Showing papers by "University of York published in 2001"
TL;DR: Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments and to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.
Abstract: The ecological consequences of biodiversity loss have aroused considerable interest and controversy during the past decade. Major advances have been made in describing the relationship between species diversity and ecosystem processes, in identifying functionally important species, and in revealing underlying mechanisms. There is, however, uncertainty as to how results obtained in recent experiments scale up to landscape and regional levels and generalize across ecosystem types and processes. Larger numbers of species are probably needed to reduce temporal variability in ecosystem processes in changing environments. A major future challenge is to determine how biodiversity dynamics, ecosystem processes, and abiotic factors interact.
4,070 citations
TL;DR: Five experiments reported in which the goal either to perform well or to cooperate was activated, without the awareness of participants, through a priming manipulation demonstrated that action guided by nonconsciously activated goals effectively guide action, enabling adaptation to ongoing situational demands.
Abstract: It is proposed that goals can be activated outside of awareness and then operate nonconsciously to guide self-regulation effectively (J. A. Bargh, 1990). Five experiments are reported in which the goal either to perform well or to cooperate was activated, without the awareness of participants, through a priming manipulation. In Experiment 1 priming of the goal to perform well caused participants to perform comparatively better on an intellectual task. In Experiment 2 priming of the goal to cooperate caused participants to replenish a commonly held resource more readily. Experiment 3 used a dissociation paradigm to rule out perceptual-construal alternative explanations. Experiments 4 and 5 demonstrated that action guided by nonconsciously activated goals manifests two classic content-free features of the pursuit of consciously held goals. Nonconsciously activated goals effectively guide action, enabling adaptation to ongoing situational demands.
1,782 citations
TL;DR: The implementation of the TLS parameterization in the macromolecular refinement program REFMAC is described, which gives improved refinement statistics and in particular an improvement in R and free R values of several percent.
Abstract: An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.
1,711 citations
TL;DR: The dual forces of habitat modification and climate change are likely to cause specialists to decline, leaving biological communities with reduced numbers of species and dominated by mobile and widespread habitat generalists.
Abstract: Habitat degradation and climate change are thought to be altering the distributions and abundances of animals and plants throughout the world, but their combined impacts have not been assessed for any species assemblage1,2,3,4. Here we evaluated changes in the distribution sizes and abundances of 46 species of butterflies that approach their northern climatic range margins in Britain—where changes in climate and habitat are opposing forces. These insects might be expected to have responded positively to climate warming over the past 30 years, yet three-quarters of them declined: negative responses to habitat loss have outweighed positive responses to climate warming. Half of the species that were mobile and habitat generalists increased their distribution sites over this period (consistent with a climate explanation), whereas the other generalists and 89% of the habitat specialists declined in distribution size (consistent with habitat limitation). Changes in population abundances closely matched changes in distributions. The dual forces of habitat modification and climate change are likely to cause specialists to decline, leaving biological communities with reduced numbers of species and dominated by mobile and widespread habitat generalists.
1,273 citations
TL;DR: It is shown that SCFTIR1 is required for AUX/IAA degradation, and it is proposed that auxin promotes the degradation of this large family of transcriptional regulators, leading to diverse downstream effects.
Abstract: The plant hormone auxin is central in many aspects of plant development. Previous studies have implicated the ubiquitin-ligase SCFTIR1 and the AUX/IAA proteins in auxin response. Dominant mutations in several AUX/IAA genes confer pleiotropic auxin-related phenotypes, whereas recessive mutations affecting the function of SCFTIR1 decrease auxin response. Here we show that SCFTIR1 is required for AUX/IAA degradation. We demonstrate that SCFTIR1 interacts with AXR2/IAA7 and AXR3/IAA17, and that domain II of these proteins is necessary and sufficient for this interaction. Further, auxin stimulates binding of SCFTIR1 to the AUX/IAA proteins, and their degradation. Because domain II is conserved in nearly all AUX/IAA proteins in Arabidopsis, we propose that auxin promotes the degradation of this large family of transcriptional regulators, leading to diverse downstream effects.
