bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncertainty and the double dividend hypothesis
Authors: SARTZETAKIS EFTICHIOS S. , TSIGARIS PANAGIOTIS D. 
Published: March 2009

ABSTRACTThis paper examines the double dividend hypothesis in the presence of labour income uncertainty. Empirical evidence shows that uncertainty over labour income is particularly significant in developing, while not negligible in developed countries. Under uncertainty, and assuming incomplete capital markets, the tax system plays a role in providing social insurance, and a green tax reform influences its effectiveness. We show that the increase in environmental tax reduces consumption risk, while the balanced budget decrease in labour income tax increases income risk. We find that the total welfare effect of a green tax reform differs substantially from the case of certainty. The critical parameters determining the existence of a second dividend are the lump-sum transfers, the relative substitutability of the two goods for leisure, and the initial tax rates relative to their optimal that determine also the response of labour supply to a change in the tax mix.
An end to 40 years of mistakes in DNA–protein association kinetics?
Authors: Halford Stephen E. 
Published: March 2009

Proteins that bind to specific sequences in long DNA molecules have to locate their target sites amid myriad alternative sequences, yet they do so at remarkably rapid rates, sometimes approaching 1010 M−1·s−1. Hence, it has been asserted widely that binding to specific DNA sites can surpass the maximal rate for 3D (three-dimensional) diffusion through solution and that this could only be accounted for by a reduction in the dimensionality of the search for the target in effect by 1D (one-dimensional) diffusion (or ‘sliding’) along the DNA contour. It will be shown here that there is, in fact, no known example of a protein binding to a specific DNA site at a rate above the diffusion limit, and that the rapidity of these reactions is due primarily to electrostatic interactions between oppositely charged molecules. It will also be shown that, contrary to popular belief, reduced dimensionality does not, in general, increase the rate of target-site location but instead reduces it. Finally, it will be demonstrated that proteins locate their target sites primarily by multiple dissociation/reassociation events to other (nearby or distant) sites within the same DNA molecule, and that 1D diffusion is limited to local searches covering ∼50 bp around each landing site.
Probing coupled motions in enzymatic hydrogen tunnelling reactions
Authors: Allemann Rudolf K. , Evans Rhiannon M. , Loveridge E. Joel 
Published: March 2009

Much work has gone into understanding the physical basis of the enormous catalytic power of enzymes over the last 50 years or so. Nevertheless, the detailed mechanism used by Nature's catalysts to speed chemical transformations remains elusive. DHFR (dihydrofolate reductase) has served as a paradigm to study the relationship between the structure, function and dynamics of enzymatic transformations. A complex reaction cascade, which involves rearrangements and movements of loops and domains of the enzyme, is used to orientate cofactor and substrate in a reactive configuration from which hydride is transferred by quantum mechanical tunnelling. In the present paper, we review results from experiments that probe the influence of protein dynamics on the chemical step of the reaction catalysed by TmDHFR (DHFR from Thermotoga maritima). This enzyme appears to have evolved an optimal structure that can maintain a catalytically competent conformation under extreme conditions.
Optical fibre-based detection of DNA hybridization
Authors: Hine Anna V. , Chen Xianfeng , Hughes Marcus D. , Zhou Kaiming , Davies Edward , Sugden Kate , Bennion Ian , Zhang Lin 
Published: March 2009

A dual-peak LPFG (long-period fibre grating), inscribed in an optical fibre, has been employed to sense DNA hybridization in real time, over a 1 h period. One strand of the DNA was immobilized on the fibre, while the other was free in solution. After hybridization, the fibre was stripped and repeated detection of hybridization was achieved, so demonstrating reusability of the device. Neither strand of DNA was fluorescently or otherwise labelled. The present paper will provide an overview of our early-stage experimental data and methodology, examine the potential of fibre gratings for use as biosensors to monitor both nucleic acid and other biomolecular interactions and then give a summary of the theory and fabrication of fibre gratings from a biological standpoint. Finally, the potential of improving signal strength and possible future directions of fibre grating biosensors will be addressed.
Oxidative stress but not endothelial dysfunction exists in non‐obese, young group of patients with polycystic ovary syndrome
Authors: KUŞÇU NACI KEMAL , VAR AHMET 
Published: March 2009

