Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.Comment: 17 pages, 8 figure

Industry in trouble : economics and politics of the New England fisheries

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Urban Studies and Planning, 1979.MICROFICHE COPY AVAILABLE IN ARCHIVES AND ROTCH.Includes bibliographical references.by Margaret E. Dewar.Ph.D

Development and evaluation of inductive and deductive models of elk (Cervus elaphus) summer resource suitability in Northwestern Ontario

Resource-selection modelling techniques take either a deductive or inductive approach. Deductive methods take a “bottom-up” approach, where individual wildlife-resource relationships are the building blocks that define the suitability of a landscape. Conversely, inductive models imply a “top-down approach”; the suitability of a landscape is predefined by animal use, and statistics are used to identify wildlife-resource relationships. Current modelling caters towards the inductive approach even though a formal comparison between inductive and deductive techniques has yet to identify the superior method. The Ontario Elk Restoration Project re-introduced 104 elk (Cervus elaphus) to the Lake of the Woods (LOW) region in 2000 and 2001. The population diminished substantially over the following four years bringing concern to the successful re-establishment of elk in northwestern Ontario. At present, explanations for this decline are speculative in nature, but one possibility is that the landscape does not contain the resources required to support a viable population. To address this concern, I investigated the ability of the landscape to support elk by creating a series of deductive (Habitat Suitability Index; HSI) models for the summer season based on published elk-resource relationships. I also created an inductive (Resource Utilization Function; RUE) model based on radiotelemetry location data collected weekly throughout 2000-2005 in an effort to improve upon the initial deductive model. Finally, I compared the two modelling approaches to address the growing disparity between modelling methods. Models were validated by comparing model suitability to elk resource use using weighted overlap (WO) and average overlap (AO) indices, and by comparing model suitability to elk space use (utilization distributions; UDs) using the deviation from a ‘no selection’ pattern (DVI Index); a modification of the Volume of Intersection (VI) Index. Comparison to a null model was also used to benchmark each index. I also calculated the VI Index between the predicted suitability’s of RUF and HSI models to compare their overall similarity

Compassion in the nursing curriculum: making it more explicit

Working with student nurses has taught me that the majority join the profession because they genuinely want to care compassionately but this does not mean that they know what this looks like in practice. I wanted to share with students what patients and relatives say about their experiences of care, to encourage them to ask what is most important to patients, and to respond to them in a compassionate way whatever the circumstance

Asymptomatic people with well-controlled HIV do not have abnormal left ventricular global longitudinal strain

BackgroundPrevious studies have reported impairment in systolic and diastolic function in people with HIV (PWHIV). Our aim was to determine if echocardiographically measured left ventricular (LV) global longitudinal strain (GLS) is abnormal in asymptomatic PWHIV.MethodsA cross-sectional study of PWHIV (n = 98, 89% male, median age 53 years) and HIV-negative people (n = 50, median age 53 years) without known cardiovascular disease were recruited from a single centre. All participants completed a health/lifestyle questionnaire, provided a fasting blood sample, and underwent a comprehensive echocardiogram for assessment of diastolic and systolic LV function, including measurement of GLS.ResultsAll PWHIV were receiving antiretroviral therapy (ART) for a median of 12 years (IQR: 6.9, 22.4), the majority with good virological control (87% suppressed) and without immunological compromise (median CD4 598 cells/µl, IQR: 388, 841). Compared with controls of similar age and gender, there was no difference in GLS [mean GLS −20.3% (SD 2.5%) vs. −21.0% (SD 2.5%), p = 0.14] or left ventricular ejection fractions [65.3% (SD 6.3) vs. 64.8% (SD 4.8), p = 0.62]. Following adjustment for covariates (gender, heart rate, systolic and diastolic blood pressure, and fasting glucose), the difference in GLS remained non-significant. There were no differences in LV diastolic function between the groups. Exposure to at least one mitochondrially toxic ART drug (didanosine, stavudine, zidovudine, or zalcitabine) was not associated with impairment of LV systolic function.ConclusionNo clinically significant impairment of myocardial systolic function, as measured by LV GLS, was detected in this predominantly Caucasian male population of PWHIV on long-term ART, with no history of cardiovascular disease