Showing papers by "University of British Columbia published in 2002"
TL;DR: DNA microarrays can be used to formulate a molecular predictor of survival after chemotherapy for diffuse large-B-cell lymphoma and this gene-based predictor and the international prognostic index were independent prognostic indicators.
Abstract: Background The survival of patients with diffuse large-B-cell lymphoma after chemotherapy is influenced by molecular features of the tumors. We used the gene-expression profiles of these lymphomas to develop a molecular predictor of survival. Methods Biopsy samples of diffuse large-B-cell lymphoma from 240 patients were examined for gene expression with the use of DNA microarrays and analyzed for genomic abnormalities. Subgroups with distinctive gene-expression profiles were defined on the basis of hierarchical clustering. A molecular predictor of risk was constructed with the use of genes with expression patterns that were associated with survival in a preliminary group of 160 patients and was then tested in a validation group of 80 patients. The accuracy of this predictor was compared with that of the international prognostic index. Results Three gene-expression subgroups — germinal-center B-cell–like, activated B-cell–like, and type 3 diffuse large-B-cell lymphoma — were identified. Two common oncogeni...
3,510 citations
TL;DR: In this paper, the authors evaluated the Dark Triad of personality traits, namely Machiavellianism, subclinical narcissism, and subclinical psychopathy, in a sample of 245 students and concluded that they are overlapping but distinct constructs.
3,353 citations
TL;DR: Zoning the oceans into unfished marine reserves and areas with limited levels of fishing effort would allow sustainable fisheries, based on resources embedded in functional, diverse ecosystems.
Abstract: Fisheries have rarely been 'sustainable'. Rather, fishing has induced serial depletions, long masked by improved technology, geographic expansion and exploitation of previously spurned species lower in the food web. With global catches declining since the late 1980s, continuation of present trends will lead to supply shortfall, for which aquaculture cannot be expected to compensate, and may well exacerbate. Reducing fishing capacity to appropriate levels will require strong reductions of subsidies. Zoning the oceans into unfished marine reserves and areas with limited levels of fishing effort would allow sustainable fisheries, based on resources embedded in functional, diverse ecosystems.
2,896 citations
TL;DR: It is reported that newly generated cells in the adult mouse hippocampus have neuronal morphology and can display passive membrane properties, action potentials and functional synaptic inputs similar to those found in mature dentate granule cells.
Abstract: There is extensive evidence indicating that new neurons are generated in the dentate gyrus of the adult mammalian hippocampus, a region of the brain that is important for learning and memory1,2,3,4,5. However, it is not known whether these new neurons become functional, as the methods used to study adult neurogenesis are limited to fixed tissue. We use here a retroviral vector expressing green fluorescent protein that only labels dividing cells, and that can be visualized in live hippocampal slices. We report that newly generated cells in the adult mouse hippocampus have neuronal morphology and can display passive membrane properties, action potentials and functional synaptic inputs similar to those found in mature dentate granule cells. Our findings demonstrate that newly generated cells mature into functional neurons in the adult mammalian brain.
2,822 citations
TL;DR: Observations of neutral-current nu interactions on deuterium in the Sudbury Neutrino Observatory are reported, providing strong evidence for solar nu(e) flavor transformation.
Abstract: Observations of neutral-current nu interactions on deuterium in the Sudbury Neutrino Observatory are reported. Using the neutral current (NC), elastic scattering, and charged current reactions and assuming the standard 8B shape, the nu(e) component of the 8B solar flux is phis(e) = 1.76(+0.05)(-0.05)(stat)(+0.09)(-0.09)(syst) x 10(6) cm(-2) s(-1) for a kinetic energy threshold of 5 MeV. The non-nu(e) component is phi(mu)(tau) = 3.41(+0.45)(-0.45)(stat)(+0.48)(-0.45)(syst) x 10(6) cm(-2) s(-1), 5.3sigma greater than zero, providing strong evidence for solar nu(e) flavor transformation. The total flux measured with the NC reaction is phi(NC) = 5.09(+0.44)(-0.43)(stat)(+0.46)(-0.43)(syst) x 10(6) cm(-2) s(-1), consistent with solar models.
