Genome-Wide Association Study of age at puberty and its (co)variances with fertility and stature in growing and lactating Holstein-Friesian dairy cattle

Reproductive performance is a key determinant of cow longevity in a pasture-based, seasonal dairy system. Unfortunately, direct fertility phenotypes such as inter-calving interval or pregnancy rate tend to have low heritabilities and occur relatively late in an animal's life. In contrast, age at puberty (AGEP) is a moderately heritable, early-in-life trait, that may be estimated using an animal's age at first measured elevation in blood plasma progesterone (AGEP4) concentrations. Understanding the genetic architecture of AGEP4 in addition to genetic relationships between AGEP4 and fertility traits in lactating cows is important, as is its relationship with body size in the growing animal. Thus, the objectives of this research were 3-fold. First, to estimate the genetic and phenotypic (co)variances between AGEP4 and subsequent fertility during first and second lactations. Second, to quantify the associations between AGEP4 and height, length, and body weight (BW) measured when animals were around 11 mo old (SD = 0.5). Third, to identify genomic regions that are likely to be associated with variation in AGEP4. We measured AGEP4, height, length, and BW in around 5,000 Holstein-Friesian or Holstein-Friesian x Jersey crossbred yearling heifers, across 54 pasture-based herds managed in seasonal calving farm systems. We also obtained calving rate (CR42: success or failure to calve within the first 42 d of the seasonal calving period), breeding rate (PB21: success or failure to be presented for breeding within the first 21 d of the seasonal breeding period) and pregnancy rate (PR42: success or failure to become pregnant within the first 42 d of the seasonal breeding period) phenotypes from their first and second lactations. The animals were genotyped using the Weatherby's Versa 50K SNP array (Illumina, USA). The estimated heritabilities of AGEP4, height, length, and BW were 0.34 (0.30, 0.37), 0.28 (0.25, 0.31), 0.21 (0.18, 0.23), and 0.33 (0.30, 0.36), respectively. In contrast, the heritabilities of CR42, PB21 and PR42 were all < 0.05 in both first and second lactations. The genetic correlations between AGEP4 and these fertility traits were generally moderate ranging from 0.11 to 0.60, whereas genetic correlations between AGEP4 and yearling body conformation traits ranged from 0.02 to 0.28. Our genome wide association study (GWAS) highlighted a genomic window on chromosome 5 that was strongly associated with variation in AGEP4. We also identified 4 regions, located on chromosomes 14, 6, 1 and 11 (in order of decreasing importance), that exhibited suggestive associations with AGEP4. Our results show that AGEP4 is a reasonable predictor of estimated breeding values (EBVs) for fertility traits in lactating cows. While the GWAS provided insights into genetic mechanisms underpinning AGEP4, further work is required to test genomic predictions of fertility that use this information.

Theories of disorder and order, energy and information, in sociological thought

There has always been a close relation between thermodynamic theory and sociological theory, although they repeatedly part company and later rejoin. I discuss some of the most important ways in which the two have been in contact, focusing on the potential passage from theories of energy to theories of information and vice versa. I close by discussing how a closer engagement with classic thermodynamics may continue to be fruitful for sociological theorizing. This article is part of the theme issue 'Thermodynamics 2.0: Bridging the natural and social sciences (Part 2)'.

Gibbs Samplers for Logistic Item Response Models via the Pólya-Gamma Distribution: A Computationally Efficient Data-Augmentation Strategy

Fully Bayesian estimation of item response theory models with logistic link functions suffers from low computational efficiency due to posterior density functions that do not have known forms. To improve algorithmic computational efficiency, this paper proposes a Bayesian estimation method by adopting a new data-augmentation strategy in uni- and multidimensional IRT models. The strategy is based on the Pólya-Gamma family of distributions which provides a closed-form posterior distribution for logistic-based models. In this paper, an overview of Pólya-Gamma distributions is described within a logistic regression framework. In addition, we provide details about deriving conditional distributions of IRT, incorporating Pólya-Gamma distributions into the conditional distributions for Bayesian samplers' construction, and random drawing from the samplers such that a faster convergence can be achieved. Simulation studies and applications to real datasets were conducted to demonstrate the efficiency and utility of the proposed method.

The chemical (not mechanical) paradigm of thermodynamics of colloid and interface science

In the most influential monograph on colloid and interfacial science by Adamson three fundamental equations of "physical chemistry of surfaces" are identified: the Laplace equation, the Kelvin equation and the Gibbs adsorption equation, with a mechanical definition of surface tension by Young as a starting point. Three of them (Young, Laplace and Kelvin) are called here the "mechanical paradigm". In contrary it is shown here that there is only one fundamental equation of the thermodynamics of colloid and interface science and all the above (and other) equations of this field follow as its derivatives. This equation is due to chemical thermodynamics of Gibbs, called here the "chemical paradigm", leading to the definition of surface tension and to 5 rows of equations (see Graphical abstract). The first row is the general equation for interfacial forces, leading to the Young equation, to the Bakker equation and to the Laplace equation, etc. Although the principally wrong extension of the Laplace equation formally leads to the Kelvin equation, using the chemical paradigm it becomes clear that the Kelvin equation is generally incorrect, although it provides right results in special cases. The second row of equations provides equilibrium shapes and positions of phases, including sessile drops of Young, crystals of Wulff, liquids in capillaries, etc. The third row of equations leads to the size-dependent equations of molar Gibbs energies of nano-phases and chemical potentials of their components; from here the corrected versions of the Kelvin equation and its derivatives (the Gibbs-Thomson equation and the Freundlich-Ostwald equation) are derived, including equations for more complex problems. The fourth row of equations is the nucleation theory of Gibbs, also contradicting the Kelvin equation. The fifth row of equations is the adsorption equation of Gibbs, and also the definition of the partial surface tension, leading to the Butler equation and to its derivatives, including the Langmuir equation and the Szyszkowski equation. Positioning the single fundamental equation of Gibbs into the thermodynamic origin of colloid and interface science leads to a coherent set of correct equations of this field. The same provides the chemical (not mechanical) foundation of the chemical (not mechanical) discipline of colloid and interface science.