Showing papers by "Uppsala University published in 2002"

NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks

Abstract: We introduce NeighborNet, a network construction and data representation method that combines aspects of the neighbor joining (NJ) and SplitsTree. Like NJ, NeighborNet uses agglomeration: taxa are combined into progressively larger and larger overlapping clusters. Like SPLITSTREE, NeighborNet constructs networks rather than trees, and so can be used to represent multiple phylogenetic hypotheses simultaneously, or to detect complex evolutionary processes like recombination, lateral transfer and hybridization. NeighborNet tends to produce networks that are substantially more resolved than those made with SPLITSTREE. The method is efficient (O(n3) time) and is well suited for the preliminary analyses of complex phylogenetic data. We report results of three case studies: one based on mitochondrial gene order data from early branching eukaryotes, another based on nuclear sequence data from New Zealand alpine buttercups (Ranunculi), and a third on poorly corrected synthetic data.

The Elusive Concept of Localization Economies: Towards a Knowledge-Based Theory of Spatial Clustering

Abstract: A number of possible advantages of industry agglomeration—or spatial clustering—have been identified in the research literature, notably those related to shared costs for infrastructure, the build-up of a skilled labour force, transaction efficiency, and knowledge spillovers leading to firm learning and innovation. We identify two shortcomings of existing research on the clustering phenomenon. First, the abundance of theoretical concepts and explanations stands in sharp contrast with the general lack of work aimed at validating these mechanisms empirically and the contradictory evidence found in recent empirical work in the field. Second, there is still a lack of a unified theoretical framework for analyzing spatial clustering. In an attempt to remedy the latter shortcoming, this paper investigates the nature of the cluster from a knowledge-creation or learning perspective. We argue for the need to establish a specific theory of the cluster where learning occupies centre stage. The basic requirements for ...

The strategic impact of external networks: Subsidiary performance and competence development in the multinational corporation

Abstract: A special feature of multinational firms (MNCs) is the notion that their sub-units (subsidiaries) are embedded in different local networks (Ghoshal and Bartlett, 1990; Ghoshal and Nohria, 1997; Fors-gren, Johanson, and Sharma, 2000). Each subsidiary maintains unique and idiosyncratic patterns of network linkages and consequently is differentially exposed to new knowledge, ideas and opportunities (McEvily and Zaheer, 1999). In fact, this differential exposure has been put forward as one of the basic competitive advantages of the multinational firm, because it increases the breadth and variety of its network resources (Malnight, 1996). It is also in line with recent trends in foreign direct investment theory, in which foreign investments are viewed as series of attempts to selectively tap knowledge linked to specific local business contexts (Cantwell, 1990; Almeida, 1996; Dunning, 1996).

EDUTELLA: a P2P networking infrastructure based on RDF

Abstract: Metadata for the World Wide Web is important, but metadata for Peer-to-Peer (P2P) networks is absolutely crucial. In this paper we discuss the open source project Edutella which builds upon metadata standards defined for the WWW and aims to provide an RDF-based metadata infrastructure for P2P applications, building on the recently announced JXTA Framework. We describe the goals and main services this infrastructure will provide and the architecture to connect Edutella Peers based on exchange of RDF metadata. As the query service is one of the core services of Edutella, upon which other services are built, we specify in detail the Edutella Common Data Model (ECDM) as basis for the Edutella query exchange language (RDF-QEL-i) and format implementing distributed queries over the Edutella network. Finally, we shortly discuss registration and mediation services, and introduce the prototype and application scenario for our current Edutella aware peers.

Optimal designs for space-time linear precoders and decoders

Abstract: We introduce a new paradigm for the design of transmitter space-time coding that we refer to as linear precoding. It leads to simple closed-form solutions for transmission over frequency-selective multiple-input multiple-output (MIMO) channels, which are scalable with respect to the number of antennas, size of the coding block, and transmit average/peak power. The scheme operates as a block transmission system in which vectors of symbols are encoded and modulated through a linear mapping operating jointly in the space and time dimension. The specific designs target minimization of the symbol mean square error and the approximate maximization of the minimum distance between symbol hypotheses, under average and peak power constraints. The solutions are shown to convert the MIMO channel with memory into a set of parallel flat fading subchannels, regardless of the design criterion, while appropriate power/bits loading on the subchannels is the specific signature of the different designs. The proposed designs are compared in terms of various performance measures such as information rate, BER, and symbol mean square error.