2,732 citations
TL;DR: In this paper, a set of MATLAB programs have been written to perform classical harmonic analysis for periods of about 1 year or shorter, account for unresolved constituents using nodal corrections, and compute confidence intervals for the analyzed components.
2,403 citations
National Institutes of Health1, Science Applications International Corporation2, Invitrogen3, University of California, Berkeley4, University of Iowa5, Lawrence Livermore National Laboratory6, Incyte7, Baylor College of Medicine8, Institute for Systems Biology9, Stanford University10, University of British Columbia11
TL;DR: The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene.
Abstract: The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene. ESTs were generated from libraries enriched for full-length cDNAs and analyzed to identify candidate full-ORF clones, which then were sequenced to high accuracy. The MGC has currently sequenced and verified the full ORF for a nonredundant set of >9,000 human and >6,000 mouse genes. Candidate full-ORF clones for an additional 7,800 human and 3,500 mouse genes also have been identified. All MGC sequences and clones are available without restriction through public databases and clone distribution networks (see http:mgc.nci.nih.gov).
2,184 citations
TL;DR: A form of k -fold cross validation for evaluating prediction success is proposed for presence/available RSF models, which involves calculating the correlation between RSF ranks and area-adjusted frequencies for a withheld sub-sample of data.
2,107 citations
28 May 2002
TL;DR: This work shows how to cluster words that individually are difficult to predict into clusters that can be predicted well, and cannot predict the distinction between train and locomotive using the current set of features, but can predict the underlying concept.
Abstract: We describe a model of object recognition as machine translation. In this model, recognition is a process of annotating image regions with words. Firstly, images are segmented into regions, which are classified into region types using a variety of features. A mapping between region types and keywords supplied with the images, is then learned, using a method based around EM. This process is analogous with learning a lexicon from an aligned bitext. For the implementation we describe, these words are nouns taken from a large vocabulary. On a large test set, the method can predict numerous words with high accuracy. Simple methods identify words that cannot be predicted well. We show how to cluster words that individually are difficult to predict into clusters that can be predicted well -- for example, we cannot predict the distinction between train and locomotive using the current set of features, but we can predict the underlying concept. The method is trained on a substantial collection of images. Extensive experimental results illustrate the strengths and weaknesses of the approach.
1,765 citations
TL;DR: It is shown that the biomass, growth and reproduction of alpine plant species are higher when other plants are nearby, and that competition generally, but not exclusively, dominates interactions at lower elevations where conditions are less physically stressful.
Abstract: Plants can have positive effects on each other. For example, the accumulation of nutrients, provision of shade, amelioration of disturbance, or protection from herbivores by some species can enhance the performance of neighbouring species. Thus the notion that the distributions and abundances of plant species are independent of other species may be inadequate as a theoretical underpinning for understanding species coexistence and diversity. But there have been no large-scale experiments designed to examine the generality of positive interactions in plant communities and their importance relative to competition. Here we show that the biomass, growth and reproduction of alpine plant species are higher when other plants are nearby. In an experiment conducted in subalpine and alpine plant communities with 115 species in 11 different mountain ranges, we find that competition generally, but not exclusively, dominates interactions at lower elevations where conditions are less physically stressful. In contrast, at high elevations where abiotic stress is high the interactions among plants are predominantly positive. Furthermore, across all high and low sites positive interactions are more important at sites with low temperatures in the early summer, but competition prevails at warmer sites.
1,587 citations
TL;DR: Various risk factors were shown to be positively associated with a risk for, or protection from, specific injuries, and future research should include a non-injured control group and a more precise measure of weekly running distance and running experience to validate these results.
Abstract: Results: Most of the study group were women (54%). Some injuries occurred with a significantly higher frequency in one sex. Being less than 34 years old was reported as a risk factor across the sexes for patellofemoral pain syndrome, and in men for iliotibial band friction syndrome, patellar tendinopathy, and tibial stress syndrome. Being active for less than 8.5 years was positively associated with injury in both sexes for tibial stress syndrome; and women with a body mass index less than 21 kg/m 2 were at a significantly higher risk for tibial stress fractures and spinal injuries. Patellofemoral pain syndrome was the most common injury, followed by iliotibial band friction syndrome, plantar fasciitis, meniscal injuries of the knee, and tibial stress syndrome. Conclusions: Although various risk factors were shown to be positively associated with a risk for, or protection from, specific injuries, future research should include a non-injured control group and a more precise measure of weekly running distance and running experience to validate these results.
