Showing papers by "University of Ottawa published in 1993"

Very Simple Classification Rules Perform Well on Most Commonly Used Datasets

Abstract: This article reports an empirical investigation of the accuracy of rules that classify examples on the basis of a single attribute. On most datasets studied, the best of these very simple rules is as accurate as the rules induced by the majority of machine learning systems. The article explores the implications of this finding for machine learning research and applications.

Linear Model Selection by Cross-validation

Abstract: We consider the problem of selecting a model having the best predictive ability among a class of linear models. The popular leave-one-out cross-validation method, which is asymptotically equivalent to many other model selection methods such as the Akaike information criterion (AIC), the C p , and the bootstrap, is asymptotically inconsistent in the sense that the probability of selecting the model with the best predictive ability does not converge to 1 as the total number of observations n → ∞. We show that the inconsistency of the leave-one-out cross-validation can be rectified by using a leave-n v -out cross-validation with n v , the number of observations reserved for validation, satisfying n v /n → 1 as n → ∞. This is a somewhat shocking discovery, because nv/n → 1 is totally opposite to the popular leave-one-out recipe in cross-validation. Motivations, justifications, and discussions of some practical aspects of the use of the leave-n v -out cross-validation method are provided, and results ...

Development of obesity in transgenic mice after genetic ablation of brown adipose tissue

Abstract: Brown adipose tissue, because of its capacity for uncoupled mitochondrial respiration, has been implicated as an important site of facultative energy expenditure. This has led to speculation that this tissue normally functions to prevent obesity. Attempts to ablate or denervate brown adipose tissue surgically have been uninformative because it exists in diffuse depots and has substantial capacity for regeneration and hypertrophy. Here we have used a transgenic toxigene approach to create two lines of transgenic mice with primary deficiency of brown adipose tissue. At 16 days, both lines have decreased brown fat and obesity. In one line, brown fat subsequently regenerates and obesity resolves. In the other line, the deficiency persists and obesity, with its morbid complications, advances. Obesity develops in the absence of hyperphagia, indicating that brown fat deficient mice have increased metabolic efficiency. As obesity progresses, transgenic animals develop hyperphagia. This study supports a critical role for brown adipose tissue in the nutritional homeostasis of mice.

On the Assessment of Intrinsic, Extrinsic, and Amotivation in Education: Evidence on the Concurrent and Construct Validity of the Academic Motivation Scale:

Abstract: A new measure of motivation toward education has been developed in French, namely the "Echelle de Motivation en Education" (EME). The EME is based on the tenets of self-determination theory and is ...

Guidelines for the recording and quantitative analysis of electroencephalographic activity in research contexts.

Abstract: Developments in technologic and analytical procedures applied to the study of brain electrical activity have intensified interest in this modality as a means of examining brain function. The impact of these new developments on traditional methods of acquiring and analyzing electroencephalographic activity requires evaluation. Ultimately, the integration of the old with the new must result in an accepted standardized methodology to be used in these investigations. In this paper, basic procedures and recent developments involved in the recording and analysis of brain electrical activity are discussed and recommendations are made, with emphasis on psychophysiological applications of these procedures.

Direct gene transfer into skeletal muscle in vivo: factors affecting efficiency of transfer and stability of expression.

Abstract: Striated muscle is the only tissue found to be capable of taking up and expressing reporter genes that are transferred in the form of plasmid DNA. Thus, direct gene transfer is a potential method of gene therapy for the primary inherited myopathies. However, results to date have had insufficient and too variable expression to consider using direct gene transfer in human trials. We have determined that much of the variability of expression is due to nonuniform distribution of substances injected into skeletal muscle in vivo, and have developed a model to ameliorate this. Preinjection of muscles with a relatively large volume of hypertonic sucrose improves the distribution of injected substances and results in significantly less variable expression of reporter genes for luciferase or β-galactosidase; the coefficient of variation for mean luciferase activity was reduced from about 120% to 25%. Expression is not directly proportional to dose, but is more so if the muscles are preinjected with sucrose...

