CiteULike: Author Kremer

Planar negative refractive index media using periodically L-C loaded transmission lines

GV Eleftheriades — 2008-08-11T17:20:42-00:00

Microwave Theory and Techniques, IEEE Transactions on, Vol. 50, No. 12. (2002), pp. 2702-2712.

Recent demonstrations of negative refraction utilize three-dimensional collections of discrete periodic scatterers to synthesize artificial dielectrics with simultaneously negative permittivity and permeability. In this paper, we propose an alternate perspective on the design and function of such materials that exploits the well-known L-C distributed network representation of homogeneous dielectrics. In the conventional low-pass topology, the quantities L and C represent a positive equivalent permeability and permittivity, respectively. However, in the dual configuration, in which the positions of L and C are simply interchanged, these equivalent material parameters assume simultaneously negative values. Two-dimensional periodic versions of these dual networks are used to demonstrate negative refraction and focusing; phenomena that are manifestations of the fact that such media support a propagating fundamental backward harmonic. We hereby present the characteristics of these artificial transmission-line media and propose a suitable means of implementing them in planar form. We then present circuit and full-wave field simulations illustrating negative refraction and focusing, and the first experimental verification of focusing using such an implementation.

A Bioinformatics Perspective on Proteomics: Data Storage, Analysis, and Integration

Andreas Kremer — 2005-10-17T12:26:17-00:00

Bioscience Reports, Vol. 25, No. 1-2. (February 2005), pp. 95-106.

Mycolic acid biosynthesis and enzymic characterization of the beta-ketoacyl-ACP synthase A-condensing enzyme from Mycobacterium tuberculosis.

L Kremer — 2008-08-09T05:42:29-00:00

The Biochemical journal, Vol. 364, No. Pt 2. (1 June 2002), pp. 423-430.

Mycolic acids consist of long-chain alpha-alkyl-beta-hydroxy fatty acids that are produced by successive rounds of elongation catalysed by a type II fatty acid synthase (FAS-II). A key feature in the elongation process is the condensation of a two-carbon unit from malonyl-acyl-carrier protein (ACP) to a growing acyl-ACP chain catalysed by a beta-ketoacyl-ACP synthase (Kas). In the present study, we provide evidence that kasA from Mycobacterium tuberculosis encodes an enzyme that elongates in vivo the meromycolate chain, in both Mycobacterium smegmatis and Mycobacterium chelonae. We demonstrate that KasA belongs to the FAS-II system, which utilizes primarily palmitoyl-ACP rather than short-chain acyl-ACP primers. Furthermore, in an in vitro condensing assay using purified recombinant KasA, palmitoyl-AcpM and malonyl-AcpM, KasA was found to express Kas activity. Also, mutated KasA proteins, with mutation of Cys(171), His(311), Lys(340) and His(345) to Ala abrogated the condensation activity of KasA in vitro completely. Finally, purified KasA was highly sensitive to cerulenin, a well-known inhibitor of Kas, which may lead to the development of novel anti-mycobacterial drugs targeting KasA.

Identification and substrate specificity of beta -ketoacyl (acyl carrier protein) synthase III (mtFabH) from Mycobacterium tuberculosis.

KH Choi — 2008-08-09T05:29:37-00:00

The Journal of biological chemistry, Vol. 275, No. 36. (8 September 2000), pp. 28201-28207.

The long-chain alpha-alkyl-beta-hydroxy fatty acids, termed mycolic acids, which are characteristic components of the mycobacterial cell wall are produced by successive rounds of elongation catalyzed by a multifunctional (type I) fatty acid synthase complex followed by a dissociated (type II) fatty acid synthase. In bacterial type II systems, the first initiation step in elongation is the condensation of acetyl-CoA with malonyl-acyl carrier protein (ACP) catalyzed by beta-ketoacyl-ACP III (FabH). An open reading frame in the Mycobacterium tuberculosis genome (Rv0533c), now termed mtfabH, was 37.3% identical to Escherichia coli ecFabH and contained the Cys-His-Asn catalytic triad signature. However, the purified recombinant mtFabH clearly preferred long-chain acyl-CoA substrates rather than acyl-ACP primers and did not utilize acetyl-CoA as a primer in comparison to ecFabH. In addition, purified mtFabH was sensitive to thiolactomycin and resistant to cerulenin in an in vitro assay. However, mtFabH overexpression in Mycobacterium bovis BCG did not confer thiolactomycin resistance, suggesting that mtFabH may not be the primary target of thiolactomycin inhibition in vivo and led to several changes in the lipid composition of the bacilli. The data presented is consistent with a role for mtFabH as the pivotal link between the type I and type II fatty acid elongation systems in M. tuberculosis. This study opens up new avenues for the development of selective and novel anti-mycobacterial agents targeted against mtFabH.

