EcoLens: Integration and interactive visualization of ecological datasets

Complex multi-dimensional datasets are now pervasive in science and elsewhere in society. Better interactive tools are needed for visual data exploration so that patterns in such data may be easily discovered, data can be proofread, and subsets of data can be chosen for algorithmic analysis. In particular, synthetic research such as ecological interaction research demands effective ways to examine multiple datasets. This paper describes our integration of hundreds of food-web datasets into a common platform, and the visualization software, EcoLens, we developed for exploring this information. This publicly-available application and integrated dataset have been useful for our research predicting large complex food webs, and EcoLens is favorably reviewed by other researchers. Many habitats are not well represented in our large database. We confirm earlier results about the small size and lack of taxonomic resolution in early food webs but find that they and a non-food-web source provide trophic information about a large number of taxa absent from more modern studies. Corroboration of Tuesday Lake trophic links across studies is usually possible, but lack of links among congeners may have several explanations. While EcoLens does not provide all kinds of analytical support, its label- and item-based approach is effective at addressing concerns about the comparability and taxonomic resolution of food-web data.     

Proteolytic processing of human preproapolipoprotein A-I. A proposed defect in the conversion of pro A-I to A-I in Tangier's disease

The primary translation product of human intestinal apolipoprotein A-I mRNA was isolated from wheat germ and ascites cell-free translation systems. Comparison of its NH2-terminal sequence with that of plasma high density lipoprotein-associated A-I showed that it is initially synthesized as a preproprotein. Like rat preproapolipoprotein A-I, it contains an 18-amino acid prepeptide and a 6-amino acid propeptide. The highly unusual COOH-terminal Gln-Gln dipeptide present in the rat pro-segment is also represented at the same position in the human sequence. The functional division of the 24-amino acid NH2-terminal extention into pro- and presegments was verified by finding that the stable intracellular form of A-I in a human hepatoma cell line was the proprotein. Edman degradation of radiolabeled intracellular and extracellular A-I indicated that this apolipoprotein was secreted without proteolytic cleavage of its hexapeptide prosegment. Therefore, it appears that apolipoprotein A-I undergoes an additional proteolytic processing step before it is fully integrated into plasma high density lipoprotein. Two-dimensional gel electrophoresis of purified proapolipoprotein A-I isolated from the hepatocyte cell culture media indicated that it corresponds to isoforms 2 and 3, the basic A-I isoproteins which are the precursors of plasma A-I and the predominant plasma A-I isoforms found in patients with Tangier's disease (Zannis, V. I., Lees, A. M., Lees, R. S., and Breslow, J. L. (1982) J. Biol. Chem., 257, 4978-4986). Therefore this pathologic state probably arises from a defect in the conversion of proapolipoprotein A-I to apolipoprotein A-I.     

Meal frequency differentially alters postprandial triacylglycerol and insulin concentrations in obese women

Objective:

The aim of this study was to compare postprandial lipemia, oxidative stress, antioxidant activity, and insulinemia between a three and six isocaloric high‐carbohydrate meal frequency pattern in obese women.

Design and Methods:

In a counterbalanced order, eight obese women completed two, 12‐h conditions in which they consumed 1,500 calories (14% protein, 21% fat, and 65% carbohydrate) either as three 500 calorie liquid meals every 4‐h or six 250 calorie liquid meals every 2‐h. Blood samples were taken every 30 min and analyzed for triacylglycerol (TAG), total cholesterol, high‐density lipoprotein cholesterol, low‐density lipoprotein cholesterol, oxidized low‐density lipoprotein cholesterol, myeloperoxidase, paraoxonase‐1 activity, and insulin.

Results:

The TAG incremental area under the curve (iAUC) during the three meal condition (321 ± 129 mg/dl·12 h) was significantly lower (P = 0.04) compared with the six meal condition (481 ± 155 mg/dl·12 h). The insulin iAUC during the three meal condition (5,549 ± 1,007 pmol/l^.12 h) was significantly higher (P = 0.05) compared with the six meal condition (4,230 ± 757 pmol/l^.12 h). Meal frequency had no influence on the other biochemical variables.