1,262 citations
TL;DR: A review of the literature that examines event-related brain potentials (ERPs) and novelty processing reveals that the orienting response engendered by deviant or unexpected events consists of a characteristic ERP pattern, comprised sequentially of the mismatch negativity (MMN) and the novelty P3 or P3a.
1,220 citations
TL;DR: There is much inconsistency regarding emotional and cognitive care, although one relatively consistent finding is that physicians who adopt a warm, friendly, and reassuring manner are more effective than those who keep consultations formal and do not offer reassurance.
1,206 citations
TL;DR: This analysis has focused on cation transporter gene families for which initial characterizations have been achieved for individual members, including potassium transporters and channels, sodium transporter, calcium antiporters, cyclic nucleotide-gated channels, cation diffusion facilitator proteins, natural resistance-associated macrophage proteins, and Zn-regulated transporter Fe-regulatedporter-like proteins.
Abstract: Uptake and translocation of cationic nutrients play essential roles in physiological processes including plant growth, nutrition, signal transduction, and development. Approximately 5% of the Arabidopsis genome appears to encode membrane transport proteins. These proteins are classified in 46 unique families containing approximately 880 members. In addition, several hundred putative transporters have not yet been assigned to families. In this paper, we have analyzed the phylogenetic relationships of over 150 cation transport proteins. This analysis has focused on cation transporter gene families for which initial characterizations have been achieved for individual members, including potassium transporters and channels, sodium transporters, calcium antiporters, cyclic nucleotide-gated channels, cation diffusion facilitator proteins, natural resistance-associated macrophage proteins (NRAMP), and Zn-regulated transporter Fe-regulated transporter-like proteins. Phylogenetic trees of each family define the evolutionary relationships of the members to each other. These families contain numerous members, indicating diverse functions in vivo. Closely related isoforms and separate subfamilies exist within many of these gene families, indicating possible redundancies and specialized functions. To facilitate their further study, the PlantsT database (http://plantst.sdsc.edu) has been created that includes alignments of the analyzed cation transporters and their chromosomal locations.
1,164 citations
TL;DR: It is shown that marine reserves in Florida (United States) and St. Lucia have enhanced adjacent fisheries, confirming theoretical predictions that marine reserve can play a key role in supporting fisheries.
Abstract: Marine reserves have been widely promoted as conservation and fishery management tools. There are robust demonstrations of conservation benefits, but fishery benefits remain controversial. We show that marine reserves in Florida (United States) and St. Lucia have enhanced adjacent fisheries. Within 5 years of creation, a network of five small reserves in St. Lucia increased adjacent catches of artisanal fishers by between 46 and 90%, depending on the type of gear the fishers used. In Florida, reserve zones in the Merritt Island National Wildlife Refuge have supplied increasing numbers of world record-sized fish to adjacent recreational fisheries since the 1970s. Our study confirms theoretical predictions that marine reserves can play a key role in supporting fisheries.
1,024 citations
TL;DR: It is shown that the arbuscular mycorrhizal symbiosis can both enhance decomposition of and increase nitrogen capture from complex organic material (grass leaves) in soil.
Abstract: Arbuscular mycorrhizal fungi (order Glomales), which form mycorrhizal symbioses with two out of three of all plant species, are believed to be obligate biotrophs that are wholly dependent on the plant partner for their carbon supply. It is thought that they possess no degradative capability and that they are unable to decompose complex organic molecules, the form in which most soil nutrients occur. Earlier suggestions that they could exist saprotrophically were based on observation of hyphal proliferation on organic materials. In contrast, other mycorrhizal types have been shown to acquire nitrogen directly from organic sources. Here we show that the arbuscular mycorrhizal symbiosis can both enhance decomposition of and increase nitrogen capture from complex organic material (grass leaves) in soil. Hyphal growth of the fungal partner was increased in the presence of the organic material, independently of the host plant.
1,005 citations
TL;DR: The introduction of a new concept more relevant to decision-making, that of the cost-effectiveness frontier, is suggested, and the use of these techniques when considering decisions involving multiple interventions is clarified, in the hope that as a result it can encourage the greater use ofThese techniques.
