Parametric Inference for Biological Sequence Analysis

One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems associated with different statistical models. This paper introduces the \emph{polytope propagation algorithm} for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.Comment: 15 pages, 4 figures. See also companion paper "Tropical Geometry of Statistical Models" (q-bio.QM/0311009

Serum Biochemical Phenotypes in the Domestic Dog

The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species

B. Garden to John Kean, March 23, 1788

B. Garden wrote to John Kean, addressed to Beaufort, SC regarding a bond of Mr. H Wiggs that he previously had in his possession. He had sent the bond to his attorney in the event he needed to take legal action to collect the money.https://digitalcommons.kean.edu/lhc_1780s/1188/thumbnail.jp

HIGH-LEVEL SPILL AT THE HILAC

On July 3, 1959, an incident occurred in the Hilac Building when the turning of the wrong valve resulted in pressurizing a helium cooling box, with a resultant blowout of a thin foil. The burst of He gas disintegrated experimental foils made up with 10/sup 11/ dpm of Cm/sup 244/. The resultant activity was quickly dispersed as airborne particulates throughout the building. The 27 people in the building were evacuated within 10 minutes under surveillance of the Health Chemistry personnel; wherever clothing proved to be contaminated it was removed, and in cases where nose swipes were pertinent they were taken. Although an assumption of a combination of the worst conditions could conceivably have resulted in 1 man's inhsling between 2 and 4 times the (alculated allowable inhalation for shont bursts,. evaluation from air analysis and medical tests indicate that it is unlikely that anyone actually did receive this amount. The bullding was closed during decontamination procedures, which required about 30 people for 3 weeks in direct decontamination work and 30 people for 3 weeks in indirect work. The cost of labor, material, and other charges related to the spill amounted to about 0,500 without overhead; equipment loss was held to less than 00. The lost time of operation of the Hilac has been evaluated at ,000, so that the total loss from the incident amounts to roughly 8,500. The primary cause of the accident was determined to be an error by the experimenter. Steps were taken to help insure against any recurrence of an uncontained radiation spill at the Hilac, and to decrease the danger of exposure to personnel in the event that a spill should occur in the future. (auth

Diagnosis of anaplastic large-cell lymphoma in a dog using CD30 immunohistochemistry

Anaplastic large-cell lymphoma or null-cell lymphoma is a clinical entity reported in people, classified according to the unique appearance of large pleomorphic cells that express CD30. Null-cell lymphoma has also been described in dogs when neither CD3 nor CD79α is expressed by the tumor. We describe a case of lymphoma in the dog in which neoplastic cells did not express routine B- or T-lymphocyte markers on flow cytometry or immunohistochemistry; however, cells immunohistochemically labeled for CD30. The dog in our case died 5 mo after initial presentation, confirming a poor prognosis. Identification of further similar cases in dogs would provide additional prognostic information for this subset of lymphomas. CD30 may also serve as a potential therapeutic target in anaplastic large-cell lymphomas

Phenotypic heterogeneity of peripheral monocytes in healthy dogs

Monocytes are key cells of the innate immune system. Their phenotypic and functional roles have been investigated in humans, mice and other animals, such as the rat, pig and cow. To date, detailed phenotypic analysis of monocytes has not been undertaken in dogs. Two important surface markers in human monocytes are CD14 and MHC class II (MHC II). By flow cytometry, we demonstrated that canine monocytes can be subdivided into three separate populations: CD14posMHC IIneg, CD14posMHC IIpos and CD14negMHC IIpos. Both light and transmission electron microscopy confirmed the monocytic identity of all three populations. The CD14posMHC IIneg population could be distinguished on an ultrastructural level by their smaller size, the presence of more numerous, larger granules, and more pseudopodia than both of the other populations

Topological susceptibility in the SU(3) gauge theory

We compute the topological susceptibility for the SU(3) Yang--Mills theory by employing the expression of the topological charge density operator suggested by Neuberger's fermions. In the continuum limit we find r_0^4 chi = 0.059(3), which corresponds to chi=(191 +/- 5 MeV)^4 if F_K is used to set the scale. Our result supports the Witten--Veneziano explanation for the large mass of the eta'.Comment: Final version to appear on Phys. Rev. Let

Serum anti-Müllerian hormone concentrations before and after treatment of an ovarian granulosa cell tumour in a cat

Case summary A 15-year-old female cat was presented for investigation of progressive behavioural changes, polyuria, polydipsia and periuria. An ovarian granulosa cell tumour was identified and the cat underwent therapeutic ovariohysterectomy (OHE). The cat’s clinical signs resolved, but 6 months later it was diagnosed as having an anaplastic astrocytoma and was euthanased. Serum anti-Müllerian hormone (AMH) concentration prior to OHE was increased vs a control group of entire and neutered female cats. Following OHE, serum AMH concentration decreased to <1% of the original value. Relevance and novel information Serum AMH measurement may represent a novel diagnostic and monitoring tool for functional ovarian neoplasms in cats

Infant and early childhood dietary predictors of overweight at age 8 years in the CAPS population

BACKGROUND/OBJECTIVES: Programs to address obesity are a high priority for public policy especially for young children. Research into dietary determinants of obesity is challenging but important for rational planning of interventions to prevent obesity, given that both diet and energy expenditure influence weight status. We investigated whether early life dietary factors were predictive of weight status at 8 years in a cohort of Australian children. SUBJECTS/METHODS: We used data from the Childhood Asthma Prevention Study-a birth cohort at high risk of asthma. Dietary data (3-day weighed food records) were collected at 18 months and height, weight and waist circumference were collected at 8 years. We assessed the relationship between dietary predictor variables and measures of adiposity using linear regression. RESULTS: Intakes of protein, meat and fruit at age 18 months were positively associated with measures of adiposity at age 8 years, namely, body mass index and/or waist circumference. We also showed a significant negative relationship between these measures of adiposity at 8 years and intake at 18 months of dairy foods as a percent of total energy, and intake of energy dense cereal-based foods such as cookies and crackers. CONCLUSIONS: This birth cohort study with rigorous design, measures and analyses, has shown a number of associations between early dietary intake and subsequent adiposity that contribute to the growing evidence base in this important field.National Health and Medical Research Council of AustraliaHjärt- och LungfondenSvenska LäkarsällskapetManuscrip