scholarly journals Probability of pregnancy before ninety days postpartum in water buffaloes

2021 ◽  
Vol 30 (1) ◽  
pp. 29-34
Author(s):  
Hector Nava-Trujillo ◽  
Robert Valeris-Chacin ◽  
Adriana Morgado-Osorio ◽  
Javier Hernández ◽  
Janeth Caamaño ◽  
...  
Keyword(s):  
Mixed Model ◽  
Linear Mixed Model ◽  
Water Buffalo ◽  
Mixed Effects ◽  
Short Photoperiod ◽  
Water Buffaloes ◽  
Negative Effect ◽  
Log Odds ◽  
First 90 Days ◽  
Long Photoperiod

This study aimed to determine the effect of parity and season of calving on the probability of water buffalo cows becoming pregnant before 90 days postpartum. A retrospective analysis of reproductive records of 1,465 water buffaloes with 3,181 pregnancies was carried out. Buffaloes were grouped according to parity in one, two, or three and more calvings. Season of calving was created with the following values: long photoperiod (March-August) and short photoperiod (September-February) and predicted probabilities from the mixed-effects logistic regression model were calculated, and a generalized linear mixed model was fitted with random intercepts to calculate the log odds of becoming pregnant ≤90 days postpartum. The probability of pregnancy ≤90 days postpartum was 0.3645, and this was lower in primiparous (0.2717) in comparison with two-calved (0.3863) and three or more calving buffaloes (0.5166). Probability of pregnancy ≤90 days postpartum increased 1.77 odds by each increase in parity. The probability of becoming pregnant ≤90 days postpartum was higher in water buffaloes calving during the short photoperiod season (0.4239 vs. 0.2474, P>0.000), and water buffaloes calving during the long photoperiod season only had 0.2645 odds to become pregnant than those calving during the short photoperiod season. The negative effect of long photoperiod was observed indifferently of parity. In conclusion, primiparity and the long photoperiod affect water buffalo cow's reproductive performance, decreasing pregnancy probability during the first 90 days postpartum.

scholarly journals Effect of season and parity on water buffalo calving distribution throughout the year in Venezuela

2019 ◽  
Vol 17 ◽  
pp. 1
Author(s):  
Héctor Nava-Trujillo ◽  
Robert Valeris-Chacin ◽  
Javier Hernandez ◽  
Mariano Duran Nuñez ◽  
Adriana Morgado-Osorio ◽  
...  
Keyword(s):  
Retrospective Study ◽  
Confidence Interval ◽  
Reproductive Behavior ◽  
Water Buffalo ◽  
Short Photoperiod ◽  
Water Buffaloes ◽  
Long Photoperiod

The aim of this study was to determine the effect of season and parity on water buffalo calving distribution throughout the year in Venezuela. A retrospective study analyzing records of 3,192 crossbred (Murrah/Mediterranean) buffaloes including 7,790 calvings was carried out in Venezuela. Two seasons were evaluated according to the length of the photoperiod: September-February (short photoperiod; autumn-winter) and March-August (long photoperiod; spring-summer). Parity order was categorized in parity 1, parity 2, parity 3, and parity 4. Photoperiod was shorter between September and February in comparison with March-August (11.81 ± 0.08 h/day and 12.42±0.08 h/day, respectively, p < 0.05). Percentage of calving varied between the two seasons (p < 0.05), and 63.7% (95% Confidence Interval (CI): 62.5%-64.9%) of calving occurred during the season of short photoperiod in comparison with that of the season of long photoperiod (36.3%, 95% CI: 35.1%-37.5%), and this effect was observed in all parities. The proportion of calvings during the short photoperiod season was greater as parity increased. The percentage of calving during the short photoperiod season was lower in primiparous water buffalo cows in comparison with that of multiparous water buffalo cows; conversely, the percentage of calving during the long photoperiod season was higher in primiparous water buffalo cows in comparison with that of multiparous water buffalo cows. Eight percent of water buffalo cows having their first calving in the long photoperiod season had the next calvings during this season. In conclusion, results confirm the seasonal reproductive behavior of water buffaloes with a concentration of calvings during the months with short photoperiod; this seasonality becomes stronger as parity increases; even though a small percentage of water buffalo cows has the ability of calving constantly during long photoperiod.  