University of Cambridge1, Conservation International2, University of East Anglia3, University of Maryland Center for Environmental Science4, University of Pittsburgh5, Royal Society for the Protection of Birds6, World Conservation Monitoring Centre7, University of British Columbia8, University of Washington9, Stanford University10
TL;DR: It is estimated that the overall benefit:cost ratio of an effective global program for the conservation of remaining wild nature is at least 100:1.
Abstract: On the eve of the World Summit on Sustainable Development, it is timely to assess progress over the 10 years since its predecessor in Rio de Janeiro. Loss and degradation of remaining natural habitats has continued largely unabated. However, evidence has been accumulating that such systems generate marked economic benefits, which the available data suggest exceed those obtained from continued habitat conversion. We estimate that the overall benefit:cost ratio of an effective global program for the conservation of remaining wild nature is at least 100:1.
TL;DR: It is now recognized that MMP activity is tightly regulated at several levels, providing new avenues for blocking these enzymes and leading to new therapeutic strategies for cancer.
Abstract: For more than two decades, the view that tumour-associated matrix metalloproteinases (MMPs) were required for peritumour tissue degradation and metastasis dominated the drive to develop MMP inhibitors as anticancer therapeutics. Until recently, clinical trials with MMP inhibitors have yielded disappointing results, highlighting the need for better insight into the mechanisms by which this growing family of multifunctional enzymes contribute to tumour growth. It is now recognized that MMP activity is tightly regulated at several levels, providing new avenues for blocking these enzymes. What are the different approaches that can be used to target MMPs, and which of these might lead to new therapeutic strategies for cancer?
TL;DR: The results of field injection of molasses, nitrate, and low-arsenic water show that organic carbon or its degradation products may quickly mobilize arsenic, oxidants may lower arsenic concentrations, and sorption of arsenic is limited by saturation of aquifer materials.
Abstract: High levels of arsenic in well water are causing widespread poisoning in Bangladesh. In a typical aquifer in southern Bangladesh, chemical data imply that arsenic mobilization is associated with recent inflow of carbon. High concentrations of radiocarbon-young methane indicate that young carbon has driven recent biogeochemical processes, and irrigation pumping is sufficient to have drawn water to the depth where dissolved arsenic is at a maximum. The results of field injection of molasses, nitrate, and low-arsenic water show that organic carbon or its degradation products may quickly mobilize arsenic, oxidants may lower arsenic concentrations, and sorption of arsenic is limited by saturation of aquifer materials.
TL;DR: A new clustering method is proposed, called CLARANS, whose aim is to identify spatial structures that may be present in the data, and two spatial data mining algorithms that aim to discover relationships between spatial and nonspatial attributes are developed.
Abstract: Spatial data mining is the discovery of interesting relationships and characteristics that may exist implicitly in spatial databases. To this end, this paper has three main contributions. First, it proposes a new clustering method called CLARANS, whose aim is to identify spatial structures that may be present in the data. Experimental results indicate that, when compared with existing clustering methods, CLARANS is very efficient and effective. Second, the paper investigates how CLARANS can handle not only point objects, but also polygon objects efficiently. One of the methods considered, called the IR-approximation, is very efficient in clustering convex and nonconvex polygon objects. Third, building on top of CLARANS, the paper develops two spatial data mining algorithms that aim to discover relationships between spatial and nonspatial attributes. Both algorithms can discover knowledge that is difficult to find with existing spatial data mining algorithms.
TL;DR: This paper found negative correlations between maximizing and happiness, optimism, self-esteem, and life satisfaction, and positive correlations between maximization and depression, perfectionism, and regret, and found that maximizers are less satisfied than non-maximizers with consumer decisions, and more likely to engage in social comparison.
Abstract: Can people feel worse off as the options they face increase? The present studies suggest that some people--maximizers--can. Study 1 reported a Maximization Scale, which measures individual differences in desire to maximize. Seven samples revealed negative correlations between maximization and happiness, optimism, self-esteem, and life satisfaction, and positive correlations between maximization and depression, perfectionism, and regret. Study 2 found maximizers less satisfied than nonmaximizers (satisficers) with consumer decisions, and more likely to engage in social comparison. Study 3 found maximizers more adversely affected by upward social comparison. Study 4 found maximizers more sensitive to regret and less satisfied in an ultimatum bargaining game. The interaction between maximizing and choice is discussed in terms of regret, adaptation, and self-blame.
