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Showing papers by "McGill University published in 2004"


Journal ArticleDOI
TL;DR: It is shown that an epigenomic state of a gene can be established through behavioral programming, and it is potentially reversible, suggesting a causal relation among epigenomicState, GR expression and the maternal effect on stress responses in the offspring.
Abstract: Here we report that increased pup licking and grooming (LG) and arched-back nursing (ABN) by rat mothers altered the offspring epigenome at a glucocorticoid receptor (GR) gene promoter in the hippocampus. Offspring of mothers that showed high levels of LG and ABN were found to have differences in DNA methylation, as compared to offspring of 'low-LG-ABN' mothers. These differences emerged over the first week of life, were reversed with cross-fostering, persisted into adulthood and were associated with altered histone acetylation and transcription factor (NGFI-A) binding to the GR promoter. Central infusion of a histone deacetylase inhibitor removed the group differences in histone acetylation, DNA methylation, NGFI-A binding, GR expression and hypothalamic-pituitary-adrenal (HPA) responses to stress, suggesting a causal relation among epigenomic state, GR expression and the maternal effect on stress responses in the offspring. Thus we show that an epigenomic state of a gene can be established through behavioral programming, and it is potentially reversible.

5,514 citations


Journal ArticleDOI
TL;DR: This framework is used to discuss why the metacommunity concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples.
Abstract: The metacommunity concept is an important way to think about linkages between different spatial scales in ecology. Here we review current understanding about this concept. We first investigate issues related to its definition as a set of local communities that are linked by dispersal of multiple potentially interacting species. We then identify four paradigms for metacommunities: the patch-dynamic view, the species-sorting view, the mass effects view and the neutral view, that each emphasizes different processes of potential importance in metacommunities. These have somewhat distinct intellectual histories and we discuss elements related to their potential future synthesis. We then use this framework to discuss why the concept is useful in modifying existing ecological thinking and illustrate this with a number of both theoretical and empirical examples. As ecologists strive to understand increasingly complex mechanisms and strive to work across multiple scales of spatio-temporal organization, concepts like the metacommunity can provide important insights that frequently contrast with those that would be obtained with more conventional approaches based on local communities alone.

4,266 citations


Journal ArticleDOI
TL;DR: Both the upstream components of the signaling pathway(s) that activates mammalian TOR (mTOR) and the downstream targets that affect protein synthesis are described.
Abstract: The evolutionarily conserved checkpoint protein kinase, TOR (target of rapamycin), has emerged as a major effector of cell growth and proliferation via the regulation of protein synthesis. Work in the last decade clearly demonstrates that TOR controls protein synthesis through a stunning number of downstream targets. Some of the targets are phosphorylated directly by TOR, but many are phosphorylated indirectly. In this review, we summarize some recent developments in this fast-evolving field. We describe both the upstream components of the signaling pathway(s) that activates mammalian TOR (mTOR) and the downstream targets that affect protein synthesis. We also summarize the roles of mTOR in the control of cell growth and proliferation, as well as its relevance to cancer and synaptic plasticity.

4,074 citations


Journal ArticleDOI
TL;DR: This commentary summarizes the Workshop presentations on HNPCC and MSI testing; presents the issues relating to the performance, specificity, and specificity of the Bethesda Guidelines; outlines the revised Bethesda Guidelines for identifying individuals at risk for H NPCC; and recommend criteria for MSI testing.
Abstract: Hereditary nonpolyposis colorectal cancer (HNPCC), also known as Lynch syndrome, is a common autosomal dominant syndrome characterized by early age at onset, neoplastic lesions, and microsatellite instability (MSI). Because cancers with MSI account for approximately 15% of all colorectal cancers and because of the need for a better understanding of the clinical and histologic manifestations of HNPCC, the National Cancer Institute hosted an international workshop on HNPCC in 1996, which led to the development of the Bethesda Guidelines for the identification of individuals with HNPCC who should be tested for MSI. To consider revision and improvement of the Bethesda Guidelines, another HNPCC workshop was held at the National Cancer Institute in Bethesda, MD, in 2002. In this commentary, we summarize the Workshop presentations on HNPCC and MSI testing; present the issues relating to the performance, sensitivity, and specificity of the Bethesda Guidelines; outline the revised Bethesda Guidelines for identifying individuals at risk for HNPCC; and recommend criteria for MSI testing.