Abstract: Decision-making in health care is inevitably undertaken in a context of uncertainty concerning the effectiveness and costs of health care interventions and programmes. One method that has been suggested to represent this uncertainty is the cost-effectiveness acceptability curve. This technique, which directly addresses the decision-making problem, has advantages over confidence interval estimation for incremental cost-effectiveness ratios. However, despite these advantages, cost-effectiveness acceptability curves have yet to be widely adopted within the field of economic evaluation of health care technologies. In this paper we consider the relationship between cost-effectiveness acceptability curves and decision-making in health care, suggest the introduction of a new concept more relevant to decision-making, that of the cost-effectiveness frontier, and clarify the use of these techniques when considering decisions involving multiple interventions. We hope that as a result we can encourage the greater use of these techniques.
TL;DR: The AAA+ proteins represent a novel type of molecular chaperone and are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure.
Abstract: The AAA+ superfamily of ATPases, which contain a homologous ATPase module, are found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Recent structural studies have revealed that they usually form ring-shaped oligomers, which are crucial for their ATPase activities and mechanisms of action. These ring-shaped oligomeric complexes are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure; unfolding of proteins, disassembly of protein complexes, unwinding of DNA, or alteration of the state of DNA–protein complexes. Thus, the AAA+ proteins represent a novel type of molecular chaperone. Comparative analyses have also revealed significant similarities and differences in structure and molecular mechanism between AAA+ ATPases and other ring-shaped ATPases.
TL;DR: Exercise-based cardiac rehabilitation is effective in reducing cardiac deaths, but it is not clear from this review whether exercise only or a comprehensive cardiac rehabilitation intervention is more beneficial.
Abstract: BACKGROUND: The burden of cardiovascular disease world-wide is one of great concern to patients and health care agencies alike. Cardiac rehabilitation aims to restore patients with heart disease to health through exercise only based rehabilitation or comprehensive cardiac rehabilitation. OBJECTIVES: To determine the effectiveness of exercise only or exercise as part of a comprehensive cardiac rehabilitation programme on the mortality, morbidity, health-related quality of life (HRQoL) and modifiable cardiac risk factors of patients with coronary heart disease. SEARCH STRATEGY: Electronic databases were searched for randomised controlled trials, using standardised trial filters, from the earliest date available to December 31st 1998. SELECTION CRITERIA: Men and women of all ages, in hospital or community settings, who have had myocardial infarction, coronary artery bypass graft or percutaneous transluminal coronary angioplasty, or who have angina pectoris or coronary artery disease defined by angiography. DATA COLLECTION AND ANALYSIS: Studies were selected independently by two reviewers, and data extracted independently. Authors were contacted where possible to obtain missing information. MAIN RESULTS: This systematic review has allowed analysis of an increased number of patients from approximately 4500 in earlier meta-analyses to 8440 (7683 contributing to the total mortality outcome). The pooled effect estimate for total mortality for the exercise only intervention shows a 27% reduction in all cause mortality (random effects model OR 0.73 (0.54, 0.98)). Comprehensive cardiac rehabilitation reduced all cause mortality, but to a lesser degree (OR 0.87 (0.71, 1.05)). Total cardiac mortality was reduced by 31% (random effects model OR 0.69 (0.51, 0.94)) and 26% (random effects model OR 0.74 (0.57, 0.96)) in the exercise only and comprehensive cardiac rehabilitation groups respectively. Neither intervention had any effect on the occurrence of non-fatal myocardial infarction. There was a significant net reduction in total cholesterol (pooled WMD random effects model -0.57 mmol/l (-0.83, -0.31)) and LDL (pooled WMD random effects model -0.51 mmol/l (-0.82, -0.19) in the comprehensive cardiac rehabilitation group. REVIEWER'S CONCLUSIONS: Exercise-based cardiac rehabilitation is effective in reducing cardiac deaths. It is not clear from this review whether exercise only or a comprehensive cardiac rehabilitation intervention is more beneficial. The population studied in this review is still predominantly male, middle aged and low risk. Identification of the ethnic origin of the participants was seldom reported. It is possible that patients who would have benefited most from the intervention were excluded from the trials on the grounds of age, sex or co-morbidity.
