Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets

The objective of this study was to model differences in pedigree accuracy caused by selective genotyping. As genotypes are used to correct pedigree errors, some pedigree relationships are more accurate than others. These accuracy differences can be modeled with uncertain parentage models that distribute the paternal (maternal) contribution across multiple sires (dams). In our case, the parents were the parent on record and an unknown parent group to account for pedigree relationships that were not confirmed through genotypes. Pedigree accuracy was addressed through simulation and through North American Holstein data. Data were simulated to be representative of the dairy industry with heterogeneous pedigree depth, pedigree accuracy, and genotyping. Holstein data were obtained from the official evaluation for milk, fat, and protein. Two models were compared: the traditional approach, assuming accurate pedigrees, and uncertain parentage, assuming variable pedigree accuracy. The uncertain parentage model was used to add pedigree relationships for alternative parents when pedigree relationships were not certain. The uncertain parentage model included 2 possible sires (dams) when the sire (dam) could not be confirmed with genotypes. The 2 sires (dams) were the sire (dam) on record with probability 0.90 (0.95) and the unknown parent group for the birth year of the sire (dam) with probability 0.10 (0.05). An additional set of assumptions was tested in simulation to mimic an extensive dairy production system by using a sire probability of 0.75, a dam probability of 0.85, and the remainder attributed to the unknown parent groups. In the simulation, small bias differences occurred between models based on pedigree accuracy and genotype status. Rank correlations were strong between traditional and uncertain parentage models in simulation (≥0.99) and in Holstein (≥0.99). For Holsteins, the estimated breeding value differences between models were small for most animals. Thus, traditional models can continue to be used for dairy genomic prediction despite using genotypes to improve pedigree accuracy. Those genotypes can also be used to discover maternal parentage, specifically maternal grandsires and great grandsires when the dam is not known. More research is needed to understand how to use discovered maternal pedigrees in genetic prediction.     

Digitization and profitability

Information Systems and e-Business Management - Consider a monopolistic vendor who faces a known demand curve. By setting a price that equates marginal revenue with marginal cost, the vendor will...     

Estimation of long-term dietary exposure to acrylamide of the Japanese people

Acrylamide is a probable human carcinogen and known human neurotoxin. This study estimated hypothetical long-term dietary exposure to acrylamide of the Japanese people using probabilistic and deterministic approaches by combining the concentration of acrylamide in foods with the amount and frequency of food consumption in the population. Data included acrylamide concentrations in more than 2400 individual food samples from a national survey and the literature from 2004 to 2013. Food consumption amounts were derived from the data of 24,293 Japanese citizens aged 1 year and older in the 2012 National Health and Nutrition Survey. Median lifetime average dietary exposure to acrylamide was estimated as 147–154 ng/kg body weight (bw)/day (95th percentile, 226–261 ng/kg bw/day). The deterministic estimate of lifetime exposure was 158 ng/kg bw/day and ranged from 119 ng/kg bw/day for the period of life after 60 years old to 409 ng/kg bw/day for the period between 1 and 6 years old. This study found that vegetables cooked at a high temperature, coffee and cooked potato were the major food groups contributing to long-term dietary acrylamide exposure of the Japanese people.     

Pyrolytic transformation from polydihydrosilane to hydrogenated amorphous silicon film

The fabrication of thin film silicon devices based on solution processes rather than on conventional vacuum processes is of substantial interest since cost reductions may result. Using a solution process, we coated substrates with polydihydrosilane solution and studied the pyrolytic transformation of the material into hydrogenated amorphous silicon (a-Si:H). From thermal gravimetry and differential thermal analysis data a significant reduction in weight of the material and a construction of SiSi bonds are concluded for the pyrolysis temperature T_p = 270 to 360 °C. The appearance of amorphous silicon phonon bands in Raman spectra for films prepared at T_p ≥ 330 °C suggests the construction of a three-dimensional amorphous silicon network. Films prepared at T_p ≥ 360 °C exhibit a hydrogen content near 10 at.% and an optical gap near 1.6 eV similar to device-grade vacuum processed a-Si:H. However, the infrared microstructure factor, the spin density, and the photosensitivity require significant improvements.     

Note: Light output enhanced fast response and low afterglow 6Li glass scintillator as potential down-scattered neutron diagnostics for inertial confinement fusion

The characteristics of an APLF80+3Ce scintillator are presented. Its sufficiently fast decay profile, low afterglow, and an improved light output compared to the recently developed APLF80+3Pr, were experimentally demonstrated. This scintillator material holds promise for applications in neutron imaging diagnostics at the energy regions of 0.27 MeV of DD fusion down-scattered neutron peak at the world's largest inertial confinement fusion facilities such as the National Ignition Facility and the Laser Me?gajoule.     