2,899 citations


Journal ArticleDOI
TL;DR: A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) can accurately identify basal-like tumors using standard available clinical tools and shows high specificity.
Abstract: Purpose: Expression profiling studies classified breast carcinomas into estrogen receptor (ER)+/luminal, normal breast-like, HER2 overexpressing, and basal-like groups, with the latter two associated with poor outcomes. Currently, there exist clinical assays that identify ER+/luminal and HER2-overexpressing tumors, and we sought to develop a clinical assay for breast basal-like tumors. Experimental Design: To identify an immunohistochemical profile for breast basal-like tumors, we collected a series of known basal-like tumors and tested them for protein patterns that are characteristic of this subtype. Next, we examined the significance of these protein patterns using tissue microarrays and evaluated the prognostic significance of these findings. Results: Using a panel of 21 basal-like tumors, which was determined using gene expression profiles, we saw that this subtype was typically immunohistochemically negative for estrogen receptor and HER2 but positive for basal cytokeratins, HER1, and/or c-KIT. Using breast carcinoma tissue microarrays representing 930 patients with 17.4-year mean follow-up, basal cytokeratin expression was associated with low disease-specific survival. HER1 expression was observed in 54% of cases positive for basal cytokeratins ( versus 11% of negative cases) and was associated with poor survival independent of nodal status and size. c-KIT expression was more common in basal-like tumors than in other breast cancers but did not influence prognosis. Conclusions: A panel of four antibodies (ER, HER1, HER2, and cytokeratin 5/6) can accurately identify basal-like tumors using standard available clinical tools and shows high specificity. These studies show that many basal-like tumors express HER1, which suggests candidate drugs for evaluation in these patients.

2,562 citations



Journal ArticleDOI
06 Feb 2004-Science
TL;DR: Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.
Abstract: A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.

2,037 citations


Journal ArticleDOI
TL;DR: Patients with fistulizing Crohn's disease who have a response to induction therapy with inflIXimab have an increased likelihood of a sustained response over a 54-week period if infliximab treatment is continued every 8 weeks.
Abstract: BACKGROUND: Infliximab, a monoclonal antibody against tumor necrosis factor, is an effective maintenance therapy for patients with Crohn's disease without fistulas. It is not known whether infliximab is an effective maintenance therapy for patients with fistulas. METHODS: We performed a multicenter, double-blind, randomized, placebo-controlled trial to evaluate the efficacy of infliximab maintenance therapy in 306 adult patients with Crohn's disease and one or more draining abdominal or perianal fistulas of at least three months' duration. Patients received 5 mg of infliximab per kilogram of body weight intravenously on weeks 0, 2, and 6. A total of 195 patients who had a response at weeks 10 and 14 and 87 patients who had no response were then randomly assigned to receive placebo or 5 mg of infliximab per kilogram every eight weeks and to be followed to week 54. The primary analysis was the time to the loss of response among patients who had a response at week 14 and underwent randomization. RESULTS: The time to loss of response was significantly longer for patients who received infliximab maintenance therapy than for those who received placebo maintenance (more than 40 weeks vs. 14 weeks, P<0.001). At week 54, 19 percent of patients in the placebo maintenance group had a complete absence of draining fistulas, as compared with 36 percent of patients in the infliximab maintenance group (P=0.009). CONCLUSIONS: Patients with fistulizing Crohn's disease who have a response to induction therapy with infliximab have an increased likelihood of a sustained response over a 54-week period if infliximab treatment is continued every 8 weeks.

2,006 citations


Journal ArticleDOI
TL;DR: In this paper, a method for minimizing the effect of leaf chlorophyll content on the prediction of green LAI was presented, and new algorithms that adequately predict the LAI of crop canopies.

1,915 citations


Journal ArticleDOI
TL;DR: In a qualitative study of the emerging field of HIV/AIDS treatment advocacy in Canada, it was found that institutional entrepreneurship involved three sets of critical activities: the occupation of “subject positions” that have wide legitimacy and bridge diverse stakeholders.
Abstract: In a qualitative study of the emerging field of HIV/AIDS treatment advocacy in Canada, we found that institutional entrepreneurship involved three sets of critical activities: (1) the occupation of “subject positions” that have wide legitimacy and bridge diverse stakeholders, (2) the theorization of new practices through discursive and political means, and (3) the institutionalization of these new practices by connecting them to stakeholders’ routines and values.

1,876 citations


Journal ArticleDOI
TL;DR: The growth of understanding of the pulmonary hypertensive diseases that has enabled the development of a clinical classification oriented towards prevention and treatment is traced.


Journal ArticleDOI
TL;DR: Converging results from epidemiological research and in vivo carcinogenesis models indicate that high levels of circulating IGF1 are associated with increased risk of several common cancers, and ongoing research seeks to clarify the mechanisms underlying these observations.
Abstract: The insulin-like growth factor 1 (IGF1) signalling pathway has important roles in regulating cellular proliferation and apoptosis. Converging results from epidemiological research and in vivo carcinogenesis models indicate that high levels of circulating IGF1 are associated with increased risk of several common cancers. Ongoing research seeks to clarify the mechanisms underlying these observations and to determine the extent to which IGF physiology influences patterns of cancer incidence. Various therapeutic strategies that target the IGF1 receptor have demonstrated impressive antineoplastic activity in laboratory models, and clinical trials of several novel drug candidates are planned.