TL;DR: This work combines production of compressed matter in a laser-driven implosion with picosecond-fast heating by a laser pulse timed to coincide with the peak compression, allowing efficient compression and heating to be carried out simultaneously, providing a route to efficient fusion energy production.
Abstract: Modern high-power lasers can generate extreme states of matter that are relevant to astrophysics, equation-of-state studies and fusion energy research. Laser-driven implosions of spherical polymer shells have, for example, achieved an increase in density of 1,000 times relative to the solid state. These densities are large enough to enable controlled fusion, but to achieve energy gain a small volume of compressed fuel (known as the 'spark') must be heated to temperatures of about 108 K (corresponding to thermal energies in excess of 10 keV). In the conventional approach to controlled fusion, the spark is both produced and heated by accurately timed shock waves, but this process requires both precise implosion symmetry and a very large drive energy. In principle, these requirements can be significantly relaxed by performing the compression and fast heating separately; however, this 'fast ignitor' approach also suffers drawbacks, such as propagation losses and deflection of the ultra-intense laser pulse by the plasma surrounding the compressed fuel. Here we employ a new compression geometry that eliminates these problems; we combine production of compressed matter in a laser-driven implosion with picosecond-fast heating by a laser pulse timed to coincide with the peak compression. Our approach therefore permits efficient compression and heating to be carried out simultaneously, providing a route to efficient fusion energy production.
TL;DR: The amygdala is involved in processing facial signals of fear and in fear conditioning, and this conclusion has emerged from evidence converging from the analysis of animals with amygdala lesions, from patients with bilateral amygdala damage and from functional imaging experiments in healthy individuals.
Abstract: For over 60 years, ideas about emotion in neuroscience and psychology have been dominated by a debate on whether emotion can be encompassed within a single, unifying model. In neuroscience, this approach is epitomized by the limbic system theory and, in psychology, by dimensional models of emotion. Comparative research has gradually eroded the limbic model, and some scientists have proposed that certain individual emotions are represented separately in the brain. Evidence from humans consistent with this approach has recently been obtained by studies indicating that signals of fear and disgust are processed by distinct neural substrates. We review this research and its implications for theories of emotion.
TL;DR: The authors examined the empirical determinants of borrowing decisions of firms and the role of adjustment process and found that firms have long-term target borrowing ratios and they adjust to their target ratios relatively fast, which might suggest that the costs of being away from their target ratio are significant.
Abstract: This paper examines the empirical determinants of borrowing decisions of firms and the role of adjustment process. A partial adjustment model is estimated by GMM estimation procedure using data for an unbalanced panel of 390 UK firms over the period of 1984–1996. Our results suggest that firms have long-term target borrowing ratios and they adjust to their target ratios relatively fast, which might suggest that the costs of being away from their target ratios are significant. The results also provide support for positive impact of size, and negative effects of growth opportunities, liquidity, profitability of firms and non-debt tax shields on the borrowing decisions of companies.
TL;DR: The ability of the root system to respond to phosphate availability was found to be independent of sucrose supply and auxin signaling, and shoot phosphate status was finding to influence theRoot system architecture response to phosphateavailability.
Abstract: Plant root systems are highly plastic in their development and can adapt their architecture in response to the prevailing environmental conditions. One important parameter is the availability of phosphate, which is highly immobile in soil such that the arrangement of roots within the soil will profoundly affect the ability of the plant to acquire this essential nutrient. Consistent with this, the availability of phosphate was found to have a marked effect on the root system architecture of Arabidopsis. Low phosphate availability favored lateral root growth over primary root growth, through increased lateral root density and length, and reduced primary root growth mediated by reduced cell elongation. The ability of the root system to respond to phosphate availability was found to be independent of sucrose supply and auxin signaling. In contrast, shoot phosphate status was found to influence the root system architecture response to phosphate availability.
TL;DR: This textbook for advanced undergraduates and graduate students emphasizes algorithms for a range of strategies for locomotion, sensing, and reasoning in mobile robots, including significant coverage of SLAM (simultaneous localization and mapping) and multi-robot systems.