Stochastic resonance in neuron models

Abstract: Periodically stimulated sensory neurons typically exhibit a kind of “statistical phase locking” to the stimulus: they tend to fire at a preferred phase of the stimulus cycle, but not at every cycle. Hence, the histogram of interspike intervals (ISIH), i.e., of times between successive firings, is multimodal for these neurons, with peaks centered at integer multiples of the driving period. A particular kind of residence time histogram for a large class of noisy bistable systems has recently been shown to exhibit the major features of the neural data. In the present paper, we show that an excitable cell model, the Fitzhugh-Nagumo equations, also reproduces these features when driven by additive periodic and stochastic forces. This model exhibits its own brand of stochastic resonance as the peaks of the ISIH successively go through a maximum when the noise intensity is increased. Further, the presence of a noise-induced limit cycle introduces a third time scale in the problem. This limit cycle is found to modify qualitatively the phase-locking picture, e.g., by suppressing certain peaks in the ISIH. Finally, the role of noise and possibly of stochastic resonance (SR) in the neural encoding of sensory information is discussed.

Decision Rules for the Use of Radiography in Acute Ankle Injuries: Refinement and Prospective Validation

Abstract: In the second stage, the refined rules proved to have sensitivities of 1.0 (95% CI, 0.93 to 1.0) for 50 malleolar zone fractures, and 1.0 (95% CI, 0.83 to 1.0) for 19 midfoot zone fractures. The potential reduction in radiography is estimated to be 34% for the ankle series and 30% for the foot series. The probability of fracture, if the corresponding decision rule were "negative," is estimated to be 0% (95% CI, 0% to 0.8%) in the ankle series, and 0% (95% CI, 0% to 0.4%) in the foot series. Conclusion.\p=m-\Refinementand validation have shown the Ottawa ankle rules to be 100% sensitive for fractures, to be reliable, and to have the potential to allow physicians to safely reduce the number of radiographs ordered in patients with ankle injuries by one third. Field trials will assess the feasibility of implementing these rules into clinical practice.

DNA-based immunization induces continuous secretion of hepatitis B surface antigen and high levels of circulating antibody

Abstract: The possibility of inducing an immune response to a protein expressed directly from an introduced gene represents an alternative to classic vaccination. We evaluated the ability of plasmid-based eukaryotic expression vectors to produce the Hepatitis B surface antigen (HBsAg) after injection of pure DNA into mouse tibialis anterior muscles. DNA was injected into either normal mature muscle, or regenerating muscle following cardiotoxin-induced degeneration. The sera obtained from these animals contained significant levels of HBsAg as early as 10 days after gene transfer, at which time low levels of antibodies to HBsAg (anti-HBsAg) were already present. Between 15-60 d after DNA transfer, serum levels of anti-HBsAg steadily increased whereas those for HbsAg fell, most likely due to the neutralizing effect of the antibodies. Analysis of proportions of HBs-seropositive mice showed that within 2 wk of injection of 100 micrograms pCMV-HBs in regenerating muscle, 91% of the mice were seropositive [defined as having more than 1 milli-International Unit/ml (mIU/ml) of anti-HBsAg]. Even at that early time, 68% had titers of anti-HBsAg greater than 10 mlU/ml, a level that is recognized as being sufficient in humans to confer protection against natural Hepatitis B virus infection. The proportion of seropositive animals rose to 95% by 4 wk, and 100% by 8 wk, at which time all mice had greater than 100 mIU anti-HBsAg in their sera. We have thus demonstrated that direct intramuscular injection of a plasmid vector encoding the HBsAg will give rise to secretion of the viral surface protein into the circulation which leads to an appropriate antibody response.(ABSTRACT TRUNCATED AT 250 WORDS)

P19 embryonal carcinoma cells.