Journal ArticleDOI
TL;DR: 1,25(OH)2D3 thus directly regulates antimicrobial peptide gene expression, revealing the potential of its analogues in treatment of opportunistic infections.
Abstract: The hormonal form of vitamin D3, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), is an immune system modulator and induces expression of the TLR coreceptor CD14. 1,25(OH)2D3 signals through the vitamin D receptor, a ligand-stimulated transcription factor that recognizes specific DNA sequences called vitamin D response elements. In this study, we show that 1,25(OH)2D3 is a direct regulator of antimicrobial innate immune responses. The promoters of the human cathelicidin antimicrobial peptide (camp) and defensin β2 (defB2) genes contain consensus vitamin D response elements that mediate 1,25(OH)2D3-dependent gene expression. 1,25(OH)2D3 induces antimicrobial peptide gene expression in isolated human keratinocytes, monocytes and neutrophils, and human cell lines, and 1,25(OH)2D3 along with LPS synergistically induce camp expression in neutrophils. Moreover, 1,25(OH)2D3 induces corresponding increases in antimicrobial proteins and secretion of antimicrobial activity against pathogens including Pseudomonas aeruginosa. 1,25(OH)2D3 thus directly regulates antimicrobial peptide gene expression, revealing the potential of its analogues in treatment of opportunistic infections.

Journal ArticleDOI
TL;DR: In this 52-week trial, adalimumab was more effective than placebo at inhibiting the progression of structural joint damage, reducing the signs and symptoms, and improving physical function in patients with active RA who had demonstrated an incomplete response to MTX.
Abstract: Objective Tumor necrosis factor (TNF) is an important proinflammatory cytokine that mediates inflammatory synovitis and articular matrix degradation in rheumatoid arthritis (RA). We investigated the ability of adalimumab, a human anti–TNF monoclonal antibody, to inhibit the progression of structural joint damage, reduce the signs and symptoms, and improve physical function in patients with active RA receiving concomitant treatment with methotrexate (MTX). Methods In this multicenter, 52-week, double-blind, placebo-controlled study, 619 patients with active RA who had an inadequate response to MTX were randomized to receive adalimumab 40 mg subcutaneously every other week (n = 207), adalimumab 20 mg subcutaneously every week (n = 212), or placebo (n = 200) plus concomitant MTX. The primary efficacy end points were radiographic progression at week 52 (total Sharp score by a modified method [TSS]), clinical response at week 24 (improvements of at least 20% in the American College of Rheumatology core criteria [ACR20]), and physical function at week 52 (disability index of the Health Assessment Questionnaire [HAQ]). Results At week 52, there was statistically significantly less radiographic progression, as measured by the change in TSS, in the patients receiving adalimumab either 40 mg every other week (mean ± SD change 0.1 ± 4.8) or 20 mg weekly (0.8 ± 4.9) as compared with that in the placebo group (2.7 ± 6.8) (P ≤ 0.001 for each comparison). In addition, there were statistically significant changes in the components of the TSS. At week 24, ACR20 responses were achieved by 63% and 61% of patients in the adalimumab 40 mg every other week and 20 mg weekly groups, respectively, versus 30% of patients in the placebo group (P ≤ 0.001 for each comparison). At week 52, ACR20 responses were achieved by 59% and 55% of patients taking adalimumab 40 mg every other week and 20 mg weekly, respectively, versus 24% of patients taking placebo (P ≤ 0.001 for each comparison). At week 52, physical function as measured by the HAQ demonstrated statistically significant improvement with adalimumab 40 mg every other week and 20 mg weekly compared with placebo (mean change in HAQ score −0.59 and −0.61, respectively, versus −0.25; P ≤ 0.001 for each comparison). A total of 467 patients (75.4%) completed 52 weeks of treatment. Adalimumab was generally well tolerated. Discontinuations occurred in 22.0% of adalimumab-treated patients and in 30.0% of placebo-treated patients. The rate of adverse events (both serious and nonserious) was comparable in the adalimumab and placebo groups, although the proportion of patients reporting serious infections was higher in patients receiving adalimumab (3.8%) than in those receiving placebo (0.5%) (P ≤ 0.02), and was highest in the patients receiving 40 mg every other week. Conclusion In this 52-week trial, adalimumab was more effective than placebo at inhibiting the progression of structural joint damage, reducing the signs and symptoms, and improving physical function in patients with active RA who had demonstrated an incomplete response to MTX.