A Cre-inducible diphtheria toxin receptor mediates cell lineage ablation after toxin administration

Thorsten Buch — 2005-05-20T19:06:38-00:00

Nature Methods, Vol. 2, No. 6. (20 May 2005), pp. 419-426.

Unexpectedly robust assembly of the Axin destruction complex regulates Wnt/Wg signaling in Drosophila as revealed by analysis in vivo.

W Peterson-Nedry — 2008-07-31T18:52:15-00:00

Developmental biology, Vol. 320, No. 1. (1 August 2008), pp. 226-241.

Secreted proteins in the Wnt family regulate gene expression in target cells by causing the accumulation of the transcriptional activator beta-catenin. In the absence of Wnt, a protein complex assembled around the scaffold protein Axin targets beta-catenin for destruction, thereby preventing it from transducing inappropriate signals. Loss of Axin or its binding partners APC and GSK3 results in aberrant activation of the Wnt signaling response. We have analyzed the effects of mutant forms of Drosophila Axin with large internal deletions when expressed at physiological levels in vivo, either in the presence or absence of wild type Axin. Surprisingly, even deletions that completely remove the binding sites for fly APC, GSK3 or beta-catenin, though they fail to rescue to viability, these mutant forms of Axin cause only mild developmental defects, indicating largely retained Axin function. Furthermore, two lethal Axin deletion constructs, AxinDeltaRGS and AxinDeltabeta cat(DeltaArm), can complement each other and restore viability. Our findings support a model in which the Axin complex is assembled through cooperative tripartite interactions among the binding partners, making the assembly of functional complexes surprisingly robust.

Bridging the Gap Between Atomistic and Coarse-Grained Models of Polymers: Status and Perspectives

Jörg Baschnagel — 2008-07-24T14:02:58-00:00

Viscoelasticity, Atomistic Models, Statistical Chemistry (2000), pp. 41-156.

Recent developments that increase the time and distance scales accessible in the simulations of specific polymers are reviewed. Several different techniques are similar in that they replace a model expressed in fully atomistic detail with a coarse-grained model of the same polymer, atomistic → coarse-grained (and beyond!), thereby increasing the time and distance scales accessible within the expenditure of reasonable computational resources. The bridge represented by the right-pointing arrow can be constructed via different procedures, which are reviewed here. The review also considers the status of methods which reverse this arrow, atomistic ← coarse-grained. This “reverse-mapping” recovers a model expressed in fully atomistic detail from an arbitrarily chosen replica generated during the simulation of the coarse-grained system. Taken in conjunction with the efficiency of the simulation when the system is in its coarse-grained representation, the overall process permits a much more complete equilibration of the system (larger effective size of Δt) when that equilibration is performed with the coarse-grained replicas (II → III) than if it were attempted with the fully atomistic replicas (I → IV).

Anorexia nervosa, perfectionism, and dopamine D4 receptor (DRD4).

R Bachner-Melman — 2007-12-31T04:43:20-00:00

Am J Med Genet B Neuropsychiatr Genet, Vol. 144, No. 6. (5 September 2007), pp. 748-756.

The dopamine D4 receptor (DRD4), a well-characterized, polymorphic gene, is an attractive candidate for contributing risk to disordered eating and anorexia nervosa (AN). We tested association using UNPHASED for 5 DRD4 polymorphic loci, 3 promoter region SNPs (C-521T, C-616G, A-809G), the 120 bp promoter region tandem duplication and the exon III repeat, in 202 AN trios and 418 control families. Since perfectionism characterizes AN, we tested these five loci for association with the Child and Adolescent Perfectionism Scale (CAPS) in the AN and control groups. Single locus analysis showed significant association between the 'C' C-521T allele and AN. Haplotype analysis also showed significant association, particularly a 4-locus haplotype (exon III&120 bp repeat&C-521T&A-809G). Association was also observed between DRD4 and CAPS scores both for AN and control subjects. The insulin-like growth factor 2 (IGF2) and the arginine vasopressin 1a receptor (AVPR1a), previously shown to be associated with disordered eating, were also associated with CAPS scores. Three genes associated with AN were also associated with perfectionism. Personality traits are potential endophenotypes for understanding the etiology of eating disorders and one of the several pathways to eating pathology may be mediated by the impact of DNA sequences on perfectionism.

