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Background Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs. Methods In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data. Results The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations. Conclusions This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden. Electronic supplementary material The online version of this article (10.1186/s13073-019-0636-8) contains supplementary material, which is available to users.

The objective of this study was to determine the effects of liver abscess severity in beef cattle at slaughter on meat tenderness and sensory attributes of steaks from USDA Low Choice and Select quality grades. Liver abscesses at the time of slaughter have been shown to decrease hot carcass weight, dressing percentage, yield grade, and marbling scores. However, little research has focused on the effects of animal health and disease parameters, including liver abscesses, on meat tenderness and sensory attributes., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2017

Yearling Red Angus or Black Angus bulls (n = 24; initial BW = 1,336 ± 25.1 lb; (606 ± 11.4 kg); average 16 mo of age) were used to evaluate the effects of castration and use of growth promoting technology (STR) on performance, carcass traits, and meat quality characteristics when compared to intact (BULL) post-pubertal male cattle. The STR treatment included administration of a combination 120 mg trenbolone acetate + 24 mg estradiol growth-promoting implant on d 0 and feeding ractopamine hydrochloride the last 28 d on feed. Cattle were individually fed a corn-based finishing diet for 62 d and harvested at a commercial abattoir. Intact bulls had greater average daily gain (4.08 vs 3.19 lb or 1.85 vs 1.45 kg/d; P = 0.02) and feed:gain ratio (8.54 vs 10.97; P = 0.02) than STR. There were no treatment differences for dry-matter intake, quality or yield grade, hot carcass weight, back-fat thickness, or dressing percent (P < 0.05). Longissimus muscle area was greater in BULL compared to STR carcasses (16.6 vs 15.0 in2 or 106.9 vs 96.8 cm2; P < 0.01). Warner-Bratzler Shear Force was not affected (P > 0.05) by treatment. Intact bulls had improved performance with no differences in carcass characteristics, tenderness, or sensory panel measurements compared to STR treatment., The Bovine Practitioner, Vol. 51, No. 1 (2017 Spring)

This was a dynamic population longitudinal study to determine the association of lameness diagnosis and locomotion score at time of initial lameness diagnosis with case outcome in feedlot cattle, and provide beef cattle feedlot lameness morbidity, mortality, and realizer incidence due to different lameness etiologies., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2016

Bruising in cattle is an indicator of poor welfare, as well as a significant cause of economic loss due to decreased carcass value. Vehicle design, transport conditions, and loading/unloading procedures are considered potential sources of carcass bruising; however, none of these have been explored extensively. The objective of the current study was to determine whether a relationship exists between trauma incurred during unloading and prevalence of carcass bruising in finished beef cattle at commercial slaughter facilities., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2016

In this Letter, a novel all-polymer arrayed waveguide grating (AWG) device with an operating wavelength around 850 nm is reported. The all-polymer AWG consists of polymer ridge waveguides fabricated on a thin poly(methyl methacrylate) foil via microscope projection photolithography. The developed device is suitable to be integrated into optical circuits, e.g., a planar polymer foil and, along with other optical integrated devices, to be used for different sensing applications. The functionality of the device is demonstrated by using a fiber Bragg grating sensor and performing strain measurements.

Veterinary consultants routinely give recommendations to feedlot employees and managers on all areas of cattle health and well-being. Recommendations are made based on veterinarians’ field experience and review of peer-reviewed literature. However, there is little data available about how the literature is merged with field experience and the actual recommendations given by consulting veterinarians to feedlot employees and managers. A survey conducted by Vasconcelos and Galyean (2007) reported baseline recommendations of select feedlot nutritionists in the United States. This survey is to be repeated every 4 to 5 years, as changes in recommendations can be useful in determining areas in nutritional practices that warrant further research. A similar study was conducted for feedlot veterinary recommendations in 2009 to establish a baseline for recommendations of feedlot veterinary consultants in the United States and Canada. The objective of the current survey was to report specific recommendations currently made by feedlot consulting veterinarians and to compare the current recommended practices to those recommended in the survey conducted 5 years ago., American Association of Bovine Practitioners Proceedings of the Annual Conference, 2015