Journal ArticleDOI
TL;DR: Given the complexity of processes that underlie biological invasions, it is argued against a simple relationship between enemy ‘release’ and the vigour, abundance or impact of NIS.
Abstract: A recent trend in invasion ecology relates the success of non-indigenous species (NIS) to reduced control by enemies such as pathogens, parasites and predators (i.e. the enemy release hypothesis, ERH). Despite the demonstrated importance of enemies to host population dynamics, studies of the ERH are split – biogeographical analyses primarily show a reduction in the diversity of enemies in the introduced range compared with the native range, while community studies imply that NIS are no less affected by enemies than native species in the invaded community. A broad review of the invasion literature implies at least eight non-exclusive explanations for this enigma. In addition, we argue that the ERH has often been accepted uncritically wherever (i) NIS often appear larger, more fecund, or somehow ‘better’ than either congeners in the introduced region, or conspecifics in the native range; and (ii) known enemies are conspicuously absent from the introduced range. However, all NIS, regardless of their abundance or impact, will lose natural enemies at a biogeographical scale. Given the complexity of processes that underlie biological invasions, we argue against a simple relationship between enemy ‘release’ and the vigour, abundance or impact of NIS.

Journal ArticleDOI
TL;DR: This study shows that weight-loss surgery significantly decreases overall mortality as well as the development of new health-related conditions in morbidly obese patients.
Abstract: Objective: This study tested the hypothesis that weight-reduction (bariatric) surgery reduces long-term mortality in morbidly obese patients. Background: Obesity is a significant cause of morbidity and mortality. The impact of surgically induced, long-term weight loss on this mortality is unknown. Methods: We used an observational 2-cohort study. The treatment cohort (n = 1035) included patients having undergone bariatric surgery at the McGill University Health Centre between 1986 and 2002. The control group (n = 5746) included age- and gender-matched severely obese patients who had not undergone weight-reduction surgery identified from the Quebec provincial health insurance database. Subjects with medical conditions (other then morbid obesity) at cohort-inception into the study were excluded. The cohorts were followed for a maximum of 5 years from inception. Results: The cohorts were well matched for age, gender, and duration of follow-up. Bariatric surgery resulted in significant reduction in mean percent excess weight loss (67.1%, P < 0.001). Bariatric surgery patients had significant risk reductions for developing cardiovascular, cancer, endocrine, infectious, psychiatric, and mental disorders compared with controls, with the exception of hematologic (no difference) and digestive diseases (increased rates in the bariatric cohort). The mortality rate in the bariatric surgery cohort was 0.68% compared with 6.17% in controls (relative risk 0.11, 95% confidence interval 0.04-0.27), which translates to a reduction in the relative risk of death by 89%. Conclusions: This study shows that weight-loss surgery significantly decreases overall mortality as well as the development of new health-related conditions in morbidly obese patients.

Journal ArticleDOI
TL;DR: In the cytosol of prokaryotic and eukaryotic cells, molecular chaperones of different structural classes form a network of pathways that can handle substrate polypeptides from the point of initial synthesis on ribosomes to the final stages of folding.
Abstract: Cells are faced with the task of folding thousands of different polypeptides into a wide range of conformations. For many proteins, the folding process requires the action of molecular chaperones. In the cytosol of prokaryotic and eukaryotic cells, molecular chaperones of different structural classes form a network of pathways that can handle substrate polypeptides from the point of initial synthesis on ribosomes to the final stages of folding.

Journal ArticleDOI
TL;DR: In this paper, the authors take stock of the large body of extant research and provide a systematic assessment of empirical evidence and conclude that a more thorough empirical grounding of the theory's foundation is crucial to its future development, and offer several strategies for doing this.
Abstract: Transaction cost economics (TCE) is one of the leading perspectives in management and organizational studies, yet debate continues regarding its empirical support. In this paper, we take stock of the large body of extant research and provide a systematic assessment of empirical evidence. In all, 308 statistical tests from 63 articles, selected according to a set of clear criteria, were examined across various dimensions. We assess not only the level of empirical support for the theory, but also the degree of paradigm consensus present in the empirical literature. Our analysis shows that results are mixed: while we found support in some areas (e.g., with regard to asset specificity), we also found considerable disagreement on how to operationalize some of TCE's central constructs and propositions, and relatively low levels of empirical support in other core areas (e.g., surrounding uncertainty and performance). We conclude that a more thorough empirical grounding of the theory's foundation is crucial to its future development, and offer several strategies for doing this. Copyright © 2003 John Wiley & Sons, Ltd.