Potential Applications and Pitfalls of Bayesian Inference of Phylogeny

Abstract: Only recently has Bayesian inference of phylogeny been proposed. The method is now a practical alternative to the other methods; indeed, the method appears to possess advantages over the other methods in terms of ability to use complex models of evolution, ease of interpretation of the results, and computational efeciency. However, the method should be used cautiously. The results of a Bayesian analysis should be examined with respect to the sensitivity of the results to the priors used and the reliability of the Markov chain Monte Carlo approximation of the probabilities of trees. (Bayesian inference; Markov chain Monte Carlo; phylogeny; posterior probability.)

The catalytic pathway of horseradish peroxidase at high resolution

Abstract: A molecular description of oxygen and peroxide activation in biological systems is difficult, because electrons liberated during X-ray data collection reduce the active centres of redox enzymes catalysing these reactions. Here we describe an effective strategy to obtain crystal structures for high-valency redox intermediates and present a three-dimensional movie of the X-ray-driven catalytic reduction of a bound dioxygen species in horseradish peroxidase (HRP). We also describe separate experiments in which high-resolution structures could be obtained for all five oxidation states of HRP, showing such structures with preserved redox states for the first time.

A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans

Abstract: Systemic lupus erythematosus (SLE, OMIM 152700) is a complex autoimmune disease that affects 0.05% of the Western population, predominantly women. A number of susceptibility loci for SLE have been suggested in different populations, but the nature of the susceptibility genes and mutations is yet to be identified. We previously reported a susceptibility locus (SLEB2) for Nordic multi-case families. Within this locus, the programmed cell death 1 gene (PDCD1, also called PD-1) was considered the strongest candidate for association with the disease. Here, we analyzed 2,510 individuals, including members of five independent sets of families as well as unrelated individuals affected with SLE, for single-nucleotide polymorphisms (SNPs) that we identified in PDCD1. We show that one intronic SNP in PDCD1 is associated with development of SLE in Europeans (found in 12% of affected individuals versus 5% of controls; P = 0.00001, r.r. (relative risk) = 2.6) and Mexicans (found in 7% of affected individuals versus 2% of controls; P = 0.0009, r.r. = 3.5). The associated allele of this SNP alters a binding site for the runt-related transcription factor 1 (RUNX1, also called AML1) located in an intronic enhancer, suggesting a mechanism through which it can contribute to the development of SLE in humans.

Microwave-accelerated homogeneous catalysis in organic chemistry.

Abstract: The efficiency of microwave flash heating in accelerating organic transformations (reaction times reduced from days and hours to minutes and seconds) has recently been proven in several different fields of organic chemistry. This specific account mainly summarizes our own experiences in developing rapid, robust, and selective microwave-assisted transition metal-catalyzed homogeneous reactions. Applications include selective Heck couplings, cross-couplings, and asymmetric substitutions. The science of green chemistry was developed to meet the increasing demand for environmentally benign chemical processes. We believe the combination of metal catalysis and microwave heating will be of importance in the search for green laboratory-scale synthesis.

Quantum origin of the oxygen storage capability of ceria.

Abstract: The microscopic mechanism behind the extraordinary ability of ceria to store, release, and transport oxygen is explained on the basis of first-principles quantum mechanical simulations. The oxygen-vacancy formation energy in ceria is calculated for different local environments. The reversible CeO2-Ce2O3 reduction transition associated with oxygen-vacancy formation and migration is shown to be directly coupled with the quantum process of electron localization.

Surface Characterization of Electrodes from High Power Lithium-Ion Batteries

Abstract: X-ray photoelectron spectroscopy and scanning electron microscopy were used to study electrode samples obtained from 18650-type lithium-ion cells subjected to accelerated calendar-life testing at temperatures ranging from 25 to 70 C and at states-of-charge from 40 to 80%. The cells contained LiNi{sub 0.8}Co{sub 0.2}O{sub 2}-based positive electrodes (cathodes), graphite-based negative electrodes (anodes), and a 1 M LiPF{sub 6} ethylene carbonate:diethyl carbonate (1:1) electrolyte. The results from electrochemically treated samples showed surface film formation on both electrodes. The positive electrode laminate surfaces contained a mixture of organic species that included polycarbonates, and LiF, Li{sub x}PF{sub y}-type and Li{sub x}PF{sub y}O{sub z}-type compounds. The same surface compounds were observed regardless of test temperature, test duration, and state-of-charge. On the negative electrode laminates lithium alkyl carbonates (ROCO{sub 2}Li) and Li{sub 2}CO{sub 3} were found in addition to the above-mentioned compounds. Decomposition of lithium alkyl carbonates to Li{sub 2}CO{sub 3} occurred on negative electrodes stored at elevated temperature. Initial depth-profiling results suggest that the surface layer thickness is greater on positive electrode samples from cells stored at high temperature than on samples from cells stored at room temperature. This observation is significant because positive electrode impedance, and more specifically, charge-transfer resistance at the electrode/electrolytemore » interface, has been shown to be the main contributor to impedance rise in these cells.« less

50 Million Years of Genomic Stasis in Endosymbiotic Bacteria

Abstract: Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acqui ...