Abstract: P19 cells are a line of pluripotent embryonal carcinoma able to grow continuously in serum-supplemented media. The differentiation of these cells can be controlled by nontoxic drugs. Retinoic acid effectively induces the development of neurons, astroglia and microglia--cell types normally derived from the neuroectoderm. Aggregates of P19 cells exposed to dimethyl sulfoxide differentiate into endodermal and mesodermal derivatives including cardiac and skeletal muscle. P19 cells can be effectively transfected with DNA encoding recombinant genes and stable lines expressing these genes can be readily isolated. These manipulations make P19 cells suitable material for investigating the molecular mechanisms governing developmental decision made by differentiating pluripotent cells.

Two Controlled Trials of Rifabutin Prophylaxis against Mycobacterium avium Complex Infection in AIDS

Abstract: Background Disseminated Mycobacterium avium complex infection eventually develops in most patients with the acquired immunodeficiency syndrome (AIDS). This infection results in substantial morbidity and reduces survival by about six months. Methods We conducted two randomized, double-blind, multicenter trials of daily prophylactic treatment with either rifabutin (300 mg) or placebo. All the patients had AIDS and CD4 cell counts ≤ 200 per cubic millimeter. The primary end point was M. avium complex bacteremia as assessed monthly by blood culture. The secondary end points were signs and symptoms associated with disseminated M. avium complex infection, adverse events, hospitalization, and survival. Results In the first trial, M. avium complex bacteremia developed in 51 of 298 patients (17 percent) assigned to placebo and 24 of 292 patients (8 percent) assigned to rifabutin (P<0.001). In the second trial, bacteremia developed in 51 of 282 patients in the placebo group (18 percent) and 24 of 274 patients in th...

Partners in defense, vitamin E and vitamin C

Abstract: In addition to the enzymic mechanism of free-radical removal, essential nutrients that can scavenge free radicals, such as vitamins E and C, constitute a strong line of defense in retarding free radical induced cellular damage. Distinct pathways for the repair of oxidized vitamin E in human cells have been recently identified. Within 0.5 min after the addition of arachidonic acid to a human platelet homogenate, over half of the platelet vitamin E and added arachidonate were metabolized by platelet cyclooxygenase and lipoxygenase pathways. After adding nordihydroguaiaretic acid, a lipoxygenase inhibitor and a strong reductant, over 60% of the oxidized vitamin E was regenerated. To test other physiological, water-soluble reductants that may help regenerate vitamin E, eicosatetraynoic acid, a lipoxygenase inhibitor that is not an antioxidant, was used. In this system, both ascorbate and glutathione provided significant vitamin E regeneration. Kinetic analysis and studies of vitamin E regeneration in a protein-denaturing system revealed that ascorbate regenerates vitamin E by a nonenzymic mechanism, whereas glutathione regenerates vitamin E enzymatically. These studies suggest that significant interaction occurs between water- and lipid-soluble molecules at the membrane-cytosol interface and that vitamin C may function in vivo to repair the membrane-bound oxidized vitamin E.

Plasmid DNA Is Superior to Viral Vectors for Direct Gene Transfer into Adult Mouse Skeletal Muscle

Abstract: Direct gene transfer into skeletal muscle offers several therapeutic possibilities. We assessed direct intramuscular injection of recombinant plasmids, adenovirus, or retrovirus in normal or regenerating muscles of mice. The incorporation and expression of reporter genes introduced by any of these three vectors is greater in regenerating than in mature muscle. In regenerating muscle, pure DNA and adenovirus result in equivalent numbers of fibers expressing reporter gene (> 10%), but adenovirus also induces considerable cellular infiltration. In mature muscle, recombinant DNA is better than adenovirus. Retrovirus failed to infect mature muscle fibers and was less effective than plasmid DNA or adenovirus in regenerating muscle. The surprisingly high relative efficiency of pure plasmid DNA suggests that this method will provide a simple, safe and viable alternative for gene therapy involving muscle tissue.

Can disturbed brain microcirculation cause Alzheimer’s disease?

Abstract: Recent ultrastructural studies demonstrate characteristic and extensive angioarchitectural distortions of cerebral capillaries in Alzheimer’s brains. Alzheimer’s disease subjects additionally show ...

Ocular artifacts in EEG and event-related potentials. I: Scalp topography.