How food supply in rubbish dumps affects the breeding success and offspring mortality of cattle Egret Bubulcus ibis?

2021 ◽  
pp. 175815592110660
Author(s):  
Rachida Gherbi-Salmi ◽  
Abdelkrim Si Bachir ◽  
Cherif Ghazi ◽  
Salah Eddine Doumandji
Keyword(s):  
Clutch Size ◽  
Breeding Success ◽  
Food Supply ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Cattle Egret ◽  
Bubulcus Ibis ◽  
Negative Effect ◽  
Effect Of Food ◽  
The Mean

The objective of this study was to evaluate the effect of food supply in garbage dumps on the reproductive fitness of Cattle Egret Bubulcus ibis and offspring losses. A total of 236 nests were monitored during two distinct periods of 2 years for each: 146 nests during a period without food supply in dumps (1998–1999) and 90 with food supply in dumps (2007–2008). The study was carried out in the colony of El-Kseur in the Lower Soummam Valley (northeast Algeria). For the entire study period, the mean of clutch size, average number of hatched chicks, productivity, and breeding success varied significantly between years (Kruskal–Wallis test: p < .05). Also, the average calculated losses for eggs, chicks, and total offspring vary significantly (Chi2 test: p > .0001). The clutch size and the number of hatched chicks per nest were highest during the period with food supply in garbage dump (respectively: 3.46 ± 0.86; 2.85 ± 1.11), compared to the period when cattle egrets feed in natural or agricultural habitats (3.04 ± 0.87; 2.54 ± 1.03). However, productivity and breeding success were highest during the period without food supply (respectively: 2.11 ± 1.16 fledging’s/nest; 0.70 ± 0.35) than in the period with food supply (1.14 ± 0.91; 0.35 ± 0.30). While egg losses were substantially similar between the two study periods, chick’s mortality (59.9%) and total offspring losses (36.7%) were higher during the period with food supply. The generalized linear mixed model (GLMM) analysis indicated a large negative effect of food supply in dumps on the productivity, on the chick’s losses; and a positive effect on the total offspring losses ( p < .001). Also, feed in dump garbage revealed a significant negative effect on the breeding success linear mixed model (LMM, p = .01). However, no significant effects (GLMM, p > .05) of food supply in dumps were noted on average clutch size, the mean number of hatched chicks per nest, and egg losses.

scholarly journals Poisson–Tweedie mixed-effects model: A flexible approach for the analysis of longitudinal RNA-seq data

2020 ◽  
pp. 1471082X2093601
Author(s):  
Mirko Signorelli ◽  
Pietro Spitali ◽  
Roula Tsonaka
Keyword(s):  
Rna Sequencing ◽  
Heavy Tails ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Simulated Data ◽  
Likelihood Estimation ◽  
Mixed Effects ◽  
Repeated Measurements ◽  
Mixed Effects Model ◽  
Rna Seq

We present a new modelling approach for longitudinal overdispersed counts that is motivated by the increasing availability of longitudinal RNA-sequencing experiments. The distribution of RNA-seq counts typically exhibits overdispersion, zero-inflation and heavy tails; moreover, in longitudinal designs repeated measurements from the same subject are typically (positively) correlated. We propose a generalized linear mixed model based on the Poisson–Tweedie distribution that can flexibly handle each of the aforementioned features of longitudinal overdispersed counts. We develop a computational approach to accurately evaluate the likelihood of the proposed model and to perform maximum likelihood estimation. Our approach is implemented in the R package ptmixed, which can be freely downloaded from CRAN. We assess the performance of ptmixed on simulated data, and we present an application to a dataset with longitudinal RNA-sequencing measurements from healthy and dystrophic mice. The applicability of the Poisson–Tweedie mixed-effects model is not restricted to longitudinal RNA-seq data, but it extends to any scenario where non-independent measurements of a discrete overdispersed response variable are available.

scholarly journals Combination of longitudinal biomarkers in predicting binary events