Abstract: Mobile robotics is a multidisciplinary field involving both computer science and engineering. Addressing the design of automated systems, it lies at the intersection of artificial intelligence, computational vision, and robotics. This textbook for advanced undergraduates and graduate students emphasizes algorithms for a range of strategies for locomotion, sensing, and reasoning. It concentrates on wheeled and legged mobile robots but discusses a variety of other propulsion systems. The new edition includes advances in robotics and intelligent machines over the last ten years, including significant coverage of SLAM (simultaneous localization and mapping) and multi-robot systems. It includes additional mathematical background and an extensive list of sample problems. Various mathematical techniques that were assumed in the first edition are now briefly introduced in appendices at the end of the text to make the book more self-contained. Researchers as well as students in the field of mobile robotics will appreciate this comprehensive treatment of state-of-the-art methods and key technologies.
TL;DR: In this paper, the extent to which behavior in games reflects attempts to predict others' decisions, taking their incentives into account, was investigated, where subjects' initial responses to normal-form games with various patterns of iterated dominance and unique pure-strategy equilibria without dominance, using a computer interface that allowed them to search for hidden payoff information.
Abstract: This paper reports experiments designed to study strategic sophistication, the extent to which behavior in games reflects attempts to predict others' decisions, taking their incentives into account. We studied subjects' initial responses to normal-form games with various patterns of iterated dominance and unique pure-strategy equilibria without dominance, using a computer interface that allowed them to search for hidden payoff information, while recording their searches. Monitoring subjects' information searches along with their decisions allows us to better understand how their decisions are determined, and subjects' deviations from the search patterns suggested by equilibrium analysis help to predict their deviations from equilibrium decisions.
TL;DR: There appear to be important inequities in access to some types of health care in the UK, but that the evidence is often methodologically inadequate, making it difficult to draw firm conclusions.
TL;DR: A general catalytic mechanism for all retaining β-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate is formulated.
Abstract: Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques. A catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-building studies. The 'Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta-glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta-glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated. Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by X-ray diffraction. We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate.
TL;DR: In this article, a connection between the theories of ordinary differential equations and integrable models is made, and generalized supersymmetry transformations acting at the quasi-exactly solvable points are also pointed out, and an efficient numerical procedure for the study of these and related problems is described.
Abstract: The one-dimensional Schrodinger equation for the potential x6 + αx2 + l(l + 1)/x2 has many interesting properties. For certain values of the parameters l and α the equation is in turn supersymmetric (Witten) and quasi-exactly solvable (Turbiner), and it also appears in Lipatov's approach to high-energy QCD. In this paper we signal some further curious features of these theories, namely novel spectral equivalences with particular second- and third-order differential equations. These relationships are obtained via a recently observed connection between the theories of ordinary differential equations and integrable models. Generalized supersymmetry transformations acting at the quasi-exactly solvable points are also pointed out, and an efficient numerical procedure for the study of these and related problems is described. Finally we generalize slightly and then prove a conjecture due to Bessis, Zinn-Justin, Bender and Boettcher, concerning the reality of the spectra of certain -symmetric quantum mechanical systems.
TL;DR: To assess the effectiveness of all interventions that have been evaluated for use in the treatment or management of CFS in adults or children, 350 studies initially identified demonstrated mixed results in terms of effectiveness.
Abstract: ContextA variety of interventions have been used in the treatment and management
of chronic fatigue syndrome (CFS). Currently, debate exists among health care
professionals and patients about appropriate strategies for management.ObjectiveTo assess the effectiveness of all interventions that have been evaluated
for use in the treatment or management of CFS in adults or children.Data SourcesNineteen specialist databases were searched from inception to either
January or July 2000 for published or unpublished studies in any language.
The search was updated through October 2000 using PubMed. Other sources included
scanning citations, Internet searching, contacting experts, and online requests
for articles.Study SelectionControlled trials (randomized or nonrandomized) that evaluated interventions
in patients diagnosed as having CFS according to any criteria were included.
Study inclusion was assessed independently by 2 reviewers. Of 350 studies
initially identified, 44 met inclusion criteria, including 36 randomized controlled
trials and 8 controlled trials.Data ExtractionData extraction was conducted by 1 reviewer and checked by a second.