Abstract: The ocular artifacts that contaminate the EEG derive from the potential difference between the cornea and the fundus of the eye. This corneofundal or corneoretinal potential can be considered as an equivalent dipole with its positive pole directed toward the cornea. The cornea shows a steady DC potential of approximately +13 mV relative to the forehead. Blink potentials are caused by the eyelids sliding down over the positively charged cornea. The artifacts from eye-movements result from changes in orientation of the corneo-fundal potential. The scalp-distribution of the ocular artifacts can be described in terms of propagation factors--the fraction of the EOG signal at periocular electrodes that is recorded at a particular scalp location. These factors vary with the location of the scalp electrode. Propagation factors for blinks and upward eye-movements are significantly different.

Relative Power of the Wilcoxon Test, the Friedman Test, and Repeated-Measures ANOVA on Ranks

Abstract: Many introductory statistics textbooks in education, psychology, and the social sciences consider the Friedman test to be a nonparametric counterpart of repeated-measures ANOVA, just as the Kruskal-Wallis test is a counterpart of oneway ANOVA However, it is known in theoretical statistics that the Friedman test is a generalization of the sign test and possesses the modest statistical power of the sign test for normal as well as many nonnormal distributions Although not familiar to researchers, another significance test that can be regarded as a nonparametric counterpart of repeated-measures ANOVA is a rank-transformation procedure, in which the usual parametric statistical analysis is performed on ranks replacing the original scores In the present computer simulation study we compared the ordinary paired-samples Student t test, the Wilcoxon signed-ranks test, and the sign test for correlated samples from normal, uniform, mixed-normal, exponential, Laplace, and Cauchy distributions, for which t

The Maslach Burnout Inventory: Testing for factorial validity and invariance across elementary, intermediate and secondary teachers

Abstract: The purposes of the study were: (a) to test for the factorial validity of the Maslach Burnout Inventory (MBI) separately for elementary (N = 1159), intermediate (N = 388) and secondary (N = 1384) teachers; (b) given findings of inadequate model fit, to propose and test an alternative factorial structure; (c) to cross-validate this structure across an independent sample for each teacher group; and (d) to test for the equivalence of item measurements and theoretical structure across these three teaching panels. Although confirmatory and exploratory factor analytic findings supported a three-factor structure, the deletion of two items (nos 12 and 16) yielded a better fitting model that was, for the most part, psychometrically and structurally invariant across groups. This study is the most rigorous to date in testing the factorial validity of the MBI in general, and as it bears on members of the teaching profession in particular.