Rapid Regulation of Light Harvesting and Plant Fitness in the Field

Abstract: We used Arabidopsis thaliana mutants to examine how a photosynthetic regulatory process, the qE-type or ΔpH-dependent nonphotochemical quenching, hereafter named feedback de-excitation, influences plant fitness in different light environments. We show that the feedback de-excitation is important for plant fitness in the field and in fluctuating light in a controlled environment but that it does not affect plant performance under constant light conditions. Our findings demonstrate that the feedback de-excitation confers a strong fitness advantage under field conditions and suggest that this advantage is due to the increase in plant tolerance to variation in light intensity rather than tolerance to high-intensity light itself.

On the Vote-Purchasing Behavior of Incumbent Governments

Abstract: A couple of months before the Swedish election in 1998, the incumbent government distributed 2.3 billion SEK to 42 out of 115 applying municipalities. This was the first wave of a four-year long grant program intended to support local investment programs aimed at an ecological sustainable development. This temporary grant program differs from traditional intergovernmental grants in several aspects, most importantly in the sovereign decision making power given to the incumbent central government. In this paper we investigate whether there were any tactical motives behind the distribution of these grants. We find support for the hypothesis that the incumbent government used the grant program under study in order to win votes. In particular, we find strong support for the Lindbeck-Weibull/Dixit-Londregan model in which parties distribute transfers to regions where there are many swing voters. This result is statistically as well as economically significant. We do however not find any support for the model that predicts that the incumbent government transfer money to its own supporters.

Public Information and Breeding Habitat Selection in a Wild Bird Population

Abstract: According to the “public information” hypothesis, some animal species may monitor the current reproductive success of conspecifics to assess local habitat quality and to choose their own subsequent breeding site. To test this hypothesis experimentally, we manipulated two components of public information, the mean number of offspring raised locally (“quantity”) and their condition (“quality”), in the collared flycatcher Ficedula albicollis. Immigration rate decreased with local offspring quantity but did not depend on local offspring quality, suggesting that immigrants are deprived of information regarding local quality. Conversely, emigration rate increased both when local offspring quantity or quality decreased, suggesting that residents can use both components of public information.

Lung Cancer Following Chemotherapy and Radiotherapy for Hodgkin's Disease

Abstract: Background: Lung cancer is a frequent cause of death in patients cured of Hodgkin’s disease, but the contributions of chemotherapy, radiotherapy, and smoking are not well described.We quantified the risk of treatment-associated lung cancer, taking into account tobacco use. Methods: Within a population-based cohort of 19 046 Hodgkin’s disease patients (diagnosed from 1965 through 1994), a case–control study of lung cancer was conducted.The cumulative amount of cytotoxic drugs, the radiation dose to the specific location in the lung where cancer developed, and tobacco use were compared for 222 patients who developed lung cancer and for 444 matched control patients.All statistical tests were twosided. Results: Treatment with alkylating agents without radiotherapy was associated with increased lung cancer risk (relative risk [RR] = 4.2; 95% confidence interval [CI] = 2.1 to 8.8), as was radiation dose of 5 Gy or more without alkylating agents (RR = 5.9; 95% CI = 2.7 to 13.5). Risk increased with both increasing number of cycles of alkylating agents and increasing radiation dose (P for trend <.001). Among patients treated with mechlorethamine, vincristine, procarbazine, and prednisone (MOPP), risk increased with cumulative amounts of mechlorethamine and procarbazine (P<.001) when evaluated separately. Statistically significantly elevated risks of lung cancer were apparent within 1–4 years after treatment with alkylating agents, whereas excess risk after radiotherapy began 5 years after treatment and persisted for more than 20 years.Risk after treatment with alkylating agents and radiotherapy together was as expected if individual excess risks were summed.Tobacco use increased lung cancer risk more than 20-fold; risks from smoking appeared to multiply risks from treatment. Conclusions: Past treatments with alkylating agents and radiation therapy for Hodgkin’s disease were associated with an increased risk of lung cancer in a dose-dependent and additive fashion.The precise risk estimates, however, should be interpreted cautiously, given the possible residual and enhancing effects of tobacco.[J Natl Cancer Inst 2002;94:182–92] Second malignant neoplasms constitute the number one cause of mortality in patients cured of Hodgkin’s disease, with lung cancer representing the most frequent solid tumor (1–3). Although leukemia was the first malignancy reported to be increased following Hodgkin’s disease treatments, the absolute risk of solid cancers now far exceeds that of leukemia, with estimates of 48.8 and 18.4 excess cases per 10 000 patients per