A trial of etanercept, a recombinant tumor necrosis factor receptor:Fc fusion protein, in patients with rheumatoid arthritis receiving methotrexate.

ME Weinblatt — 2008-07-19T13:15:41-00:00

The New England journal of medicine, Vol. 340, No. 4. (28 January 1999), pp. 253-259.

BACKGROUND: Patients treated with methotrexate for rheumatoid arthritis often improve but continue to have active disease. This study was undertaken to determine whether the addition of etanercept, a soluble tumor necrosis factor receptor (p75):Fc fusion protein (TNFR:Fc), to methotrexate therapy would provide additional benefit to patients who had persistent rheumatoid arthritis despite receiving methotrexate. METHODS: In a 24-week, double-blind trial, we randomly assigned 89 patients with persistently active rheumatoid arthritis despite at least 6 months of methotrexate therapy at a stable dose of 15 to 25 mg per week (or as low as 10 mg per week for patients unable to tolerate higher doses) to receive either etanercept (25 mg) or placebo subcutaneously twice weekly while continuing to receive methotrexate. The primary measure of clinical response was the American College of Rheumatology criteria for a 20 percent improvement in measures of disease activity (ACR 20) at 24 weeks. RESULTS: The addition of etanercept to methotrexate therapy resulted in rapid and sustained improvement. At 24 weeks, 71 percent of the patients receiving etanercept plus methotrexate and 27 percent of those receiving placebo plus methotrexate met the ACR 20 criteria (P<0.001); 39 percent of the patients receiving etanercept plus methotrexate and 3 percent of those receiving placebo plus methotrexate met the ACR 50 criteria (for a 50 percent improvement) (P<0.001). Patients receiving etanercept plus methotrexate had significantly better outcomes according to all measures of disease activity. The only adverse events associated with etanercept were mild injection-site reactions, and no patient withdrew from the study because of adverse events associated with etanercept. CONCLUSIONS: In patients with persistently active rheumatoid arthritis, the combination of etanercept and methotrexate was safe and well tolerated and provided significantly greater clinical benefit than methotrexate alone.

Reducing unhealthy weight gain in children through community capacity-building: results of a quasi-experimental intervention program, Be Active Eat Well

AM Sanigorski — 2008-06-10T15:48:57-00:00

International Journal of Obesity, Vol. aop, No. current.

Relaxation of randomly cross-linked polymer melts

Edgardo Duering — 2008-07-12T02:28:47-00:00

Physical Review Letters, Vol. 67, No. 25. (16 December 1991), 3531.

Incentives in Markets, Firms, and Governments

Daron Acemoglu — 2008-07-07T15:15:41-00:00

J Law Econ Organ (6 December 2007), ewm055.

We construct a simple career concerns model where high-powered incentives can distort the composition of effort by inducing excessive signaling. We show that in the presence of this type of career concerns, markets typically fail to limit competitive pressures and cannot commit to the desirable low-powered incentives. Firms may be able to weaken incentives and improve efficiency by obscuring information about individual workers' contribution to output, and thus reducing their willingness to signal through a moral-hazard-in-teams reasoning. However, firms themselves have a commitment problem, since firm owners would like to provide high-powered incentives to their employees to increase profits. When firms cannot refrain from doing so, government provision may be useful as a credible commitment to low-powered incentives. Governments may be able to achieve this even when operated by a self-interested politician. Among other reasons, this may happen because of the government's ability to limit yardstick competition and reelection uncertainty. We discuss possible applications of our theory to pervasive government involvement in predominantly private goods such as education and management of pension funds. 10.1093/jleo/ewm055

Dynamics of entangled linear polymer melts: A molecular-dynamics simulation

Kurt Kremer — 2006-08-18T11:48:45-00:00

The Journal of Chemical Physics, Vol. 92, No. 8. (1990), pp. 5057-5086.