Is the selection of statistical methods governed by level of measurement

Abstract: The notion that nonparametric methods are required as a replacement of parametric statistical methods when the scale of measurement in a research study does not achieve a certain level was discussed in light of recent developments in representational measurement theory. A new approach to examining the problem via computer simulation was introduced. Some of the beliefs that have been widely held by psychologists for several decades were examined by means of a computer simulation study that mimicked measurement of an underlying empirical structure and performed two - sample Student t - tests on the resulting sample data. It was concluded that there is no need to replace parametric statistical tests by nonparametric methods when the scale of measurement is ordinal and not interval.Stevens' (1946) classic paper on the theory of scales of measurement triggered one of the longest standing debates in behavioural science methodology. The debate -- referred to as the levels of measurement controversy, or measurement - statistics debate -- is over the use of parametric and nonparametric statistics and its relation to levels of measurement. Stevens (1946; 1951; 1959; 1968), Siegel (1956), and most recently Siegel and Castellan (1988) and Conover (1980) argue that parametric statistics should be restricted to data of interval scale or higher. Furthermore, nonparametric statistics should be used on data of ordinal scale. Of course, since each scale of measurement has all of the properties of the weaker measurement, statistical methods requiring only a weaker scale may be used with the stronger scales. A detailed historical review linking Stevens' work on scales of measurement to the acceptance of psychology as a science, and a pedagogical presentation of fundamental axiomatic (i.e., representational) measurement can be found in Zumbo and Zimmerman (1991).Many modes of argumentation can be seen in the debate about levels of measurement and statistics. This paper focusses almost exclusively on an empirical form of rhetoric using experimental mathematics (Ripley, 1987). The term experimental mathematics comes from mathematical physics. It is loosely defined as the mimicking of the rules of a model of some kind via random processes. In the methodological literature this is often referred to as monte carlo simulation. However, for the purpose of this paper, the terms experimental mathematics or computer simulation are preferred to monte carlo because the latter is typically referred to when examining the robustness of a test in relation to particular statistical assumptions. Measurement level is not an assumption of the parametric statistical model (see Zumbo & Zimmerman, 1991 for a discussion of this issue) and to call the method used herein "monte carlo" would imply otherwise. The term experimental mathematics emphasizes the modelling aspect of the present approach to the debate.The purpose of this paper is to present a new paradigm using experimental mathematics to examine the claims made in the levels of measurement controversy. As Michell (1986) demonstrated, the concern over levels of measurement is inextricably tied to the differing notions of measurement and scaling. Michell further argued that fundamental axiomatic measurement or representational theory (see, for example, Narens & Luce, 1986) is the only measurement theory which implies a relation between measurement scales and statistics. Therefore, the approach advocated in this paper is linked closely to representational theory. The novelty of this approach, to the authors knowledge, is in the use of experimental mathematics to mimic representational measurement. Before describing the methodology used in this paper, we will briefly review its motivation.Admissible TransformationsRepresentational theory began in the late 1950's with Scott and Suppes (1958) and later with Suppes and Zinnes (1963), Pfanzagl (1968), and Krantz, Luce, Suppes & Tversky (1971). …

A functional classification of wetland plants.

Abstract: . In this paper we review the search for guilds in plant communities, and provide a summary of the process, emphasizing five steps: (1) defining function, (2) selecting traits which reflect function, (3) screening for those traits, (4) constructing trait matrices, and (5) grouping species according to these traits. We illustrate this process for wetland plant species based upon a matrix of 27 traits and 43 species from across eastern North America. The 43 species were selected to represent the widest range of life history types possible as well as both common species and nationally rare or endangered species. We found three main functional groups: ruderals, matrix and interstitial species, which we subdivide into a total of seven guilds. The growing number of such studies in the literature suggest that this may be an expedient measure for conservation biology and a promising one for predictions.

Ocular artifacts in recording EEGs and event-related potentials II: Source dipoles and source components

Abstract: The source dipoles for blinks point radially whereas the source dipoles for saccades point tangentially, in the direction of the eye movement. This indicates that blink potentials are not generated by eye movements but by the eyelid sliding down over the positively charged cornea. Dipole source dipole analysis shows that the “rider artifact” at the onset of upward and lateral saccades is caused by the eyelid as it lags a little behind the eyes at the beginning of the movement. Dipole source analysis allows both the EEG and the EOG to be modeled simultaneously and EOG generators to be distinguished from nearby EEG generators. Ocular source components can be calculated from a principal component analysis of EEG and EOG recordings during blinks and saccades. The effectiveness of propagation factors, source dipoles and source components in removing ocular artifacts from EEG samples was assessed. The most effective correction procedure uses source components.

Trans-splicing of pre-mRNA in plants, animals, and protists

Abstract: Messenger RNA maturation in eukaryotes typically involves the removal of introns from long precursor molecules. An unusual form of RNA splicing in which separate precursor transcripts contribute sequences to the mature mRNA through intermolecular reactions has now been documented in a number of diverse organisms. In this review, the phenomenon of pre-mRNA trans-splicing has been divided into two categories. The "spliced leader" type, found in protozoans such as trypanosomes and lower invertebrates such as nematodes, results in the addition of a short, capped 5' noncoding sequence to the mRNA. The "discontinuous group II intron" form of trans-splicing, found in plant/algal chloroplasts and plant mitochondria, involves the joining of independently transcribed coding sequences, presumably through interactions between "intronic" RNA pieces. Both categories of trans-splicing are mechanistically similar to conventional nuclear pre-mRNA cis-splicing; potential evolutionary relationships are discussed.