Book ChapterDOI
TL;DR: The data are conflicting with respect to iron status but suggest that, at least in developing-country settings, where iron stores of newborn infants may be suboptimal, exclusive breastfeeding without iron supplementation through 6 months of age may compromise hematologic status.
Abstract: Although the health benefits of breastfeeding are acknowledged widely, opinions and recommendations are divided on the optimal duration of exclusive breastfeeding. We systematically reviewed available evidence concerning the effects on child health, growth, and development and on maternal health of exclusive breastfeeding for 6 months vs. exclusive breastfeeding for 3-4 months followed by mixed breastfeeding (introduction of complementary liquid or solid foods with continued breastfeeding) to 6 months. Two independent literature searches were conducted, together comprising the following databases: MEDLINE (as of 1966), Index Medicus (prior to 1966), CINAHL, HealthSTAR, BIOSIS, CAB Abstracts, EMBASE-Medicine, EMBASE-Psychology, Econlit, Index Medicus for the WHO Eastern Mediterranean Region, African Index Medicus, Lilacs (Latin American and Carribean literature), EBM Reviews-Best Evidence, the Cochrane Database of Systematic Reviews, and the Cochrane Controlled Trials Register. No language restrictions were imposed. The two searches yielded a total of 2,668 unique citations. Contacts with experts in the field yielded additional published and unpublished studies. Studies were stratified according to study design (controlled trials vs. observational studies) and provenance (developing vs. developed countries). The main outcome measures were weight and length gain, weight-for-age and length-for-age z-scores, head circumference, iron status, gastrointestinal and respiratory infectious morbidity, atopic eczema, asthma, neuromotor development, duration of lactational amenorrhea, and maternal postpartum weight loss. Twenty independent studies meeting the selection criteria were identified by the literature search: 9 from developing countries (2 of which were controlled trials in Honduras) and 11 from developed countries (all observational studies). Neither the trials nor the observational studies suggest that infants who continue to be exclusively breastfed for 6 months show deficits in weight or length gain, although larger sample sizes would be required to rule out modest increases in the risk of undernutrition. The data are conflicting with respect to iron status but suggest that, at least in developing-country settings, where iron stores of newborn infants may be suboptimal, exclusive breastfeeding without iron supplementation through 6 months of age may compromise hematologic status. Based primarily on an observational analysis of a large randomized trial in Belarus, infants who continue exclusive breastfeeding for 6 months or more appear to have a significantly reduced risk of one or more episodes of gastrointestinal tract infection. No significant reduction in risk of atopic eczema, asthma, or other atopic outcomes has been demonstrated in studies from Finland, Australia, and Belarus. Data from the two Honduran trials suggest that exclusive breastfeeding through 6 months of age is associated with delayed resumption of menses and more rapid postpartum weight loss in the mother. Infants who are breastfed exclusively for 6 months experience less morbidity from gastrointestinal tract infection than infants who were mixed breastfed as of 3 or 4 months of age. No deficits have been demonstrated in growth among infants from either developing or developed countries who are exclusively breastfed for 6 months or longer. Moreover, the mothers of such infants have more prolonged lactational amenorrhea and faster postpartum weight loss. Based on the results of this review, the World Health Assembly adopted a resolution to recommend exclusive breastfeeding for 6 months to its member countries. Large randomized trials are recommended in both developed and developing countries to ensure that exclusive breastfeeding for 6 months does not increase the risk of undernutrition (growth faltering), to confirm the health benefits reported thus far, and to investigate other potential effects on health and development, especially over the long term.

Journal ArticleDOI
TL;DR: In this article, the number of sulfate groups in the cellulose crystals was determined by potentiometric titration and the thermal degradation behavior was investigated by thermogravimetric analysis.