AbstractObjective. To determine if oxidative stress and endothelial dysfunction exist at the same time in a young, non‐obese group of patients with polycystic ovary syndrome (PCOS). Design. Cross‐sectional study. Setting. Celal Bayar University, School of Medicine, Manisa, Turkey. Sample. Thirty‐one young, non‐obese patients with PCOS and 23 age‐ and body mass index‐matched controls. Methods. Following clinical and biochemical diagnosis, malonyldialdehyde (MDA), superoxide dismutase (SOD), von Willebrand Factor (vWF), and nitric oxide (NO) levels of patients and controls were measured and compared. Main outcome measures. To find out oxidative stress and endothelial dysfunction parameters. Results. MDA (0.12±0.03 vs 0.10±0.03, p = 0.01) and SOD (8.0±0.7 vs 7.28±0.8, p = 0.001) levels were significantly higher in PCOS group while there was no difference in vWF (527.2±280.1 vs 568.1±276.8, p>0.05) and NO levels (169.9±47.4 vs 168.9±80, p>0.05). When the results of the PCOS patients were divided into two subgroups in terms of insulin resistance (IR– and IR +), the IR– subgroup had significantly higher MDA levels compared to the control (0.125±0.03 vs 0.101±0.03, p = 0.03). Though IR+ group also had higher MDA than the control group, it did not reach to a significant level (0.117±0.05 vs 0.101±0.03, p>0.05). Both IR– and IR+ groups had significantly higher SOD levels compared with control group (7.99±0.7 vs 7.28±0.8, p = 0.009 and 8.22±0.8 vs 7.28±0.8, p = 0.03, respectively). vWF and NO levels were not different among these three groups (p>0.05). Conclusions. Oxidative stress is prominent while endothelial dysfunction does not exist in young, non‐obese patients with PCOS.
Infernal 1.0: inference of RNA alignments
Authors: Nawrocki Eric P. , Kolbe Diana L. , Eddy Sean R. 
Published: March 2009

Abstract
Summary: infernal builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence- and structure-based multiple sequence alignments.
Availability: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.
Contact: nawrockie,kolbed,eddys@janelia.hhmi.org
A study of the relationship between tag-signal characteristics and achievable performances in acoustic fish-tag studies
Authors: Ehrenberg John E. , Steig Tracey W. 
Published: March 2009