We present an extensive molecular-dynamics simulation for a bead spring model of a melt of linear polymers. The number of monomers N covers the range from N=5 to N=400. Since the entanglement length Ne is found to be approximately 35, our chains cover the crossover from the nonentangled to the entangled regime. The Rouse model provides an excellent description for short chains N<Ne, while the dynamics of the long chains can be described by the reptation model. By mapping the model chains onto chemical species we give estimates of the times and distances of onset of the slowing down in motion due to reptation. Comparison to neutron spin-echo data confirm our mapping procedure, resolving a discrepancy between various experiments. By considering the primitive chain we are able to directly visualize the confinement to a tube. Analyzing the Rouse mode relaxation allows us to exclude the generalized Rouse models, while the original reptation prediction gives a good description of the data. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.

Forces between single pairs of charged colloids in aqueous salt solutions

C Gutsche — 2007-10-02T11:29:36-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 3. (2007)

Forces between single pairs of negatively charged micrometer-sized colloids in aqueous solutions of monovalent, divalent, or trivalent counter-ions at varying concentrations have been measured by employing optical tweezers. The experimental data have been analyzed by using the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and a numerical solution of the Poisson-Boltzmann (PB) equation. With monovalent counterions, the data are well described by the DLVO and PB theories, suggesting that the DLVO theory is adequate to describe the colloidal forces at these conditions. At higher counter-ion valence, the approximations within the two theories become evident.

A generalized concept of power helped to choose optimal endpoints in clinical trials.

GF Borm — 2008-06-09T04:59:22-00:00

Journal of clinical epidemiology, Vol. 60, No. 4. (April 2007), pp. 375-381.

OBJECTIVES: A clinical trial may have multiple objectives. Sometimes the results for several parameters may need to be significant or meet certain other criteria. In such cases, it is important to evaluate the probability that all these objectives will be met, rather than the probability that each will be met. The purpose of this article is to introduce a definition of power that is tailored to handle this situation and that is helpful for the design of such trials. STUDY DESIGN AND SETTING: We introduce a generalized concept of power. It can handle complex situations, for example, in which there is a logical combination of partial objectives. These may be formulated not only in terms of statistical tests and of confidence intervals, but also in nonstatistical terms, such as "selecting the optimal by dose." RESULTS: The power of a trial was calculated for various objectives and combinations of objectives. CONCLUSION: The generalized concept of power may lead to power calculations that closely match the objectives of the trial and contribute to choosing more efficient endpoints and designs.

Simulation approaches to soft matter: Generic statistical properties vs. chemical details

Matej Praprotnik — 2008-06-07T14:37:43-00:00

Computer Physics Communications, Vol. 179, No. 1-3. (July 2008), pp. 51-60.

The relation between atomistic structure, architecture, molecular weight and material properties is a basic concern of modern soft material science. This by now goes far beyond standard properties of bulk materials. A typical additional focus is on surface or interface aspects or on the relation between structure and function in nanoscopic molecular assemblies. This all implies a thorough understanding on many length and correspondingly time scales ranging from (sub-)atomic to macroscopic. At this point computer simulations are playing an increasingly important, if not the central role. Traditionally simulations have been separated in two main groups, namely simplified models to deal with generic or universal aspects of polymers, i.e. critical exponents, and those employing classical force field simulations with (almost) all atomistic detail, i.e. for the diffusion of small additives in a small "sample". Still characteristic problems, which require huge systems and/or long times in combination with a chemistry specific model, cannot be tackled by these methods alone. More recently with the development of scale bridging or multiscale simulation techniques, these different approaches have been combined into an emerging rather powerful tool. It is the purpose of this contribution to give a few examples of how such an approach can be used to understand specific material properties.

Entanglement effects in model polymer networks

R Everaers — 2008-06-05T12:41:26-00:00

Anomalous Diffusion From Basics to Applications (1999), pp. 221-234.