TL;DR: It is shown that infants are sensitive to the statistical distribution of speech sounds in the input language, and that this sensitivity influences speech perception.
University of California, San Diego1, Fred Hutchinson Cancer Research Center2, University of Washington3, University of California, Los Angeles4, University of British Columbia5, McGill University6, University of Alabama7, Monogram Biosciences8, Veterans Health Administration9, University of Colorado Denver10
TL;DR: Testing for resistance to drugs before therapy begins is now indicated even for recently infected patients, as the proportion of new HIV infections that involve drug-resistant virus is increasing in North America.
Abstract: Background Among persons in North America who are newly infected with the human immunodeficiency virus (HIV), the prevalence of transmitted resistance to antiretroviral drugs has been estimated at 1 to 11 percent. Methods We performed a retrospective analysis of susceptibility to antiretroviral drugs before treatment and drug-resistance mutations in HIV in plasma samples from 377 subjects with primary HIV infection who had not yet received treatment and who were identified between May 1995 and June 2000 in 10 North American cities. Responses to treatment could be evaluated in 202 subjects. Results Over the five-year period, the frequency of transmitted drug resistance increased significantly. The frequency of high-level resistance to one or more drugs (indicated by a value of more than 10 for the ratio of the 50 percent inhibitory concentration [IC50] for the subject's virus to the IC50 for a drug-sensitive reference virus) increased from 3.4 percent during the period from 1995 to 1998 to 12.4 percent dur...
Harvard University1, University of Missouri2, University of British Columbia3, Heriot-Watt University4, Indiana University5, Salk Institute for Biological Studies6, Leibniz Association7, Boyce Thompson Institute for Plant Research8, Nagoya University9, University of Copenhagen10, University of Tsukuba11
TL;DR: A simplified nomenclature for Arabidopsis MAPKs and MAPK kinases is proposed that might also serve as a basis for standard annotation of these gene families in all plants.
TL;DR: It is shown that MLL regulates target Hox gene expression through direct binding to promoter sequences and the MLL SET domain is a histone H3 lysine 4-specific methyltransferase whose activity is stimulated with acetylated H3 peptides.
TL;DR: It is shown that lymphoblast mitochondria from patients with HD have a lower membrane potential and depolarize at lower calcium loads than do mitochondriaFrom controls, and mitochondrial calcium abnormalities occur early in HD pathogenesis and may be a direct effect of mutant huntingtin on the organelle.
Abstract: Huntington's disease (HD) is caused by an expansion of exonic CAG triplet repeats in the gene encoding huntingtin protein (Htt), but the mechanisms by which this mutant protein causes neurodegeneration remain unknown. Here we show that lymphoblast mitochondria from patients with HD have a lower membrane potential and depolarize at lower calcium loads than do mitochondria from controls. We found a similar defect in brain mitochondria from transgenic mice expressing full-length mutant huntingtin, and this defect preceded the onset of pathological or behavioral abnormalities by months. By electron microscopy, we identified N-terminal mutant huntingtin on neuronal mitochondrial membranes, and by incubating normal mitochondria with a fusion protein containing an abnormally long polyglutamine repeat, we reproduced the mitochondrial calcium defect seen in human patients and transgenic animals. Thus, mitochondrial calcium abnormalities occur early in HD pathogenesis and may be a direct effect of mutant huntingtin on the organelle.
Posted Content•
TL;DR: In this article, international and inter-personal differences in subjective well-being over the final fifth of the twentieth century were explained using data from three waves of the World Values survey covering about fifty different countries.
