A Bayesian random regression method using mixture priors for genome-enabled analysis of time-series high-throughput phenotyping data.

The recent advancement in image-based phenotyping platforms enables the acquisition of large-scale nondestructive crop phenotypes measured at frequent intervals. To further understand the underlying genetic basis over a physiological process and improve plant breeding programs, the question of how to efficiently utilize these time-series measurements in genome-enabled analysis including genomic prediction and genome-wide association studies (GWASs) should be considered. In this paper, a Bayesian random regression model with mixture priors is developed to introduce more meaningful biological assumptions to the analysis of longitudinal traits.

3D imaging of the vagus nerve fascicular anatomy with cryo-imaging and UV excitation.

Vagus nerve stimulation (VNS) is a method to treat drug-resistant epilepsy and depression, but therapeutic outcomes are often not ideal. Newer electrode designs such as intra-fascicular electrodes offer potential improvements in reducing off-target effects but require a detailed understanding of the fascicular anatomy of the vagus nerve. We have adapted a section-and-image technique, cryo-imaging, with UV excitation to visualize fascicles along the length of the vagus nerve.

Salt stress responses and SNP-based phylogenetic analysis of Thai rice cultivars.

Genetic diversity is important for developing salt-tolerant rice (Oryza sativa L.) cultivars. Certain Thai rice accessions display salt tolerance at the adult or reproductive stage, but their response to salinity at the seedling stage is unknown.

Agricultural soils of the Animas River watershed after the Gold King Mine spill: An elemental spatiotemporal analysis via portable X-ray fluorescence spectroscopy.

In August 2015, 11.3 million L of heavy metal-contaminated water spilled into the Animas River from the Gold King Mine (Colorado, USA). National attention focused on water quality and agricultural production in areas affected by the spill.

Raman-based cytopathology: an approach to improve diagnostic accuracy in medullary thyroid carcinoma.

Medullary thyroid carcinoma (MTC) is a rare form of thyroid malignancy that can be diagnostically challenging on fine needle aspiration (FNA) cytology. Ancillary tests such as elevated serum or immunohistochemical positive calcitonin have been helpful, yet they can occasionally provide false positive results. In search for an alternative method to improve diagnostic accuracy (DA), we applied hyperspectral Raman spectroscopy to characterize the biochemical composition of single cells from MTC and compared their spectral information to cells from other types of thyroid nodules.

Interlaboratory Measurement of Rheological Properties of Tomato Salad Dressing.

Rheological properties of food materials are important as they influence food texture, processing properties, and stability. Rotational rheometry has been widely used for measuring rheological properties. However, the measurements obtained using different geometries and rheometers are generally not compared for precision and accuracy, so it is difficult to compare data across different studies.

Hyperspectral Raman microscopy can accurately differentiate single cells of different human thyroid nodules.

We report on the use of line-scan hyperspectral Raman microscopy in combination with multivariate statistical analyses for identifying and classifying single cells isolated from clinical samples of human thyroid nodules based on their intrinsic Raman spectral signatures. A total of 248 hyperspectral Raman images of single cells from benign thyroid (n = 127) and classic variant of papillary carcinoma (n = 121) nodules were collected. Spectral differences attributed to phenylalanine, tryptophan, proteins, lipids, and nucleic acids were identified for benign and papillary carcinoma cells.

Impact of Microclimate on Fatty Acids and Volatile Terpenes in "Kerman" and "Golden Hills" Pistachio (Pistacia vera) Kernels.

Pistachio is an economically important nut crop in California. Since temperature variations among geographical locations can influence biochemical processes during fruit development, it is of great relevance to understand the impact of growing area over the components that define the nutritional and sensory characteristics of pistachio nuts. Changes in moisture, fat content, fatty acid composition and volatile terpenes were studied during kernel development for "Kerman" and "Golden Hills" varieties in two different California Central Valley microclimates, Lost Hills and Parlier.

A Fluorescence-based Method for Estimation of Oxygen Barrier Properties of Microspheres.

In this study, we developed a fluorescence method to quantify oxygen barrier properties for wall materials used in microencapsulation of oxygen-sensitive compounds. We used a reversible, oxygen quenching dye, tris (4,7-diphenyl-1, 10-phenanthroline) ruthenium(II) dichloride complex, as a marker to monitor oxygen transport across spray-dried and freeze-dried Hi-cap100 and maltodextrin microspheres. We fit the rate of oxygen transport to Fick's second law and extrapolated an effective oxygen diffusion coefficient Deff.

Development of Protein-Based High-Oxygen Barrier Films Using an Industrial Manufacturing Facility.

In this study, protein-based high-oxygen barrier multilayer films were manufactured at a pilot plant scale by a roll-to-roll coating process and an adhesive lamination process. Also, their characteristics were examined to evaluate their industrial feasibility. Oxygen transmission rates (OTRs) of the protein-based films (polyethylene terephthalate [PET]/pea protein isolate [PPI]/nylon/cast polypropylene [CPP], PET/whey protein isolate [WPI]/CPP, PET/WPI/nylon/CPP, and PET/PPI/nylon/low-density polyethylene [LDPE]) were significantly lower than OTR of the PET/nylon/CPP film without a protein-coating layer and that of the commercial high-barrier multilayer film copolymer (PET/aluminum/CPP).

Development of A Comprehensive Biological Hazard-Proof Packaging Film with Insect-Repellent, Antibacterial, and Antifungal Activities.

A multifunctional film with insect-repellent and antimicrobial activities was developed. Star anise (Illicium verum Hook. f.