Migration of 1,3-diazacyclohexane sub-rings in ring-contracted macrocyclic silver(I) complexes

Mononuclear and dinuclear silver(I) complexes with contracted macrocyclic ligands were synthesized ([AgL^d]BPh₄, 1, and [Ag₂L^b](BPh₄)₂ · 2(DMF), 2). X-ray structural analysis revealed that in 1 the coordinated ligand L^d adopted a ring-contracted cis-form, with two 1,3-diazacyclohexane sub-rings positioned in a cis-configuration with respect to the macrocyclic ring center, while in 2 the ligand L^b adopted a ring-contracted trans-form. ¹H NMR and X-ray structural analysis revealed that the cis- and trans-forms are interconvertible depending on whether the complex is mononuclear or dinuclear and whether it is in crystalline form or in solution; i.e., the 1,3-diazacyclohexane sub-ring is capable of migration in ring-contracted macrocyclic silver(I) complexes.     

Identification of Physiological and Toxic Conformations in Aβ42 Aggregates

Aggregation of the 42‐residue amyloid β‐protein (Aβ42) plays a crucial role in the pathogenesis of Alzheimer's disease (AD). Despite numerous structural studies on Aβ aggregates, the relationship between tertiary structure and toxicity remains unclear. Our proline scanning and solid‐state NMR studies suggested that aggregates both of wild‐type Aβ42 and of E22K‐Aβ42 (one of the mutants related to cerebral amyloid angiopathy) contain two conformers: a major one with a turn at positions 25 and 26, and a minor one with a turn at positions 22 and 23. To identify the toxic conformer, the derivative Aβ42‐lactam(22K–23E), in which the side chains at positions 22 and 23 were covalently linked, was synthesized as a minor conformer surrogate, along with Aβ42‐lactam(25K–26E) as a major conformer surrogate. The Aβ42‐lactam(22K–23E) showed stronger aggregation, neurotoxicity, radical generation, and oligomerization than wild‐type Aβ42, whereas in Aβ42‐lactam(25K–26E) were weak. The transition from the physiological conformation with a turn at positions 25 and 26 to the toxic conformation with a turn at positions 22 and 23 might be a key event in the pathogenesis of AD.     

Development of quantitative analysis for the micro-relief of the skin surface using a video microscope and its application to examination of skin surface texture

We developed a new analyzing method for characterizing a skin surface morphology image obtained easily by a video microscope. For the numerical analysis of various characteristics of the skin surface morphology, three parameters were invented; 'the width of the skin furrows,'the fineness of the skin ridges,' and 'the size of the skin pores.' The width of the skin furrows was calculated as mean width of the skin furrows. The fineness of the skin ridges was calculated as number of the skin ridges. The size of the skin pores was calculated as total area of skin pores. The analyzed parameters were compared with the clinical scores evaluated by trained experts, resulting in a high correlation (r = 0.54–0.72). Upon the age related changes in the parameters described above, the number of the skin ridges decreased at around the age of 20, and the size of the skin pores became large with aging during the teens through 40's. In the analysis of seasonal changes, the ridge parameter was high in summer, and the furrow parameter was high in winter. Upon the relationship between the images (the skin surface patterns) and the skin physiological parameters, the skin with a low barrier function (high TEWL) or that with high sebum content gave a low density of the skin ridges. From these results it seems that the image analysis of skin surface morphology using a video microscope is quite useful for an easy and simple evaluation of skin condition.     

Migrated Hopene Synthases from Colysis pothifolia and Identification of a Migration Switch Controlling the Number of 1,2‐Hydride and Methyl Shifts

Ferns are known to produce triterpenes, derived from squalene, that are synthesized by squalene cyclases (SCs). Among these, Colysis species produce onoceroids, the bis‐cyclic skeleton of which can be cyclized from both termini of squalene. To gain insight into the molecular basis of triterpene structural diversity, cDNA cloning of SCs from C. elliptica and C. pothifolia was performed; this leads to the isolation of five SC cDNAs. Functional analysis of these clones revealed their enzymatic products to be hop‐22(29)‐ene, α‐polypodatetraene, and hop‐17(21)‐ene. One of these clones (CPF) is a transcribed pseudogene with a 22‐nucleotide deletion causing a nonsense mutation. To predict the inherent function of CPF, we constructed an insertion mutant of CPF that successfully converted inert CPF to the active SC, the product of which is fern‐9(11)‐ene. Subsequent mutations identified active‐site residues that control the number of 1,2‐hydride and methyl shifts.