Abstract: This paper attempts to explain international and inter-personal differences in subjective well-being over the final fifth of the twentieth century The empirical work makes use of data from three waves of the World Values survey covering about fifty different countries The analysis proceeds in stages First there is a brief review of some reasons for giving a key role to subjective measures of well-being This is followed by a survey of earlier empirical studies, a description of the main variables used, a report of results and tests, and discussion of the links among social capital, education, income and well-being The main innovation of the paper, relative to earlier studies of subjective well-being, lies in its use of large international samples of data combining individual and societal level variables, thus permitting the simultaneous identification of individual-level and societal-level determinants of well-being This is particularly useful in identifying the direct and indirect linkages between social capital and well-being
TL;DR: In this article, the authors transduced neurons with peptides that disrupted the interaction of NMDARs with the postsynaptic density protein PSD-95 without blocking synaptic activity or calcium influx.
Abstract: N-methyl-D-aspartate receptors (NMDARs) mediate ischemic brain damage but also mediate essential neuronal excitation. To treat stroke without blocking NMDARs, we transduced neurons with peptides that disrupted the interaction of NMDARs with the postsynaptic density protein PSD-95. This procedure dissociated NMDARs from downstream neurotoxic signaling without blocking synaptic activity or calcium influx. The peptides, when applied either before or 1 hour after an insult, protected cultured neurons from excitotoxicity, reduced focal ischemic brain damage in rats, and improved their neurological function. This approach circumvents the negative consequences associated with blocking NMDARs and may constitute a practical stroke therapy.
TL;DR: Although cultural experts agreed that East Asians are more collectivistic than North Americans, cross-cultural comparisons of trait and attitude measures failed to reveal such a pattern, the problematic nature of this reference-group effect was demonstrated.
Abstract: Social comparison theory maintains that people think about themselves compared with similar others. Those in one culture, then, compare themselves with different others and standards than do those in another culture, thus potentially confounding cross-cultural comparisons. A pilot study and Study 1 demonstrated the problematic nature of this reference-group effect: Whereas cultural experts agreed that East Asians are more collectivistic than North Americans, cross-cultural comparisons of trait and attitude measures failed to reveal such a pattern. Study 2 found that manipulating reference groups enhanced the expected cultural differences, and Study 3 revealed that people from different cultural backgrounds within the same country exhibited larger differences than did people from different countries. Cross-cultural comparisons using subjective Likert scales are compromised because of different reference groups. Possible solutions are discussed.
TL;DR: This work presents a simple but effective mechanism operating under full anonymity that shows that in voluntary public goods interactions, cooperators and defectors will coexist and shows that this result holds under very diverse assumptions on population structure and adaptation mechanisms.
Abstract: The evolution of cooperation among nonrelated individuals is one of the fundamental problems in biology and social sciences. Reciprocal altruism fails to provide a solution if interactions are not repeated often enough or groups are too large. Punishment and reward can be very effective but require that defectors can be traced and identified. Here we present a simple but effective mechanism operating under full anonymity. Optional participation can foil exploiters and overcome the social dilemma. In voluntary public goods interactions, cooperators and defectors will coexist. We show that this result holds under very diverse assumptions on population structure and adaptation mechanisms, leading usually not to an equilibrium but to an unending cycle of adjustments (a Red Queen type of evolution). Thus, voluntary participation offers an escape hatch out of some social traps. Cooperation can subsist in sizable groups even if interactions are not repeated, defectors remain anonymous, players have no memory, and assortment is purely random.
TL;DR: In conclusion, smoking has little or no independent effect on the risk of developing breast cancer; the effect of alcohol on breast cancer needs to be interpreted in the context of its beneficial effects, in moderation, on cardiovascular disease and its harmful effects on cirrhosis.