Structure and bonding of water on Pt(111).

Abstract: We address the adsorption of water on Pt(111) using x-ray absorption, x-ray emission, and x-ray photoelectron spectroscopy along with calculations in the framework of density functional theory. Using the direct relationship between the electronic structure and adsorbate geometry, we show that in the first layer all the molecules bind directly to the surface and to each other through the in-layer H bonds without dissociation, creating a nearly flat overlayer. The water molecules are adsorbed through alternating metal-oxygen (M-O) and metal-hydrogen (M-HO) bonds.

Hydrogenases and Hydrogen Metabolism of Cyanobacteria

Abstract: Cyanobacteria may possess several enzymes that are directly involved in dihydrogen metabolism: nitrogenase(s) catalyzing the production of hydrogen concomitantly with the reduction of dinitrogen to ammonia, an uptake hydrogenase (encoded by hupSL) catalyzing the consumption of hydrogen produced by the nitrogenase, and a bidirectional hydrogenase (encoded by hoxFUYH) which has the capacity to both take up and produce hydrogen. This review summarizes our knowledge about cyanobacterial hydrogenases, focusing on recent progress since the first molecular information was published in 1995. It presents the molecular knowledge about cyanobacterial hupSL and hoxFUYH, their corresponding gene products, and their accessory genes before finishing with an applied aspect—the use of cyanobacteria in a biological, renewable production of the future energy carrier molecular hydrogen. In addition to scientific publications, information from three cyanobacterial genomes, the unicellular Synechocystis strain PCC 6803 and the filamentous heterocystous Anabaena strain PCC 7120 and Nostoc punctiforme (PCC 73102/ATCC 29133) is included.

Antagonistic coevolution between the sexes in a group of insects

Abstract: In coevolutionary 'arms races' between the sexes, the outcome of antagonistic interactions may remain at an evolutionary standstill. The advantage gained by one sex, with any evolutionary exaggeration of arms, is expected to be matched by analogous counteradaptations in the other sex. This fundamental coevolutionary process may thus be hidden from the evolutionist's eye, and no natural examples are known. We have studied the effects of male and female armament (clasping and anti-clasping morphologies) on the outcome of antagonistic mating interactions in 15 species of water strider, using a combination of experimental and phylogenetic comparative methods. Here we present, by assessing the independent effects of both species-specific level of arms escalation and small imbalances in the amounts of arms between the sexes within species, the consequences of a sexual arms race. Evolutionary change in the balance of armament between males and females, but not in the species-specific level of escalation, has resulted in evolutionary change in the outcome of sexually antagonistic interactions such as mating rate.

Molecular basis of proton motive force generation: structure of formate dehydrogenase-N.

Abstract: The structure of the membrane protein formate dehydrogenase-N (Fdn-N), a major component of Escherichia coli nitrate respiration, has been determined at 1.6 angstroms. The structure demonstrates 11 redox centers, including molybdopterin-guanine dinucleotides, five [4Fe-4S] clusters, two heme b groups, and a menaquinone analog. These redox centers are aligned in a single chain, which extends almost 90 angstroms through the enzyme. The menaquinone reduction site associated with a possible proton pathway was also characterized. This structure provides critical insights into the proton motive force generation by redox loop, a common mechanism among a wide range of respiratory enzymes.