The influence of topological constraints on the local dynamics in cross-linked polymer melts and their contribution to the elastic properties of rubber elastic systems are a long standing problem in statistical mechanics. Polymer networks with diamond lattice connectivity (Everaers and Kremer 1995, Everaers and Kremer 1996a) are idealized model systems which isolate the effect of topology conservation from other sources of quenched disorder. We study their behavior in molecular dynamics simulations under elongational strain. In our analysis we compare the measured, purely entropic shear moduli G to the predictions of statistical mechanical models of rubber elasticity, making extensive use of the microscopic structural and topological information available in computer simulations. We find (Everaers and Kremer 1995) that the classical models of rubber elasticity underestimate the true change in entropy in a deformed network significantly, because they neglect the tension along the contour of the strands which cannot relax due to entanglements (Everaers and Kremer (in preparation)). This contribution and the fluctuations in strained systems seem to be well described by the constrained mode model (Everaers 1998) which allows to treat the crossover from classical rubber elasticity to the tube model for polymer networks with increasing strand length within one transparant formalism. While this is important for the description of the effects we try to do a first quantitative step towards their explanation by topological considerations. We show (Everaers and Kremer 1996a) that for the comparatively short strand lengths of our diamond networks the topology contribution to the shear modulus is proportional to the density of entangled mesh pairs with non-zero Gauss linking number. Moreover, the prefactor can be estimated consistently within a rather simple model developed by Vologodskii et al. and by Graessley and Pearson, which is based on the definition of an entropic interaction between the centers of mass of two loops in a conserved topological state. Polymer networks are the basic structural element of systems as different as tire rubber and gels. They are not only technically important but also commonly found in biological systems such as the cytoskeleton. Networks of flexible macromolecules display an elastic and thermoelastic behaviour quite different from ordinary solids. (Treloar 1975) Crystals, metals, ceramics, or glasses can be stretched only minimally. Small deformations of the sample extend down to atomic scales and lead to an increase of the internal energy. Rubber-like materials reversibly sustain elongations of up to 1000% with small strain elastic moduli that are four or five orders of magnitude smaller than for other solids. Most importantly, the tension induced by a deformation is almost exclusively due to a decrease in entropy. As a consequence, the underlying mechanism has to be different from the case of conventional solids.

Computer Visualization of Three-Dimensional Image Data Using IMOD

James Kremer — 2008-06-02T22:48:16-00:00

Journal of Structural Biology, Vol. 116, No. 1. (January 1996), pp. 71-76.

We have developed a computer software package, IMOD, as a tool for analyzing and viewing three-dimensional biological image data. IMOD is useful for studying and modeling data from tomographic, serial section, and optical section reconstructions. The software allows image data to be visualized by several different methods. Models of the image data can be visualized by volume or contour surface rendering and can yield quantitative information.

New directions in fuzzy automata

Mansoor Doostfatemeh — 2008-04-01T07:06:34-00:00

International Journal of Approximate Reasoning, Vol. 38, No. 2. (February 2005), pp. 175-214.

Automata are the prime example of general computational systems over discrete spaces. The incorporation of fuzzy logic into automata theory resulted in fuzzy auotomata which can handle continuous spaces. Moreover, they are able to model uncertainty which is inherent in many applications. Deterministic Finite-state Automata (DFA) have been the architecture, most used in many applications, but, the increasing interest in using fuzzy logic for many new areas necessitates that the formalism of fuzzy automata be more developed and better established to fulfill implementational requirements in a well-defined manner. This need is due to the fact that despite the long history of fuzzy automata and lots of research being done on that, there are still some issues which have not been well-established and issues which need some kind of revision. In particular, we focus on membership assignment, output mapping, multi-membership resolution, and the concept of acceptance for fuzzy automata. We develop a new general definition for fuzzy automata, and based on that, develop well-defined and application-driven methodologies to establish a better ground for fuzzy automata and pave the way for forthcoming applications.

Microscopic verification of dynamic scaling in dilute polymer solutions: A molecular-dynamics simulation

Burkhard Dã¼nweg — 2006-10-08T12:50:22-00:00

Physical Review Letters, Vol. 66, No. 23. (10 June 1991), 2996.

The dynamics of a single polymer chain immersed in a large number of solvent particles is studied by molecular dynamics. This is the first simulation where chain length (30; 40; and 60 monomers) and statistical accuracy are sufficient to test the predictions of the Zimm model as a result of the particle-particle interactions: The short-time diffusion constant is in good agreement with the Kirkwood prediction; and the monomer motions exhibit the expected dynamic scaling. The long-range hydrodynamic interaction requires a data analysis that explicitly includes the periodic images via Ewald sums.

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

Matej Praprotnik — 2008-05-21T12:41:38-00:00

Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 545-571.

The relation between atomistic chemical structure, molecular architecture, molecular weight, and material properties is of basic concern in modern soft material science and includes standard properties of bulk materials and surface and interface aspects, as well as the relation between structure and function in nanoscopic objects and molecular assemblies of both synthetic and biological origin. This all implies a thorough understanding on many length and correspondingly time scales, ranging from (sub)atomistic to macroscopic. Presently, computer simulations play an increasingly important, if not central, role. Some problems do not require specific atomistic details, whereas others require them only locally. However, in many cases this strict separation is not sufficient for a comprehensive understanding of systems, and flexible simulation schemes are required that link the different levels of resolution. We here give a general view of the problem regarding soft matter and discuss some specific examples of linked simulation techniques at different resolution levels. We then discuss a recently developed flexible simulation scheme, the AdResS method, which allows one to adaptively change the resolution in certain regions of space on demand.