Journal ArticleDOI
Gary A. Churchill, David C. Airey1, Hooman Allayee2, Joe M. Angel3, Alan D. Attie4, Jackson Beatty5, Willam D. Beavis6, John K. Belknap7, Beth Bennett8, Wade H. Berrettini9, André Bleich10, Molly A. Bogue, Karl W. Broman11, Kari J. Buck12, Edward S. Buckler13, Margit Burmeister14, Elissa J. Chesler15, James M. Cheverud16, Steven J. Clapcote17, Melloni N. Cook18, Roger D. Cox19, John C. Crabbe12, Wim E. Crusio20, Ariel Darvasi21, Christian F. Deschepper22, Rebecca W. Doerge23, Charles R. Farber24, Jiri Forejt25, Daniel Gaile26, Steven J. Garlow27, Hartmut Geiger28, Howard K. Gershenfeld29, Terry Gordon30, Jing Gu15, Weikuan Gu15, Gerald de Haan31, Nancy L. Hayes32, Craig Heller33, Heinz Himmelbauer34, Robert Hitzemann12, Kent W. Hunter35, Hui-Chen Hsu36, Fuad A. Iraqi37, Boris Ivandic38, Howard J. Jacob39, Ritsert C. Jansen31, Karl J. Jepsen40, Dabney K. Johnson41, Thomas E. Johnson8, Gerd Kempermann42, Christina Kendziorski4, Malak Kotb15, R. Frank Kooy43, Bastien Llamas22, Frank Lammert44, J. M. Lassalle45, Pedro R. Lowenstein5, Lu Lu15, Aldons J. Lusis5, Kenneth F. Manly15, Ralph S. Marcucio46, Doug Matthews18, Juan F. Medrano24, Darla R. Miller41, Guy Mittleman18, Beverly A. Mock35, Jeffrey S. Mogil47, Xavier Montagutelli48, Grant Morahan49, David G. Morris50, Richard Mott51, Joseph H. Nadeau52, Hiroki Nagase53, Richard S. Nowakowski32, Bruce F. O'Hara54, Alexander V. Osadchuk, Grier P. Page36, Beverly Paigen, Kenneth Paigen, Abraham A. Palmer, Huei Ju Pan, Leena Peltonen-Palotie5, Leena Peltonen-Palotie55, Jeremy L. Peirce15, Daniel Pomp56, Michal Pravenec25, Daniel R. Prows28, Zonghua Qi1, Roger H. Reeves11, John C. Roder17, Glenn D. Rosen57, Eric E. Schadt58, Leonard C. Schalkwyk59, Ze'ev Seltzer17, Kazuhiro Shimomura60, Siming Shou61, Mikko J. Sillanpää55, Linda D. Siracusa62, Hans-Willem Snoeck40, Jimmy L. Spearow24, Karen L. Svenson, Lisa M. Tarantino63, David W. Threadgill64, Linda A. Toth65, William Valdar51, Fernando Pardo-Manuel de Villena64, Craig H Warden24, Steve Whatley59, Robert W. Williams15, Tom Wiltshire63, Nengjun Yi36, Dabao Zhang66, Min Zhang13, Fei Zou64 
Vanderbilt University1, University of Southern California2, University of Texas MD Anderson Cancer Center3, University of Wisconsin-Madison4, University of California, Los Angeles5, National Center for Genome Resources6, Portland VA Medical Center7, University of Colorado Boulder8, University of Pennsylvania9, Hannover Medical School10, Johns Hopkins University11, Oregon Health & Science University12, Cornell University13, University of Michigan14, University of Tennessee Health Science Center15, Washington University in St. Louis16, University of Toronto17, University of Memphis18, Medical Research Council19, University of Massachusetts Medical School20, Hebrew University of Jerusalem21, Université de Montréal22, Purdue University23, University of California, Davis24, Academy of Sciences of the Czech Republic25, University at Buffalo26, Emory University27, University of Cincinnati28, University of Texas Southwestern Medical Center29, New York University30, University of Groningen31, Rutgers University32, Stanford University33, Max Planck Society34, National Institutes of Health35, University of Alabama at Birmingham36, International Livestock Research Institute37, Heidelberg University38, Medical College of Wisconsin39, Icahn School of Medicine at Mount Sinai40, Oak Ridge National Laboratory41, Charité42, University of Antwerp43, RWTH Aachen University44, Paul Sabatier University45, University of California, San Francisco46, McGill University47, Pasteur Institute48, University of Western Australia49, Yale University50, University of Oxford51, Case Western Reserve University52, Roswell Park Cancer Institute53, University of Kentucky54, University of Helsinki55, University of Nebraska–Lincoln56, Harvard University57, Merck & Co.58, King's College London59, Northwestern University60, Shriners Hospitals for Children61, Thomas Jefferson University62, Novartis63, University of North Carolina at Chapel Hill64, Southern Illinois University Carbondale65, University of Rochester66
TL;DR: The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way the authors approach human health and disease.
Abstract: The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are less effective for studying intact polygenic networks and interactions among genes, environments, pathogens and other factors. The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease.

Journal ArticleDOI
TL;DR: A nonlinear version of the recursive least squares (RLS) algorithm that uses a sequential sparsification process that admits into the kernel representation a new input sample only if its feature space image cannot be sufficiently well approximated by combining the images of previously admitted samples.
Abstract: We present a nonlinear version of the recursive least squares (RLS) algorithm. Our algorithm performs linear regression in a high-dimensional feature space induced by a Mercer kernel and can therefore be used to recursively construct minimum mean-squared-error solutions to nonlinear least-squares problems that are frequently encountered in signal processing applications. In order to regularize solutions and keep the complexity of the algorithm bounded, we use a sequential sparsification process that admits into the kernel representation a new input sample only if its feature space image cannot be sufficiently well approximated by combining the images of previously admitted samples. This sparsification procedure allows the algorithm to operate online, often in real time. We analyze the behavior of the algorithm, compare its scaling properties to those of support vector machines, and demonstrate its utility in solving two signal processing problems-time-series prediction and channel equalization.