Abstract
Ehrenberg, J. E., and Steig, T. W. 2009. A study of the relationship between tag-signal characteristics and achievable performances in acoustic fish-tag studies. – ICES Journal of Marine Science, 66: 1278–1283. Acoustic tags have been used in fish-behaviour studies in a variety of marine and freshwater environments. The intended objectives of these studies vary widely. In some cases, they require accurate three-dimensional tracking of the individual fish locations. In other cases, tags are used for estimating fish survival along a migration route. There are varieties of schemes that have been proposed and used for implementing tag systems. The purpose of this paper is to explain the relationship between the various characteristics of acoustic signals transmitted by the tags and the tag-system performance that can be achieved. In particular, the ranges at which the tags can be detected and uniquely identified, the positional accuracy, and the number of unique codes that can be assigned to individual fish are all functions of the signal type. This paper demonstrates that when the pulse-repetition period is used to encode the tag identification, the range performance for the tag is superior to that achieved using a scheme that has binary-encoded bits as part of the transmitter signal. The parametric results presented will assist investigators in their selection of the type of acoustic tags or tag parameters needed to achieve the objectives of acoustic fish-tag studies.
Comparison of nonsteroidal anti‐inflammatory drugs and cyclooxygenase‐2 (COX‐2) inhibitors use in Australia and Nova Scotia (Canada)
Authors: Barozzi Nadia , Sketris Ingrid , Cooke Charmaine , Tett Susan 
Published: March 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT • Cyclo‐oxygenase‐2 (COX‐2) inhibitors were marketed aggressively and their rapid uptake caused safety concerns and budgetary challenges in Canada and Australia. WHAT THIS STUDY ADDS • The study showed that there were similarities in the anti‐inflammatory prescribing pattern between Australia and Nova Scotia; however, volumes of both ns‐NSAIDs and COX‐2 inhibitors prescribed were higher in Australia in the study period. The remarkable increase observed in Australia in NSAIDs use was essentially due to the much higher COX‐2 inhibitor use. Differences in regulatory and marketing practices, as well as cultural and historical differences might be some of the reasons for differences in the NSAID prescribing between Australia and Nova Scotia.AIMSCyclooxygenase‐2 (COX‐2) inhibitors were marketed aggressively and their rapid uptake caused safety concerns and budgetary challenges in Canada and Australia. The objectives of this study were to compare and contrast COX‐2 inhibitors and nonselective nonsteroidal anti‐inflammatory drug (ns‐NSAID) use in Nova Scotia (Canada) and Australia and to identify lessons learned from the two jurisdictions.METHODSNs‐NSAID and COX‐2 inhibitor Australian prescription data (concession beneficiaries) were downloaded from the Medicare Australia website (2001–2006). Similar Pharmacare data were obtained for Nova Scotia (seniors and those receiving Community services). Defined daily doses per 1000 beneficiaries day−1 were calculated. COX‐2 inhibitors/all NSAIDs ratios were calculated for Australia and Nova Scotia. Ns‐NSAIDs were divided into low, moderate and high risk for gastrointestinal side‐effects and the proportions of use in each group were determined. Which drugs accounted for 90% of use was also calculated.RESULTSOverall NSAID use was different in Australia and Nova Scotia. However, ns‐NSAID use was similar. COX‐2 inhibitor dispensing was higher in Australia. The percentage of COX‐2 inhibitor prescriptions over the total NSAID use was different in the two countries. High‐risk NSAID use was much higher in Australia. Low‐risk NSAID prescribing increased in Nova Scotia over time. The low‐risk/high‐risk ratio was constant throughout over the period in Australia and increased in Nova Scotia.CONCLUSIONSThere are significant differences in Australia and Nova Scotia in use of NSAIDs, mainly due to COX‐2 prescribing. Nova Scotia has a higher proportion of low‐risk NSAID use. Interventions to provide physicians with information on relative benefits and risks of prescribing specific NSAIDs are needed, including determining their impact.
Infective dermatitis has similar immunological features to human T lymphotropic virus-type 1-associated myelopathy/tropical spastic paraparesis
Authors: Nascimento M C F , Primo J , Bittencourt A , Siqueira I , De Fátima Oliveira M , Meyer R , Schriefer A , Santos S B , Carvalho E M 
Published: March 2009

SummaryHuman T lymphotropic virus-type 1 (HTLV-1) is the causal agent of the HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), adult T cell leukaemia/lymphoma and infective dermatitis associated with HTLV-1 (IDH). Over-production of proinflammatory cytokines and an increase in HTLV-1 proviral load are features of HAM/TSP, but the immunological basis of IDH has not been established. In addition to severe cutaneous manifestations, the importance of IDH relies on the observation that up to 30% of children with IDH develop HAM/TSP in childhood and adolescence. In this study we determined the immune response in patients with IDH measuring interleukin (IL)-4, IL-5, IL-10, interferon (IFN)-γ and tumour necrosis factor (TNF)-α levels as well as the HTLV-1 proviral load. Additionally, regulatory cytokines and anti-cytokines were added to cultures to evaluate the ability of these molecules to down-modulate TNF-α and IFN-γ synthesis. HTLV-1 carriers and patients with HAM/TSP served as controls. TNF-α and IFN-γ levels were higher in IDH than in HTLV-1 carriers. There was no difference in IFN-γ and TNF-α concentrations in IDH and HAM/TSP patients. There was a tendency for higher IL-4 mRNA expression and immunoglobulin E (IgE) levels in IDH than in HTLV-1 carriers, but the difference did not reach statistical significance. The HTLV-1 proviral load was significantly higher in IDH patients than in HTLV-1 carriers. IDH is characterized by an exaggerated Th1 immune response and high HTLV-1 proviral load. The similarities between the immunological response in patients with IDH and HAM/TSP and the high proviral load observed in IDH provide support that IDH is a risk factor for development of HAM/TSP.
Activation of AMPK inhibits inflammation in MRL/lpr mouse mesangial cells
Authors: Peairs A , Radjavi A , Davis S , Li L , Ahmed A , Giri S , Reilly C M 
Published: March 2009