Concurrent triple-scale simulation of molecular liquids

Rafael Buscalioni — 2008-05-20T10:34:56-00:00

The Journal of Chemical Physics, Vol. 128, No. 11. (2008)

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Worms: Identifying Impacts on Education and Health in the Presence of Treatment Externalities

Edward Miguel — 2008-01-15T02:38:02-00:00

Econometrica, Vol. 72, No. 1. (2004), pp. 159-217.

Intestinal helminths-including hookworm, roundworm, whipworm, and schistosomiasis--infect more than one-quarter of the world's population. Studies in which medical treatment is randomized at the individual level potentially doubly underestimate the benefits of treatment, missing externality benefits to the comparison group from reduced disease transmission, and therefore also underestimating benefits for the treatment group. We evaluate a Kenyan project in which school-based mass treatment with deworming drugs was randomly phased into schools, rather than to individuals, allowing estimation of overall program effects. The program reduced school absenteeism in treatment schools by one-quarter, and was far cheaper than alternative ways of boosting school participation. Deworming substantially improved health and school participation among untreated children in both treatment schools and neighboring schools, and these externalities are large enough to justify fully subsidizing treatment. Yet we do not find evidence that deworming improved academic test scores.

Income-Distribution Dynamics with Endogenous Fertility

Michael Kremer — 2008-05-08T10:10:41-00:00

The American Economic Review, Vol. 89, No. 2. (1999), pp. 155-160.

Income Distribution Dynamics with Endogenous Fertility

Michael Kremer — 2008-05-08T10:06:27-00:00

Journal of Economic Growth, Vol. 7, No. 3. (2002), pp. 227-258.

Developing countries with highly unequal income distributions, such as Brazil or South Africa, face an uphill battle in reducing inequality. Educated workers in these countries have a much lower birthrate than uneducated workers. Assuming children of educated workers are more likely to become educated, this fertility differential increases the proportion of unskilled workers, reducing their wages, and thus their opportunity cost of having children, creating a vicious cycle. A model incorporating this effect generates multiple steady-state levels of inequality, suggesting that in some circumstances, temporarily increasing access to educational opportunities could permanently reduce inequality. Empirical evidence suggests that the fertility differential between the educated and uneducated is greater in less equal countries, consistent with the model.

Polyelectrolyte-Compression Forces between Spherical DNA Brushes

Kati Kegler — 2008-05-07T21:14:58-00:00

Physical Review Letters, Vol. 100, No. 11. (2008)

Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids, dependent on the molecular weight of the DNA chains, and the concentration and valence of the surrounding ionic medium. The resulting forces are short range and set in as the surface-to-surface distance between the colloidal cores reaches the value of the brush height. The measured force-distance relation is analyzed by means of a theoretical treatment that quantitatively describes the effects of compression of the chains on the surface of the opposite-lying colloid. Quantitative agreement with the experiment is obtained for all parameter combinations.

Transient photoconductivity measurements in semi-insulating GaAs. II. A digital approach

JC Abele — 2008-04-24T07:35:38-00:00

Journal of Applied Physics, Vol. 62, No. 6. (1987), pp. 2432-2438.

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THE SAFETY DANCE: CONFRONTING HARASSMENT, INTIMIDATION, AND VIOLENCE IN THE FIELD

Sharp — 2006-11-22T19:43:41-00:00

Sociological Methodology, Vol. 36, No. 1. (December 2006), pp. 317-327.

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota.

B Stecher — 2008-04-15T08:15:18-00:00

PLoS biology, Vol. 5, No. 10. (October 2007), pp. 2177-2189.