Conclusions:

Collectively, a three and six isocaloric high‐carbohydrate meal frequency pattern differentially alters postprandial TAG and insulin concentrations but has no effect on postprandial cholesterol, oxidative stress, or antioxidant activity in obese women.     

Thermo-optic measurements and their inter-dependencies for delineating cancerous breast biopsy tissue from adjacent normal

The histopathological diagnosis of cancer is the current gold standard to differentiate normal from cancerous tissues. We propose a portable platform prototype to characterize the tissue's thermal and optical properties, and their inter-dependencies to potentially aid the pathologist in making an informed decision. The measurements were performed on 10 samples from five subjects, where the cancerous and adjacent normal were extracted from the same patient. It was observed that thermal conductivity (k) and reduced-scattering-coefficient (μ'_s) for both the cancerous and normal tissues reduced with the rise in tissue temperature. Comparing cancerous and adjacent normal tissue, the difference in k and μ'_s (at 940 nm) were statistically significant (p = 7.94e-3), while combining k and μ'_s achieved the highest statistical significance (6.74e-4). These preliminary results promise and support testing on a large number of samples for rapidly differentiating cancerous from adjacent normal tissues.     

Diagnosis of spontaneous Clostridium spiroforme iota enterotoxemia in a barrier rabbit breeding colony

Five New Zealand White rabbits (Oryctolagus cuniculus) in a rigid barrier rabbit breeding colony developed acute diarrhea 1 week after weaning. Both Clostridium spiroforme and an iota-toxin were isolated from cecal and colon contents of all five rabbits. When pure isolates of C. spiroforme were administered to two normal healthy rabbits, the rabbits developed identical disease and shed both the organism and the iota-toxin. Results of this study suggested that C. spiroforme is an important enteric pathogen of weanling rabbits and the etiology of this diarrhea complex can be rapidly confirmed using four diagnostic criteria.     

Delayed ectopic pregnancy following vaginal hysterectomy

A patient with ectopic pregnancy occurring a considerable interval after vaginal hysterectomy is reported. She presented with recurrent lower abdominal pain and the correct diagnosis was only established at laparotomy. Although 14 cases of this late complication of hysterectomy have been reported in the literature no fatalities have been recorded.     

The woodchuck, Marmota monax, as a laboratory animal

The woodchuck or groundhog (Marmota monax) has been used as a biomedical model for studies of obesity and energy balance, endocrine and metabolic function, central nervous system control mechanisms and cardiovascular, cerebrovascular and neoplastic disease. Methods of care of a woodchuck colony, techniques for handling, restraint, anesthesia, blood sampling and breeding were developed.     

A longitudinal study of estrous cyclicity in aging C57BL/6J mice: I. Cycle frequency, length and vaginal cytology

Cycle frequency, length, and vaginal cytology were measured longitudinally in three cohorts of singly housed virgin mice staggered across a 3-year interval. The age profiles of these parameters were qualitatively similar, but quantitatively different, among cohorts. Cycle frequency was initially low (Phase I), due to prolonged cycles and late-starting cycles, and did not peak (Phase II) until mice were 3-5 months old. Phase II lasted for 7-10 months, depending on the cohort. Thereafter cycle frequency declined steadily (Phase III). The average age of cessation of cyclicity varied among cohorts, occurring between 13 and 16 months of age. Age changes in cycle length paralleled those of cycle frequency. During Phase II, median cycle length was less than 5 days and variance was lowest. During Phases I and III, variance was about twofold greater and median cycle length was greater than 5 days. Although median cycle length remained stable for several months during Phase II, the peak period of 4-day cycles was much shorter. In all cohorts, 4-day cycles did not peak until 7-8 months of age and began to decline by 9 months. The decrease in 4-day cycles was associated with a progressive lengthening of cycles-first from 4 to 5 days, then to longer cycles. The fraction of cycles with extended cornification (greater than 2 days) increased with advancing age from less than 0.35 during the initial period of cycle lengthening to a maximum of 0.60. The observation that the initial phase o cycle prolongation was not usually associated with extended cornification is consistent with earlier evidence that this period is characterized by a delayed, rather than prolonged, preovulatory rise of estradiol. However, the increased fraction of prolonged cycles with extended cornification at later ages suggests that the preovulatory elevation of estradiol may ultimately be prolonged.