SummaryRecent reports show that 5-amino-4-imidazole carboxamide riboside (AICAR), a pharmacological activator of AMP-activated protein kinase (AMPK), inhibits the lipopolysaccharide (LPS)-induced production of proinflammatory cytokines. MRL/MPJ-Faslpr (MRL/lpr) mice show an intrinsic decreased threshold for the production of inflammatory mediators when stimulated. In our current studies, we sought to determine if AMPK activation would inhibit inflammatory mediator production in stimulated kidney mesangial cells. Cultured mesangial cells from MRL/lpr mice were treated with AICAR and stimulated with LPS/interferon (IFN)-γ. AICAR decreased dose-dependently inducible nitric oxide synthase (iNOS), cyclooxygenase-2 and interleukin-6 production in LPS/IFN-γ-stimulated mesangial cells. Mechanistically, AICAR inhibited the LPS/IFN-γ-stimulated PI3K/Akt signalling inflammatory cascade but did not affect LPS/IFN-γ-mediated inhibitory kappa B phosphorylation or nuclear factor (NF)-κB (p65) nuclear translocation. Treatment with the adenosine kinase inhibitor 5′-iodotubercidin blocked the ability of AICAR to activate AMPK and prevented AICAR from inhibiting the LPS/IFN-γ-stimulated PI3K/Akt pathway and attenuating iNOS expression. Taken together, these observations suggest that AICAR inhibits LPS/IFN-γ-induced Akt phosphorylation through AMPK activation and may serve as a potential therapeutic target in inflammatory diseases.
Bleeding events in pulmonary arterial hypertension
Authors: Opitz C. F. , Kirch W. , Mueller E. A. , Pittrow D. 
Published: March 2009

AbstractDespite limited evidence from clinical studies, anticoagulant drugs such as vitamin K antagonists (VKA) (e.g., warfarin or phenprocoumon) are widely used in the background treatment of patients with pulmonary arterial hypertension (PAH). According to current guidelines, they are generally accepted as efficacious drugs, although their efficacy is neither supported by randomised controlled trials, nor formally approved by regulatory agencies for use in the specific PAH indication. The use of these drugs is not without problems, as a paradoxical situation has to be managed in the treatment of this condition. On one hand, thrombosis is one of the key pathophysiologic features of PAH (besides vasoconstriction, proliferation and inflammation). On the other hand, the incidence of bleeding events is increased in PAH patients. This applies particularly to PAH that is related to connective tissue diseases, congenital heart disease and chronic thromboembolic pulmonary hypertension. In patients receiving VKA, caution must be observed in particular when concomitantly using prostanoids or sildenafil. Similarly, VKA doses have to be adjusted according to the labelling when using sitaxentan concomitantly. Regular International Normalized Ratio monitoring contributes to the safety of PAH patients on VKA.
Endothelin‐1 and vein graft occlusion in patients undergoing bypass surgery
Authors: Dashwood M. R. 
Published: March 2009

AbstractThe saphenous vein is the most commonly used graft for revascularization procedures in patients with coronary artery disease and critical limb ischaemia. However, the patency rate of this vessel is poor, with a high proportion of patients requiring further surgery. Early graft occlusion is caused by vasoconstriction or thrombus formation, with later stages of graft failure being due to neointimal formation or atherosclerosis. Apart from its potent constrictor action, endothelin‐1 is also a potent proliferative and proinflammatory peptide that is implicated in a number of vascular diseases. The surgical trauma caused during preparation of the saphenous vein as a bypass graft stimulates the release of a number of factors affecting vascular reactivity and structure, including endothelin‐1. Endothelin‐1 not only constricts animal and human isolated saphenous vein segments but also causes vascular smooth muscle proliferation and neointimal thickeningin vitro, actions that are mediated via endothelin (A and B) receptors. Experimentally, the effects of subtype‐selective and dual receptor antagonists have been shown to inhibit endothelin‐1‐mediated constriction and cell proliferation of the saphenous vein. In this review, data supporting a role of endothelin‐1 in vein graft occlusion are presented, and the therapeutic potential of endothelin receptor antagonists in improving graft performance is discussed.
Soil phosphorus status and turnover in central‐European beech forest ecosystems with differing tree species diversity
Authors: Talkner U. , Jansen M. , Beese F. O. 
Published: March 2009