Glycosylation is necessary for the correct folding of human immunodeficiency virus gp120 in CD4 binding.

Abstract: Conflicting results have been reported regarding the role of carbohydrate on human immunodeficiency virus (HIV) envelope glycoprotein gp120 in CD4 receptor binding. Glycosylated, deglycosylated, and nonglycosylated forms of HIV type 1 (HIV-1) and HIV-2 gp120s were used to examine CD4 receptor-binding activity. Nonglycosylated forms of gp120 generated either by deletion of the signal sequence of HIV-1 gp120 or by synthesis in the presence of tunicamycin failed to bind to CD4. In contrast, highly mannosylated gp120 bound to soluble CD4 molecules well. Enzymatic removal of carbohydrate chains from glycosylated gp120 by endoglycosidase H or an endoglycosidase F/N glycanase mixture had no effect on the ability of gp120 to bind CD4. An experiment which measured the ability of gp120 to bind to CD4 as an assay of the proper conformation of gp120 showed that carbohydrate chains on gp120 are not required for the interaction between gp120 and CD4 but that N-linked glycosylation is essential for generation of the proper conformation of gp120 to provide a CD4-binding site. Images

Mouse oocytes regulate granulosa cell steroidogenesis

Abstract: Recent studies have demonstrated a critical role for the oocyte in proliferation and differentiation of granulosa cells and expansion of the cumulus oophorus in vitro The purpose of this study was to determine if steroid production by cumulus granulosa cells was also modulated by oocytes Mouse oocyte-cumulus cell complexes (intact) and complexes from which the oocytes were removed microsurgically (oocytectomized; OOX) were cultured for 24 h in the presence or absence of follicle-stimulating hormone (FSH; 150 ng/ml), testosterone (T; 5 x 10(-7) M) or both Oocytectomy had no effect on the ability of cumulus cells to produce progesterone or estradiol in control cultures or in response to T However, OOX complexes produced 17- and 36-fold more progesterone than intact complexes when cultured in the presence of FSH or FSH+T, respectively Oocyte-conditioned medium (maximum 1 oocyte/2 microliters) had no effect on progesterone production by intact cumulus complexes, but reduced the progesterone production by

Postarthroscopy analgesia with intraarticular bupivacaine/morphine. A randomized clinical trial.

Abstract: Background:Postarthroscopy analgesia has been provided with intraarticular bupivacaine, but the duration of analgesia may be only a few hours. More recently, longer-lasting analgesia has been achieved using intraarticular morphine, although the onset of analgesia may be delayed. The combination of i

pH-dissociation characteristics of cardiolipin and its 2′-deoxy analogue

Abstract: Cardiolipin (CL) is found in inner mitochondrial membranes and the plasma membrane of aerobic prokaryotes. CL is tightly bound to those transmembrane enzymes associated with oxidative phosphorylation. CL has earlier been reported to have a single pK at low pH. We have titrated CL in aqueous suspension (bilayers) and in solution in methanol/water (1∶1, vol/vol) and found it to display two different pK values, pK1 at 2.8 and pK2 initially at 7.5 but shifting upwards to 9.5 as the titration proceeds. The unusually high pK2 might be explained by the formation of a unique hydrogen bond in which the free hydroxyl on the central glycerol forms a cyclic intramolecular hydrogen-bonded structure with one protonated phosphate (P-OH group). We have therefore chemically synthesized the 2′-deoxycardiolipin analogue, which lacks the central free hydroxyl group, and measured its pH-dissociation behavior by potentiometric titration, under the same conditions as those for CL. The absence of the hydroxyl group changes the titration dramatically so that the deoxy analogue displays two closely spaced low pK values (pK1=1.8; pK2=4.0). The anomalous titration behavior of the second dissociation constant of CL may be attributed to the participation of the central glycerol OH group in stabilizing the formation of a cyclic hydrogen-bonded monoprotonated form of CL, which may function as a reservoir of protons at relatively high pH. This function may have an important bearing on proton pumping in biological membranes.