Abstract: Alcohol and tobacco consumption are closely correlated and published results on their association with breast cancer have not always allowed adequately for confounding between these exposures. Over 80% of the relevant information worldwide on alcohol and tobacco consumption and breast cancer were collated, checked and analysed centrally. Analyses included 58515 women with invasive breast cancer and 95067 controls from 53 studies. Relative risks of breast cancer were estimated, after stratifying by study, age, parity and, where appropriate, women's age when their first child was born and consumption of alcohol and tobacco. The average consumption of alcohol reported by controls from developed countries was 6.0 g per day, i.e. about half a unit/drink of alcohol per day, and was greater in ever-smokers than never-smokers, (8.4 g per day and 5.0 g per day, respectively). Compared with women who reported drinking no alcohol, the relative risk of breast cancer was 1.32 (1.19 - 1.45, P < 0.00001) for an intake of 35 - 44 g per day alcohol, and 1.46 (1.33 - 1.61, P < 0.00001) for greater than or equal to 45 g per day alcohol. The relative risk of breast cancer increased by 7.1% (95% CI 5.5-8.7%; P<0.00001) for each additional 10 g per day intake of alcohol, i.e. for each extra unit or drink of alcohol consumed on a daily basis. This increase was the same in ever-smokers and never-smokers (7.1 % per 10 g per day, P < 0.00001, in each group). By contrast, the relationship between smoking and breast cancer was substantially confounded by the effect of alcohol. When analyses were restricted to 22 255 women with breast cancer and 40 832 controls who reported drinking no alcohol, smoking was not associated with breast cancer (compared to never-smokers, relative risk for ever-smokers= 1.03, 95% CI 0.98 - 1.07, and for current smokers=0.99, 0.92 - 1.05). The results for alcohol and for tobacco did not vary substantially across studies, study designs, or according to 15 personal characteristics of the women; nor were the findings materially confounded by any of these factors. If the observed relationship for alcohol is causal, these results suggest that about 4% of the breast cancers in developed countries are attributable to alcohol. In developing countries, where alcohol consumption among controls averaged only 0.4 g per day, alcohol would have a negligible effect on the incidence of breast cancer. In conclusion, smoking has little or no independent effect on the risk of developing breast cancer; the effect of alcohol on breast cancer needs to be interpreted in the context of its beneficial effects, in moderation, on cardiovascular disease and its harmful effects on cirrhosis and cancers of the mouth, larynx, oesophagus and liver. (C) 2002 Cancer Research UK.
TL;DR: A vision-based mobile robot localization and mapping algorithm, which uses scale-invariant image features as natural landmarks in unmodified environments to localize itself accurately and build a map of the environment.
Abstract: A key component of a mobile robot system is the ability to localize itself accurately and, simultaneously, to build a map of the environment. Most of the existing algorithms are based on laser rang...
Book•
01 Jan 2002TL;DR: The cell is studied as a model for three-dimensional networks, and the role of Membrane undulations in these networks is examined.
Abstract: 1. Introduction to the cell Part I. Rods and Ropes: 2. Polymers 3. Two-dimensional networks 4. Three-dimensional networks Part II. Membranes: 5. Biomembranes 6. Membrane undulations Part III. The Whole Cell: 7. The simplest cells 8. Intermembrane forces 9. Dynamic filaments 10. Mechanical designs Appendix A. Animal cells and tissues Appendix B. The cell's molecular building blocks Appendix C. Elementary statistical mechanics Appendix D. Elasticity References Index.
TL;DR: Key hypotheses in the literature pertaining to chronic grief and resilience were tested by identifying the preloss predictors of each pattern and chronic grief was associated with preloss dependency and resilience with pre Loss acceptance of death and belief in a just world.
Abstract: The vast majority of bereavement research is conducted after a loss has occurred. Thus, knowledge of the divergent trajectories of grieving or their antecedent predictors is lacking. This study gathered prospective data on 205 individuals several years prior to the death of their spouse and at 6- and 18-months postloss. Five core bereavement patterns were identified: common grief, chronic grief, chronic depression, improvement during bereavement, and resilience. Common grief was relatively infrequent, and the resilient pattern most frequent. The authors tested key hypotheses in the literature pertaining to chronic grief and resilience by identifying the preloss predictors of each pattern. Chronic grief was associated with preloss dependency and resilience with preloss acceptance of death and belief in a just world.
TL;DR: The Sudbury Neutrino Observatory (SNO) has measured day and night solar neutrino energy spectra and rates, and a global solar neutRino analysis in terms of matter-enhanced oscillations of two active flavors strongly favors the large mixing angle solution.
Abstract: The Sudbury Neutrino Observatory (SNO) has measured day and night solar neutrino energy spectra and rates. For charged current events, assuming an undistorted 8B spectrum, the night minus day rate is 14.0%+/-6.3%(+1.5%)(-1.4%) of the average rate. If the total flux of active neutrinos is additionally constrained to have no asymmetry, the nu(e) asymmetry is found to be 7.0%+/-4.9%(+1.3%)(-1.2%). A global solar neutrino analysis in terms of matter-enhanced oscillations of two active flavors strongly favors the large mixing angle solution.