Biostatistics ◽  
2014 ◽  
Vol 15 (4) ◽  
pp. 706-718 ◽  
Author(s):  
Danping Liu ◽  
Paul S. Albert
Keyword(s):  
Random Effects ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Disease Risk ◽  
Likelihood Ratio Statistic ◽  
Disease Status ◽  
Analytical Form ◽  
Mixed Effects ◽  
Mixed Effects Model ◽  
Shared Random Effects

Abstract In disease screening, the combination of multiple biomarkers often substantially improves the diagnostic accuracy over a single marker. This is particularly true for longitudinal biomarkers where individual trajectory may improve the diagnosis. We propose a pattern mixture model (PMM) framework to predict a binary disease status from a longitudinal sequence of biomarkers. The marker distribution given the disease status is estimated from a linear mixed effects model. A likelihood ratio statistic is computed as the combination rule, which is optimal in the sense of the maximum receiver operating characteristic (ROC) curve under the correctly specified mixed effects model. The individual disease risk score is then estimated by Bayes’ theorem, and we derive the analytical form of the 95% confidence interval. We show that this PMM is an approximation to the shared random effects (SRE) model proposed by Albert (2012. A linear mixed model for predicting a binary event from longitudinal data under random effects mis-specification. Statistics in Medicine31(2), 143–154). Further, with extensive simulation studies, we found that the PMM is more robust than the SRE model under wide classes of models. This new PPM approach for combining biomarkers is motivated by and applied to a fetal growth study, where the interest is in predicting macrosomia using longitudinal ultrasound measurements.

The effect of population size of paternal groups and herds on optimal estimation of the heritability index for gestation length in cattle

2017 ◽  
Vol 13 (1) ◽  
pp. 9-17
Author(s):  
Jolanta Różańska-Zawieja ◽  
Alicja Szabelska-Beręsewicz ◽  
Zbigniew Sobek ◽  
Anna Nienartowicz-Zdrojewska ◽  
Joanna Zyprych-Walczak ◽  
...  
Keyword(s):  
Population Size ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Optimal Estimation ◽  
Farm Animals ◽  
Gestation Length ◽  
Value Assessment ◽  
Holstein Friesian ◽  
Negative Effect ◽  
Friesian Cattle

Estimation of genetic parameters is a crucial element in the process of population improvement. In the case of farm animals this process is based on a sample which is a subset of the whole population. For this reason it is important to know the effect of the size of paternal groups and of the herd on the accuracy of estimations of these parameters, particularly heritability. The aim of this study was to show the effect of the population size of paternal groups and herds on the accuracy of estimation of the heritability index (h2). The material for the analyses comprised data of Holstein-Friesian cattle born in 2005-2010 and subject to use value assessment in Poland. The trait analysed was gestation length. Calculations using a linear mixed model were performed using the R 3.1.3 platform. The analyses showed that calculations concerning daughters in paternal groups are more accurate when the daughters are in a smaller number of herds, but of greater size. An increase in the size of paternal groups at the expense of their number does not have such a negative effect on the accuracy of the estimate as in the case of a reduced number of small herds. Limiting the estimate to only the largest herds reduces its accuracy.

Analyzing discontinuities in longitudinal count data: A multilevel generalized linear mixed model.

2020 ◽  
Author(s):  
James L. Peugh ◽  
Sarah J. Beal ◽  
Meghan E. McGrady ◽  
Michael D. Toland ◽  
Constance Mara
Keyword(s):  
Count Data ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Generalized Linear Mixed Model ◽  
Longitudinal Count Data

Predicting bycatch hotspots based on suitable habitat derived from fishery-independent data

2020 ◽  
Vol 641 ◽  
pp. 159-175
Author(s):  
J Runnebaum ◽  
KR Tanaka ◽  
L Guan ◽  
J Cao ◽  
L O’Brien ◽  
...  
Keyword(s):  
Habitat Suitability ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Gulf Of Maine ◽  
Homarus Americanus ◽  
Management Tool ◽  
American Lobster ◽  
Suitable Habitat ◽  
Climate Conditions ◽  
Suitability Index