Green Tea Polyphenols Modulate Colonic Microbiota Diversity and Lipid Metabolism in High-Fat Diet Treated HFA Mice.

Unlabelled: There is an increasing interest in the effect of dietary polyphenols on the intestinal microbiota and the possible associations between this effect and the development of obesity. However, limited information is available on how these polyphenols affect the gut microbiota and lipid metabolism. The co-action of a high-fat diet (HFD) and tea polyphenol (TP) on gut microbiota and lipid metabolism using a human flora-associated (HFA) C57BL/6J mice model is studied.

Replication Improves Sorting-Task Results Analyzed by DISTATIS in a Consumer Study of American Bourbon and Rye Whiskeys.

In consumer food-sensory studies, sorting and closely related methods (for example, projective mapping) have often been applied to large product sets which are complex and fatiguing for panelists. Analysis of sorting by Multi-Dimensional Scaling (MDS) is common, but this method discards relevant individual decisions; analysis by DISTATIS, which accounts for individual differences, is gaining acceptance. This research posits that replication can improve DISTATIS analysis by stabilizing consumer sensory maps, which are often extremely unstable.

High-Density Single Nucleotide Polymorphism Linkage Maps of Lowland Switchgrass using Genotyping-by-Sequencing.

Switchgrass (Panicum virgatum L.) is a warm-season perennial grass with promising potential as a bioenergy crop in the United States. However, the lack of genomic resources has slowed the development of plant lines with optimal characteristics for sustainable feedstock production.

A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery.

Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs.

Comparative effectiveness of combined digital mammography and tomosynthesis screening for women with dense breasts.

Purpose: To evaluate the effectiveness of combined biennial digital mammography and tomosynthesis screening, compared with biennial digital mammography screening alone, among women with dense breasts.

Materials And Methods: An established, discrete-event breast cancer simulation model was used to estimate the comparative clinical effectiveness and cost-effectiveness of biennial screening with both digital mammography and tomosynthesis versus digital mammography alone among U.S.

Determination of volatile organic compound emissions and ozone formation from spraying solvent-based pesticides.

Large-scale agricultural activities have come under scrutiny for possible contributions to the emission of ozone precursors. The San Joaquin Valley (SJV) of California is an area with intense agricultural activity that exceeds the federal ozone standards for more than 30 to 40 d yr(-1) and the more stringent state standards for more than 100 d yr(-1). Pesticides are used widely in both agricultural and residential subregions of the SJV, but the largest use, by weight of "active ingredient," is in agriculture.

Permeabilization of plant tissues by monopolar pulsed electric fields: effect of frequency.

Pulsed electric fields (PEF) nonthermally induce cell membrane permeabilization and thereby improve dehydration and extraction efficiencies in food plant materials. Effects of electrical field strength and number of pulses on plant tissue integrity have been studied extensively. Two previous studies on the effect of pulse frequency, however, did not provide a clear view: one study suggested no effect of frequency, while the other found a greater impact on tissue integrity at lower frequency.

Disintegration efficiency of pulsed electric field induced effects on onion (Allium cepa L.) tissues as a function of pulse protocol and determination of cell integrity by ¹H-NMR relaxometry.

The influence of electrical pulse protocol parameters on cell rupture of onion tissues was investigated in order to improve fundamental understanding and to enhance the processing of plant tissues with pulsed electric fields (PEFs). The impact of PEF parameters on cell integrity of 20 mm dia, 4-mm thick disks of Don Victor onions (Allium cepa L.) was determined by ion leakage measurements.

Critical electric field strengths of onion tissues treated by pulsed electric fields.

The impact of pulsed electric fields (PEF) on cellular integrity and texture of Ranchero and Sabroso onions (Allium cepa L.) was investigated. Electrical properties, ion leakage rate, texture, and amount of enzymatically formed pyruvate were measured before and after PEF treatment for a range of applied field strengths and number of pulses.

Statistical and kinetic studies of the changes in soybean quality during storage as related to soymilk and tofu making.

The objective of this study was to develop statistical equations and kinetic models to describe the changes of soybean quality during storage. Significant correlations (P < 0.0001) were found among most of quality attributes including color parameters (Hunter L, a, b, and DeltaE), solid extractability (as expressed by soymilk solids content), soymilk pH and protein content, tofu yield, hardness, and protein content.

Dissolved organic nitrogen: an overlooked pathway of nitrogen loss from agricultural systems?

Conventional wisdom postulates that leaching losses of N from agriculture systems are dominated by NO(3)(-). Although the export of dissolved organic nitrogen (DON) into the groundwater has been recognized for more than 100 yr, it is often ignored when total N budgets are constructed. Leaching of DON into stream and drinking water reservoirs leads to eutrophication and acidification, and can pose a potential risk to human health.

Alcohol, volatile fatty acid, phenol, and methane emissions from dairy cows and fresh manure.

There are approximately 2.5 million dairy cows in California. Emission inventories list dairy cows and their manure as the major source of regional air pollutants, but data on their actual emissions remain sparse, particularly for smog-forming volatile organic compounds (VOCs) and greenhouse gases (GHGs).

Effects of sodium bisulfate on alcohol, amine, and ammonia emissions from dairy slurry.

Sodium bisulfate (SBS) is extensively used in the poultry industry to reduce ammonia and bacterial levels in litter. It is also used in the dairy industry to reduce bacterial counts in bedding and ammonia emissions, preventing environmental mastitis and calf respiratory stress. The present study measured the effect of SBS on the air emission of ammonia, amine, and alcohol from a dairy slurry mix.