Validity assessment was carried out by 2 reviewers with disagreements resolved
by consensus. A qualitative synthesis was carried out and studies were grouped
according to type of intervention and outcomes assessed.Data SynthesisThe number of participants included in each trial ranged from 12 to
326, with a total of 2801 participants included in the 44 trials combined.
Across the studies, 38 different outcomes were evaluated using about 130 different
scales or types of measurement. Studies were grouped into 6 different categories.
In the behavioral category, graded exercise therapy and cognitive behavioral
therapy showed positive results and also scored highly on the validity assessment.
In the immunological category, both immunoglobulin and hydrocortisone showed
some limited effects but, overall, the evidence was inconclusive. There was
insufficient evidence about effectiveness in the other 4 categories (pharmacological,
supplements, complementary/alternative, and other interventions).ConclusionsOverall, the interventions demonstrated mixed results in terms of effectiveness.
All conclusions about effectiveness should be considered together with the
methodological inadequacies of the studies. Interventions which have shown
promising results include cognitive behavioral therapy and graded exercise
therapy. Further research into these and other treatments is required using
standardized outcome measures.
TL;DR: The Politics of the Environment as mentioned in this paper provides students with a comprehensive comparative introduction to ideas, activism and policy, including discussion on climate justice, climate legislation and recent environmental struggles, such as demonstrations against fracking.
TL;DR: Differences in small subunit ribosomal RNA genes are used to identify groups of arbuscular mycorrhizal fungi that are active in the colonisation of plant roots growing in arable fields around North Yorkshire, UK.
TL;DR: Fantasy realization theory states that when people contrast their fantasies about a desired future with reflections on present reality, a necessity to act is induced that leads to the activation and use of relevant expectations.
Abstract: Fantasy realization theory states that when people contrast their fantasies about a desired future with reflections on present reality, a necessity to act is induced that leads to the activation and use of relevant expectations. Strong goal commitment arises in light of favorable expectations, and weak goal commitment arises in light of unfavorable expectations. To the contrary, when people only fantasize about a desired future or only reflect on present reality, expectancy-independent moderate goal commitment emerges. Four experiments pertaining to various life domains supported these hypotheses. Strength of goal commitment was assessed in cognitive (e.g., making plans), affective (e.g., felt attachment), and behavioral terms (e.g., effort expenditure, quality of performance). Implications for theories on goal setting and goal striving are discussed.
TL;DR: It is argued that attempts at bias correction give unsatisfactory results, and that pointwise estimation in an independent data set may be the only way of obtaining reliable estimates of locus-specific effect-and then only if one does not condition on statistical significance being obtained.
Abstract: The primary goal of a genomewide scan is to estimate the genomic locations of genes influencing a trait of interest. It is sometimes said that a secondary goal is to estimate the phenotypic effects of each identified locus. Here, it is shown that these two objectives cannot be met reliably by use of a single data set of a currently realistic size. Simulation and analytical results, based on variance-components linkage analysis as an example, demonstrate that estimates of locus-specific effect size at genomewide LOD score peaks tend to be grossly inflated and can even be virtually independent of the true effect size, even for studies on large samples when the true effect size is small. However, the bias diminishes asymptotically. The explanation for the bias is that the LOD score is a function of the locus-specific effect-size estimate, such that there is a high correlation between the observed statistical significance and the effect-size estimate. When the LOD score is maximized over the many pointwise tests being conducted throughout the genome, the locus-specific effect-size estimate is therefore effectively maximized as well. We argue that attempts at bias correction give unsatisfactory results, and that pointwise estimation in an independent data set may be the only way of obtaining reliable estimates of locus-specific effect—and then only if one does not condition on statistical significance being obtained. We further show that the same factors causing this bias are responsible for frequent failures to replicate initial claims of linkage or association for complex traits, even when the initial localization is, in fact, correct. The findings of this study have wide-ranging implications, as they apply to all statistical methods of gene localization. It is hoped that, by keeping this bias in mind, we will more realistically interpret and extrapolate from the results of genomewide scans.