Journal ArticleDOI
TL;DR: The purpose of this meeting was to define an international acceptable set of diagnostic criteria for PanINs and IPMNs and to address a number of ambiguities that exist in the previously reported classification systems for these neoplasms.
Abstract: Invasive pancreatic ductal adenocarcinoma is an almost uniformly fatal disease. Several distinct noninvasive precursor lesions can give rise to invasive adenocarcinoma of the pancreas, and the prevention, detection, and treatment of these noninvasive lesions offers the potential to cure early pancreatic cancers. Noninvasive precursors of invasive ductal adenocarcinoma of the pancreas include pancreatic intraepithelial neoplasias (PanINs), intraductal papillary mucinous neoplasms (IPMNs), and mucinous cystic neoplasms. Diagnostic criteria, including a distinct ovarian-type stroma, and a consistent nomenclature are well established for mucinous cystic neoplasms. By contrast, consistent nomenclatures and diagnostic criteria have been more difficult to establish for PanINs and IPMNs. Because both PanINs and IPMNs consist of intraductal neoplastic proliferations of columnar, mucin-containing cells with a variable degree of papilla formation, the distinction between these two classes of precursor lesions remains problematic. Thus, considerable ambiguities still exist in the classification of noninvasive neoplasms in the pancreatic ducts. A meeting of international experts on precursor lesions of pancreatic cancer was held at The Johns Hopkins Hospital from August 18 to 19, 2003. The purpose of this meeting was to define an international acceptable set of diagnostic criteria for PanINs and IPMNs and to address a number of ambiguities that exist in the previously reported classification systems for these neoplasms. We present a consensus classification of the precursor lesions in the pancreatic ducts, PanINs and IPMNs.

Journal ArticleDOI
01 Jul 2004-Immunity
TL;DR: XBP1 coordinates diverse changes in cellular structure and function resulting in the characteristic phenotype of professional secretory cells, and upregulates genes encoding many secretory pathway components.

Journal ArticleDOI
18 Mar 2004-Nature
TL;DR: It is shown that Akt promotes tumorigenesis and drug resistance by disrupting apoptosis, and that disruption of Akt signalling using the mTOR inhibitor rapamycin reverses chemoresistance in lymphomas expressing Akt, but not in those with other apoptotic defects.
Abstract: Evading apoptosis is considered to be a hallmark of cancer, because mutations in apoptotic regulators invariably accompany tumorigenesis. Many chemotherapeutic agents induce apoptosis, and so disruption of apoptosis during tumour evolution can promote drug resistance. For example, Akt is an apoptotic regulator that is activated in many cancers and may promote drug resistance in vitro. Nevertheless, how Akt disables apoptosis and its contribution to clinical drug resistance are unclear. Using a murine lymphoma model, we show that Akt promotes tumorigenesis and drug resistance by disrupting apoptosis, and that disruption of Akt signalling using the mTOR inhibitor rapamycin reverses chemoresistance in lymphomas expressing Akt, but not in those with other apoptotic defects. eIF4E, a translational regulator that acts downstream of Akt and mTOR, recapitulates Akt's action in tumorigenesis and drug resistance, but is unable to confer sensitivity to rapamycin and chemotherapy. These results establish Akt signalling through mTOR and eIF4E as an important mechanism of oncogenesis and drug resistance in vivo, and reveal how targeting apoptotic programmes can restore drug sensitivity in a genotype-dependent manner.

Journal ArticleDOI
TL;DR: The discovery of the first gene associated with hereditary breast cancer, BRCA1, was anticipated to greatly increase the understanding of both hereditary and sporadic forms of breast cancers, and to lead to therapeutic and preventive breakthroughs.
Abstract: The discovery of the first gene associated with hereditary breast cancer, BRCA1, was anticipated to greatly increase our understanding of both hereditary and sporadic forms of breast cancer, and to lead to therapeutic and preventive breakthroughs. Much has been learned during the past decade about the genetic epidemiology of breast cancer, the ethnic distribution and clinical consequences of BRCA1 and BRCA2 mutations, and the central role of DNA repair in breast cancer susceptibility. The ability to translate this knowledge into novel treatments, however, remains elusive.

