Container-based bioinformatics with Pachyderm.

Motivation: Computational biologists face many challenges related to data size, and they need to manage complicated analyses often including multiple stages and multiple tools, all of which must be deployed to modern infrastructures. To address these challenges and maintain reproducibility of results, researchers need (i) a reliable way to run processing stages in any computational environment, (ii) a well-defined way to orchestrate those processing stages and (iii) a data management layer that tracks data as it moves through the processing pipeline.

Results: Pachyderm is an open-source workflow system and data management framework that fulfils these needs by creating a data pipelining and data versioning layer on top of projects from the container ecosystem, having Kubernetes as the backbone for container orchestration.

Density functional resonance theory: complex density functions, convergence, orbital energies, and functionals.

Aspects of density functional resonance theory (DFRT) [D. L. Whitenack and A.

Density functional resonance theory of unbound electronic systems.

Density functional resonance theory (DFRT) is a complex-scaled version of ground-state density functional theory (DFT) that allows one to calculate the in-principle exact resonance energies and lifetimes of metastable anions. In this formalism, the energy and lifetime of the lowest-energy resonance of unbound systems is encoded into a complex "density" that can be obtained via complex-coordinate scaling. This complex density is used as the primary variable in a DFRT calculation, just as the ground-state density would be used as the primary variable in DFT.

Lead arsenate poisoning in a herd of beef cattle.

Lead arsenate poisoning was diagnosed in 2 beef heifers and was suspected in 6 other cattle from the same herd that had died previously and were not examined. Clinical signs in affected cattle included staggering, dehydration, hemorrhage, acidemia, and shock. Diagnosis was by arsenic and lead analysis of urine samples and kidney and liver tissue digests.

Eosinophilic mediastinitis, myositis, pleuritis, and pneumonia of cattle associated with migration of first-instar larvae of Hypoderma lineatum.

Migrating first-instar larvae of Hypoderma lineatum are a frequent cause of focal inflammatory lesions in connective tissues of the mediastinum, parietal and visceral pleura, peritoneum, lungs, diaphragm, and other loci. The lesions are characterized grossly by foci of yellowish or greenish gelatinous edema and microscopically by infiltration of the edematous tissue by a dense array of eosinophils. Lesions were recognized during a period of several weeks in late spring; the timing was attributable to events in the life cycle of the fly.

Selenium toxicosis in three California sea lions (Zalophus californianus).

Selenium poisoning occurs worldwide in nearly all domestic animals. Acute selenium poisoning is associated with feeding high levels or injecting excessive amounts of selenium and is usually fatal. The acute poisoning may cause gastrointestinal disturbance, muscle weakness, depression of the central nervous system, prostration and death (1-2).

Trypanosoma cruzi infection in a dog from Oklahoma.

A dog with signs of weakness, labored breathing, and generalized edema was examined. It was heavily infested with fleas and had wounds resulting from a recent fight. Hematologic findings were not remarkable, except for parasites in the blood.

Necropsy of the feeder and stocker calf.

Frequently occurring diseases are discussed in 2- to 12-month-old pastured or feedlot cattle. Emphasis is on gross necropsy lesions that are significant in differential diagnosis. Where applicable, practical laboratory tests that are helpful in confirming a diagnosis are described.

Characteristics of the herpesvirus of malignant catarrhal fever isolated from captive wildebeest calves.

A herpesvirus was isolated from buffy coat cells from a newborn wildebeest (Connochaetes gnou) and from tissues of a 12-day-old wildebeest during the 1982 calving season of a captive, inbred herd maintained in a zoologic collection. Both wildebeests were clinically healthy, and there was no herd record that malignant catarrhal fever (MCF) existed. Each viral isolate produced cytopathologic changes in bovine kidney cell cultures (intranuclear inclusions and massive syncytia).

A scale for measurement of the problem patient labeling process.

Physicians frequently use the term problem patient to subjectively label individuals who present with vague and shifting symptoms involving multiple organ systems, chronically complain, constantly worry about their health, and contribute in other ways to physician uncertainty and frustration. This article describes the development and reliability and validity studies of an instrument that objectively measures physicians' perceptions of problem patients. As such, the instrument quantifies a key qualitative impression that physicians may formulate.

Malignant catarrhal fever in an Indian gaur and greater kudu: experimental transmission, isolation, and identification of a herpesvirus.

Herpesviruses were isolated in bovine cell cultures from buffy coat cells obtained from an Indian gaur (Bos gaurus) and a greater kudu (Tragelaphus strepsiceros) with clinical signs of the head and eye form of malignant catarrhal fever (MCF). Both animals were from herds housed in a zoologic park in Oklahoma. Serial transmission of the head and eye form of MCF was accomplished by using whole blood from the gaur into a Hereford-Angus heifer, then whole blood from the heifer into a Holstein calf, and finally, whole blood from the calf into a white-tailed deer (Odocoileus virginianus).

Experimental malignant catarrhal fever (African form) in white-tailed deer.

White-tailed deer (Odocoileus virginianus) were experimentally infected with the African form of malignant catarrhal fever (AMCF) virus by inoculation of whole blood from experimentally infected cattle, from whole blood obtained from a greater kudu (Tragelaphus strepsiceros) and from virus isolated in cell culture. The incubation period from AMCF in experimentally infected deer ranged from 13 to 18 days. Clinical disease was characterized by lacrimation, an elevated body temperature, conjunctivitis and swelling of the external lymph nodes.

Isolation of wine influenza virus in Oklahoma.

Three isolations of swine influenca virus were made from 2 swine herds in west-central Oklahoma. Many swine in these herds had signs of respiratory tract disease, and in 1 herd, some affected animals also had diarrhea. Two isolations were made in swine testicle cell line and 1 in embryonating chicken eggs.

Visual defects in white-tailed deer from Michigan six case reports.

Six cases of unrelated visual defects in free-ranging white-tailed deer (Odocoileus virginianus) from Michigan are described. Two were congenital, two were of infectious etiology, one from central nervous neoplasia, and one from degenerative changes in lenses of both eyes.

Feline infectious peritonitis with spinal cord involvement in two cats.

Two cats from the same household had posterior paresis and hypergammaglobulinemia. Histologic evaluation of the spinal cords revealed a pyogranulomatous reaction consistent with that reported for feline infectious peritonitis.

An epizootic of cerebral nematodiasis in rabbits due to Ascaris columnarus.

An epizootic of cerebral nematodiasis due to ascaris columnaris occurred in a commercial rabbitry, and 80 diseased rabbits died or were killed. The morbidity was high in groups of recently purchased rabbits and in the offspring of 12 breeder rabbits. The breeder rabbits which had been on the farm for more than a yr survived the outbreaks.