Consumer versus resource control of species diversity and ecosystem functioning

Abstract: A key question in ecology is which factors control species diversity in a community1, 2, 3. Two largely separate groups of ecologists have emphasized the importance of productivity or resource supply, and consumers or physical disturbance, respectively. These variables show unimodal relationships with diversity when manipulated in isolation4, 5, 6, 7, 8. Recent multivariate models9, 10, however, predict that these factors interact, such that the disturbance–diversity relationship depends on productivity, and vice versa. We tested these models in marine food webs, using field manipulations of nutrient resources and consumer pressure on rocky shores of contrasting productivity. Here we show that the effects of consumers and nutrients on diversity consistently depend on each other, and that the direction of their effects and peak diversity shift between sites of low and high productivity. Factorial meta-analysis of published experiments confirms these results across widely varying aquatic communities. Furthermore, our experiments demonstrate that these patterns extend to important ecosystem functions such as carbon storage and nitrogen retention. This suggests that human impacts on nutrient supply11 and food-web structure12, 13 have strong and interdependent effects on species diversity and ecosystem functioning, and must therefore be managed together.

Model of Chemotherapy-Induced Myelosuppression With Parameter Consistency Across Drugs

Abstract: PURPOSE: To develop a semimechanistic pharmacokinetic-pharmacodynamic model describing chemotherapy-induced myelosuppression through drug-specific parameters and system-related parameters, which ar ...

Treatment With Dietary trans10cis12 Conjugated Linoleic Acid Causes Isomer-Specific Insulin Resistance in Obese Men With the Metabolic Syndrome

Abstract: OBJECTIVE —Conjugated linoleic acid (CLA) is a group of dietary fatty acids with antiobesity and antidiabetic effects in some animals. The trans 10 cis 12 ( t 10 c 12) CLA isomer seems to cause these effects, including improved insulin sensitivity. Whether such isomer-specific effects occur in humans is unknown. The aim of this study was to investigate whether t 10 c 12 CLA or a commercial CLA mixture could improve insulin sensitivity, lipid metabolism, or body composition in obese men with signs of the metabolic syndrome. RESEARCH DESIGN AND METHODS —In a randomized, double-blind controlled trial, abdominally obese men ( n = 60) were treated with 3.4 g/day CLA (isomer mixture), purified t 10 c 12 CLA, or placebo. Euglycemic-hyperinsulinemic clamp, serum hormones, lipids, and anthropometry were assessed before and after 12 weeks of treatment. RESULTS —Baseline metabolic status was similar between groups. Unexpectedly, t 10 c 12 CLA increased insulin resistance (19%; P < 0.01) and glycemia (4%; P < 0.001) and reduced HDL cholesterol (−4%; P < 0.01) compared with placebo, whereas body fat, sagittal abdominal diameter, and weight decreased versus baseline, but the difference was not significantly different from placebo. The CLA mixture did not change glucose metabolism, body composition, or weight compared with placebo but lowered HDL cholesterol (−2%; P < 0.05). CONCLUSIONS —These results reveal important isomer-specific metabolic actions of CLA in abdominally obese humans. A CLA-induced insulin resistance has previously been described only in lipodystrophic mice. Considering the use of CLA-supplements among obese individuals, it is important to clarify the clinical consequences of these results, but they also provide physiological insights into the role of specific dietary fatty acids as modulators of insulin resistance in humans.

Massless Higher Spins and Holography

Abstract: We treat free large N superconformal field theories as holographic duals of higher spin (HS) gauge theories expanded around AdS spacetime with radius R. The HS gauge theories contain massless and light massive AdS fields. The HS current correlators are written in a crossing symmetric form including only exchange of other HS currents. This and other arguments point to the existence of a consistent truncation to massless HS fields. A survey of massless HS theories with 32 supersymmetries in D=4,5,7 (where the 7D results are new) is given and the corresponding composite operators are discussed. In the case of AdS_4, the cubic couplings of a minimal bosonic massless HS gauge theory are described. We examine high energy/small tension limits giving rise to massless HS fields in the Type IIB string on AdS_5 x S^5 and M theory on AdS_{4/7} x S^{7/4}. We discuss breaking of HS symmetries to the symmetries of ordinary supergravity, and a particularly natural Higgs mechanism in AdS_5 x S^5 and AdS_4 x S^7 where the HS symmetry is broken by finite g_{YM}. In AdS_5 x S^5 it is shown that the supermultiplets of the leading Regge trajectory cross over into the massless HS spectrum. We propose that g_{YM}=0 corresponds to a critical string tension of order 1/R^2 and a finite string coupling of order 1/N. In AdS_7 x S^4 we give a rotating membrane solution coupling to the massless HS currents, and describe these as limits of Wilson surfaces in the A_{N-1}(2,0) SCFT, expandable in terms of operators with anomalous dimensions that are asymptotically small for large spin. The minimal energy configurations have semi-classical energy E=s for all s and the geometry of infinitely stretched strings with energy and spin density concentrated at the endpoints.