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TL;DR: In this paper, the authors identify the trajectories of physical aggression during early childhood and, second, identify antecedents of high-level physical aggression early in life and identify targets for preventive interventions.
Abstract: Objectives. Physical aggression in children is a major public health problem. Not only is childhood physical aggression a precursor of the physical and mental health problems that will be visited on victims, but also aggressive children themselves are at higher risk of alcohol and drug abuse, accidents, violent crimes, depression, suicide attempts, spouse abuse, and neglectful and abusive parenting. Furthermore, violence commonly results in serious injuries to the perpetrators themselves. Although it is unusual for young children to harm seriously the targets of their physical aggression, studies of physical aggression during infancy indicate that by 17 months of age, the large majority of children are physically aggressive toward siblings, peers, and adults. This study aimed, first, to identify the trajectories of physical aggression during early childhood and, second, to identify antecedents of high levels of physical aggression early in life. Such antecedents could help to understand better the developmental origins of violence later in life and to identify targets for preventive interventions. Methods. A random population sample of 572 families with a 5-month-old newborn was recruited. Assessments of physical aggression frequency were obtained from mothers at 17, 30, and 42 months after birth. Using a semiparametric, mixture model, distinct clusters of physical aggression trajectories were identified. Multivariate logit regression analysis was then used to identify which family and child characteristics, before 5 months of age, predict individuals on a high-level physical aggression trajectory from 17 to 42 months after birth. Results. Three trajectories of physical aggression were identified. The first was composed of children who displayed little or no physical aggression. These individuals were estimated to account for ∼28% of the sample. The largest group, estimated at ∼58% of the sample, followed a rising trajectory of modest aggression. Finally, a group, estimated to comprise ∼14% of the sample, followed a rising trajectory of high physical aggression. Best predictors before or at birth of the high physical aggression trajectory group, controlling for the levels of the other risk factors, were having young siblings (odds ratio [OR]: 4.00; confidence interval [CI]: 2.2–7.4), mothers with high levels of antisocial behavior before the end of high school (OR: 3.1; CI: 1.1–8.6), mothers who started having children early (OR: 3.1; CI: 1.4–6.8), families with low income (OR: 2.6; CI: 1.3–5.2), and mothers who smoked during pregnancy (OR: 2.2; CI: 1.1–4.1). Best predictors at 5 months of age were mothers’ coercive parenting behavior (OR: 2.3; CI: 1.1–4.7) and family dysfunction (OR: 2.2; CI: 1.2–4.1). The OR for a high-aggression trajectory was 10.9 for children whose mother reported both high levels of antisocial behavior and early childbearing. Conclusions. Most children have initiated the use of physical aggression during infancy, and most will learn to use alternatives in the following years before they enter primary school. Humans seem to learn to regulate the use of physical aggression during the preschool years. Those who do not, seem to be at highest risk of serious violent behavior during adolescence and adulthood. Results from the present study indicate that children who are at highest risk of not learning to regulate physical aggression in early childhood have mothers with a history of antisocial behavior during their school years, mothers who start childbearing early and who smoke during pregnancy, and parents who have low income and have serious problems living together. All of these variables are relatively easy to measure during pregnancy. Preventive interventions should target families with high-risk profiles on these variables. Experiments with such programs have shown long-term impacts on child abuse and child antisocial behavior. However, these impacts were not observed in families with physical violence. The problem may be that the prevention programs that were provided did not specifically target the parents’ control over their physical aggression and their skills in teaching their infant not to be physically aggressive. Most intervention programs to prevent youth physical aggression have targeted school-age children. If children normally learn not to be physically aggressive during the preschool years, then one would expect that interventions that target infants who are at high risk of chronic physical aggression would have more of an impact than interventions 5 to 10 years later, when physical aggression has become a way of life.

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TL;DR: Based on high-quality RCTs strong evidence was found in favour of task-oriented exercise training to restore balance and gait, and for strengthening the lower paretic limb in stroke patients.
Abstract: Objective: To determine the evidence for physical therapy interventions aimed at improving functional outcome after stroke.Methods: MEDLINE, CINAHL, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, DARE, PEDro, EMBASE and DocOnline were searched for controlled studies. Physical therapy was divided into 10 intervention categories, which were analysed separately. If statistical pooling (weighted summary effect sizes) was not possible due to lack of comparability between interventions, patient characteristics and measures of outcome, a bestresearch synthesis was performed. This best-research synthesis was based on methodological quality (PEDro score).Results: In total, 151 studies were included in this systematic review; 123 were randomized controlled trials (RCTs) and 28 controlled clinical trials (CCTs). Methodological quality of all RCTs had a median of 5 points on the 10-point PEDro scale (range 2–8 points). Based on high-quality RCTs strong evidence was found in f...

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TL;DR: The data show that combining the fMRI and lesion approaches can help reveal the source of functional modulatory influences between distant but interconnected brain regions.
Abstract: Emotional visual stimuli evoke enhanced responses in the visual cortex. To test whether this reflects modulatory influences from the amygdala on sensory processing, we used event-related functional magnetic resonance imaging (fMRI) in human patients with medial temporal lobe sclerosis. Twenty-six patients with lesions in the amygdala, the hippocampus or both, plus 13 matched healthy controls, were shown pictures of fearful or neutral faces in task-releant or task-irrelevant positions on the display. All subjects showed increased fusiform cortex activation when the faces were in task-relevant positions. Both healthy individuals and those with hippocampal damage showed increased activation in the fusiform and occipital cortex when they were shown fearful faces, but this was not the case for individuals with damage to the amygdala, even though visual areas were structurally intact. The distant influence of the amygdala was also evidenced by the parametric relationship between amygdala damage and the level of emotional activation in the fusiform cortex. Our data show that combining the fMRI and lesion approaches can help reveal the source of functional modulatory influences between distant but interconnected brain regions.