Bycatch remains a global problem in managing sustainable fisheries. A critical aspect of management is understanding the timing and spatial extent of bycatch. Fisheries management often relies on observed bycatch data, which are not always available due to a lack of reporting or observer coverage. Alternatively, analyzing the overlap in suitable habitat for the target and non-target species can provide a spatial management tool to understand where bycatch interactions are likely to occur. Potential bycatch hotspots based on suitable habitat were predicted for cusk Brosme brosme incidentally caught in the Gulf of Maine American lobster Homarus americanus fishery. Data from multiple fisheries-independent surveys were combined in a delta-generalized linear mixed model to generate spatially explicit density estimates for use in an independent habitat suitability index. The habitat suitability indices for American lobster and cusk were then compared to predict potential bycatch hotspot locations. Suitable habitat for American lobster has increased between 1980 and 2013 while suitable habitat for cusk decreased throughout most of the Gulf of Maine, except for Georges Basin and the Great South Channel. The proportion of overlap in suitable habitat varied interannually but decreased slightly in the spring and remained relatively stable in the fall over the time series. As Gulf of Maine temperatures continue to increase, the interactions between American lobster and cusk are predicted to decline as cusk habitat continues to constrict. This framework can contribute to fisheries managers’ understanding of changes in habitat overlap as climate conditions continue to change and alter where bycatch interactions could occur.

Long-term seizure outcomes after pediatric temporal lobectomy: does brain MRI lesion matter?

2019 ◽  
Vol 24 (2) ◽  
pp. 200-208
Author(s):  
Ravindra Arya ◽  
Francesco T. Mangano ◽  
Paul S. Horn ◽  
Sabrina K. Kaul ◽  
Serena K. Kaul ◽  
...  
Keyword(s):  
Repeated Measures ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Hippocampal Sclerosis ◽  
Brain Mri ◽  
Temporal Lobectomy ◽  
Seizure Freedom ◽  
Seizure Onset

OBJECTIVEThere is emerging data that adults with temporal lobe epilepsy (TLE) without a discrete lesion on brain MRI have surgical outcomes comparable to those with hippocampal sclerosis (HS). However, pediatric TLE is different from its adult counterpart. In this study, the authors investigated if the presence of a potentially epileptogenic lesion on presurgical brain MRI influences the long-term seizure outcomes after pediatric temporal lobectomy.METHODSChildren who underwent temporal lobectomy between 2007 and 2015 and had at least 1 year of seizure outcomes data were identified. These were classified into lesional and MRI-negative groups based on whether an epilepsy-protocol brain MRI showed a lesion sufficiently specific to guide surgical decisions. These patients were also categorized into pure TLE and temporal plus epilepsies based on the neurophysiological localization of the seizure-onset zone. Seizure outcomes at each follow-up visit were incorporated into a repeated-measures generalized linear mixed model (GLMM) with MRI status as a grouping variable. Clinical variables were incorporated into GLMM as covariates.RESULTSOne hundred nine patients (44 females) were included, aged 5 to 21 years, and were classified as lesional (73%), MRI negative (27%), pure TLE (56%), and temporal plus (44%). After a mean follow-up of 3.2 years (range 1.2–8.8 years), 66% of the patients were seizure free for ≥ 1 year at last follow-up. GLMM analysis revealed that lesional patients were more likely to be seizure free over the long term compared to MRI-negative patients for the overall cohort (OR 2.58, p < 0.0001) and for temporal plus epilepsies (OR 1.85, p = 0.0052). The effect of MRI lesion was not significant for pure TLE (OR 2.64, p = 0.0635). Concordance of ictal electroencephalography (OR 3.46, p < 0.0001), magnetoencephalography (OR 4.26, p < 0.0001), and later age of seizure onset (OR 1.05, p = 0.0091) were associated with a higher likelihood of seizure freedom. The most common histological findings included cortical dysplasia types 1B and 2A, HS (40% with dual pathology), and tuberous sclerosis.CONCLUSIONSA lesion on presurgical brain MRI is an important determinant of long-term seizure freedom after pediatric temporal lobectomy. Pediatric TLE is heterogeneous regarding etiologies and organization of seizure-onset zones with many patients qualifying for temporal plus nosology. The presence of an MRI lesion determined seizure outcomes in patients with temporal plus epilepsies. However, pure TLE had comparable surgical seizure outcomes for lesional and MRI-negative groups.

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