TL;DR: A phylogenetic analysis of the conserved amino acids encoded by these Arabidopsis genes reveals the presence of 14 distinct groups of UGTs, providing a foundation for further analysis of this large enzyme superfamily as well as a platform for future biotechnological applications.
Abstract: Uridine diphosphate (UDP) glycosyltransferases (UGTs) mediate the transfer of glycosyl residues from activated nucleotide sugars to acceptor molecules (aglycones), thus regulating properties of the acceptors such as their bioactivity, solubility and transport within the cell and throughout the organism. A superfamily of over 100 genes encoding UGTs, each containing a 42 amino acid consensus sequence, has been identified in the model plant Arabidopsis thaliana. A phylogenetic analysis of the conserved amino acids encoded by these Arabidopsis genes reveals the presence of 14 distinct groups of UGTs in this organism. Genes encoding UGTs have also been identified in several other higher plant species. Very little is yet known about the regulation of plant UGT genes or the localization of the enzymes they encode at the cellular and subcellular levels. The substrate specificities of these UGTs are now beginning to be established and will provide a foundation for further analysis of this large enzyme superfamily as well as a platform for future biotechnological applications.
TL;DR: The authors' meta-analysis of randomized controlled trials of HRT noted a statistically significant reduction in nonvertebral fractures, however, this effect may be attenuated in older women.
Abstract: ContextHormone replacement therapy (HRT) is widely considered to reduce fractures,
but this belief is based on observational data; evidence from randomized trials
is lacking.ObjectiveTo conduct a systematic review of all randomized trials of HRT that
have reported or collected nonvertebral fracture data but that may not have
focused on fracture prevention.Data SourcesThe MEDLINE, EMBASE, Science Citation Index, and Cochrane Controlled
Trials Register databases were searched from 1997 through 2000 and a search
was conducted of all recent systematic reviews to identify older studies.
Authors were contacted to establish whether fracture data had been collected
but not reported. Researchers in the field and pharmaceutical companies also
were contacted to try to identify unpublished studies.Study SelectionTrials were included in which participants had been randomized to at
least 12 months of therapy and data on nonvertebral fractures at any other
site and due to any cause were available. Of 70 initially identified studies,
22 were included in the analysis.Data ExtractionBoth investigators extracted data independently and appraised trial
quality according to the Jadad scale, which assesses the methods of randomization,
concealment allocation, and reporting of withdrawals and dropouts. Disagreements
were resolved by discussion.Data SynthesisThere was an overall 27% reduction in nonvertebral fractures in a pooled
analysis (reduction favoring HRT in relative risk [RR], 0.73; 95% confidence
interval [CI], 0.56-0.94; P = .02). This effect was
greater among women randomized to HRT who had a mean age younger than 60 years
(RR, 0.67; 95% CI, 0.46-0.98; P = .03). Among women
with a mean age of 60 years or older, there was a reduced effect (RR, 0.88;
95% CI, 0.71-1.08; P = .22). For hip and wrist fractures
alone, the effectiveness of HRT appeared more marked (RR, 0.60; 95% CI, 0.40-0.91; P = .02), particularly for women younger than 60 years
(RR, 0.45; 95% CI, 0.26-0.79; P = .005).ConclusionsOur meta-analysis of randomized controlled trials of HRT noted a statistically
significant reduction in nonvertebral fractures. However, this effect may
be attenuated in older women.
TL;DR: In this paper, the existence of traveling wave front solutions of reaction-diffusion systems with delay is investigated and a monotone iteration scheme is established for the corresponding wave system.
Abstract: This paper deals with the existence of traveling wave front solutions of reaction-diffusion systems with delay. A monotone iteration scheme is established for the corresponding wave system. If the reaction term satisfies the so-called quasimonotonicity condition, it is shown that the iteration converges to a solution of the wave system, provided that the initial function for the iteration is chosen to be an upper solution and is from the profile set. For systems with certain nonquasimonotone reaction terms, a convergence result is also obtained by further restricting the initial functions of the iteration and using a non-standard ordering of the profile set. Applications are made to the delayed Fishery–KPP equation with a nonmonotone delayed reaction term and to the delayed system of the Belousov–Zhabotinskii reaction model.