SummaryProblems in phosphorus (P) nutrition of forest trees raise questions concerning the soil P concentrations, pools and turnover in forests. In addition, it is not clear if, and to what extent, tree species diversity has an influence on the soil P status and turnover. The aim of this study was to investigate the P status and turnover in beech (Fagus sylvatica L.) ‐dominated forest ecosystems on loess over limestone and to elucidate what role heterogeneities in tree species diversity would play. The soils of mixed species stands contained more organically bound P (710–772 kg ha−1) than those of pure beech stands (378 kg ha−1), whereas the inorganic P content differed little between the stand types. A large proportion (44–55%) of the total soil P was organically bound. This fraction was mainly dependent on the clay content of the soils and not on the tree diversity. The P input with leaf litter (1.4–2.1 kg ha−1 year−1) showed a tendency to increase with increasing diversity. The apparent P turnover times in the organic surface layers differed, with shorter turnover times in mixed species stands (2–3 years) than in pure beech stands (10 years). Possible explanations for the different turnover times were differences in the litter quality, interactions in mixed species litters and the soil pH and base saturation. Hence, the tree species mainly influence the apparent P turnover time in the organic surface layer, whereas the P concentrations and pools in the mineral soil are determined by the soil properties, particularly the clay content.
Leaf stomatal responses to vapour pressure deficit under current and CO2‐enriched atmosphere explained by the economics of gas exchange
Authors: KATUL GABRIEL G. , PALMROTH SARI , OREN RAM 
Published: March 2009

ABSTRACTUsing the economics of gas exchange, early studies derived an expression of stomatal conductance (g) assuming that water cost per unit carbon is constant as the daily loss of water in transpiration (fe) is minimized for a given gain in photosynthesis (fc). Other studies reached identical results, yet assumed different forms for the underlying functions and defined the daily cost parameter as carbon cost per unit water. We demonstrated that the solution can be recovered when optimization is formulated at time scales commensurate with the response time of g to environmental stimuli. The optimization theory produced three emergent gas exchange responses that are consistent with observed behaviour: (1) the sensitivity of g to vapour pressure deficit (D) is similar to that obtained from a previous synthesis of more than 40 species showing g to scale as 1 − m log(D), where m ? [0.5,0.6], (2) the theory is consistent with the onset of an apparent ‘feed‐forward’ mechanism in g, and (3) the emergent non‐linear relationship between the ratio of intercellular to atmospheric [CO2] (ci/ca) and D agrees with the results available on this response. We extended the theory to diagnosing experimental results on the sensitivity of g to D under varying ca.
Regulation of isoprene emission from poplar leaves throughout a day
Authors: WIBERLEY AMY E. , DONOHUE AUTUMN R. , WESTPHAL MAIKEN M. , SHARKEY THOMAS D. 
Published: March 2009

ABSTRACTIsoprene is a biogenic hydrocarbon that significantly affects tropospheric chemistry. Numerous plant species, including many trees, emit isoprene. Isoprene is synthesized by isoprene synthase (IspS), from dimethylallyl diphosphate (DMADP) made by the methylerythritol 4‐phosphate (MEP) pathway. It has been demonstrated that in developing leaves, isoprene emission is regulated by transcriptional control of IspS, while in mature leaves subjected to changing growth temperature, regulation of emission is shared between IspS and DMADP supply from the MEP pathway. Isoprene emission also varies throughout a day, with circadian regulation implicated. This study investigated changes in isoprene emission capacity, and expression of IspS and the enzymes of the MEP pathway throughout several days, with Populus trichocarpa grown at different temperatures to induce different levels of isoprene emission. Isoprene emission capacity exhibited ultradian regulation, with a period of about 12 h; peak capacity was observed at 0300 and 1500 h daily. Several of the enzymes of the MEP pathway had previously been suggested to have regulatory roles in the production of other plastidic terpenoids, and transcript accumulation for these enzymes, combined with in silico promoter analyses, supported a regulatory role for deoxyxylulose 5‐phosphate synthase (DXS) in particular.