Most mucosal surfaces of the mammalian body are colonized by microbial communities ("microbiota"). A high density of commensal microbiota inhabits the intestine and shields from infection ("colonization resistance"). The virulence strategies allowing enteropathogenic bacteria to successfully compete with the microbiota and overcome colonization resistance are poorly understood. Here, we investigated manipulation of the intestinal microbiota by the enteropathogenic bacterium Salmonella enterica subspecies 1 serovar Typhimurium (S. Tm) in a mouse colitis model: we found that inflammatory host responses induced by S. Tm changed microbiota composition and suppressed its growth. In contrast to wild-type S. Tm, an avirulent invGsseD mutant failing to trigger colitis was outcompeted by the microbiota. This competitive defect was reverted if inflammation was provided concomitantly by mixed infection with wild-type S. Tm or in mice (IL10(-/-), VILLIN-HA(CL4-CD8)) with inflammatory bowel disease. Thus, inflammation is necessary and sufficient for overcoming colonization resistance. This reveals a new concept in infectious disease: in contrast to current thinking, inflammation is not always detrimental for the pathogen. Triggering the host's immune defence can shift the balance between the protective microbiota and the pathogen in favour of the pathogen.

Mitochondrial DNA HV lineage increases the susceptibility to schizophrenia among Israeli Arabs.

S Amar — 2008-04-12T03:57:53-00:00

Schizophrenia research, Vol. 94, No. 1-3. (August 2007), pp. 354-358.

Haplotypes and haplogroups are linked sets of common DNA variants, acting as susceptibility or protective factors to complex disorders. Growing evidence suggests that dysfunction of mitochondrial bioenergetics contributes to the schizophrenia phenotype. We studied mitochondrial DNA haplogroups in schizophrenia patients. Since mitochondria are inherited from the mothers, we used healthy fathers as an ideal case-control group. Analysis of the distribution of mitochondrial haplogroups in schizophrenia patients compared to their healthy fathers (202 pairs) resulted in an over-representation of the mtDNA lineage cluster, HV, in the patients (p=0.01), with increased relative risk (odds ratio) of 1.8. Since mitochondrial DNA is small relative to nuclear DNA, a total mitochondrial genome analysis was possible in a hypothesis-free manner. However, mitochondrial DNA haplogroups are highly variable in human population and it will be necessary to replicate our results in other human ethnic groups.

Distribution and abundance of the ctenophore, Mnemiopsis leidyi in Narragansett Bay

Patricia Kremer — 2008-04-09T21:47:29-00:00

Estuarine and Coastal Marine Science, Vol. 4, No. 6. (November 1976), pp. 627-639.

Population abundance, distribution and size composition of the ctenophore, Mnemiopsis leidyi were measured at 19 stations over three years in Narragansett Bay, Rhode Island. Continuous estimates of the relative abundance and distribution of the animals were also obtained by towing a specially designed submarine luminescence meter during five nights in the late summer and fall. While Mnemiopsis were present in the bay throughout the year, the overwintering population was extremely low (1-2 animals/104 m3). During summer, the population underwent a dramatic increase of about five orders of magnitude and reached peak densities of over 50 animals/m3. An equally sharp decline took place in the early fall. When present in the bay in large numbers, the population appeared to be relatively evenly distributed on scales of about 500 m, though clear patches of lesser dimension were also evident. The field evidence indicated that the population increases first in the upper bay and then spreads toward the mouth by mid-summer.

Predation on the ctenophore, Mnemiopsis leidyi , by butterfish, Peprilus triacanthus , in Narragansett Bay, Rhode Island

Candace Oviatt — 2008-04-09T21:43:55-00:00

Estuaries and Coasts, Vol. 18, No. 2. (22 June 1995), pp. 236-240.

Abstract Consumption rates ofMnemiopsis leidyi by butterfish,Peprilus triacanthus, ranged between 4 ml/gm dry wt/hr to 184 ml/gm dry wt/hr, depending on fish size and feeding history. These rates of comsumption supply adequate food to support the metabolism of the fish and probably account for the late summer-early fall decline in population levels ofMnemiopsis observed in Narragansett Bay.

Dynamic Stochastic General Equilibrium Models as a Tool for Policy Analysis

Jana Kremer — 2008-04-08T11:21:59-00:00

CESifo Economic Studies, Vol. 52, No. 4. (1 December 2006), pp. 640-665.

This article discusses the evolution of dynamic macroeconomic models from calibrated Real Business Cycle models to estimated dynamic stochastic general equilibrium models. The purpose is to suggest the usefulness of these models as a tool for policy analysis, with a particular emphasis on aspects of monetary policy. (JEL classification: D58, E50) 10.1093/cesifo/ifl014

Is there a correlation between chloroplastic and nuclear divergence, or what are the roles of history and selection on genetic diversity in European oaks?

Antoine Kremer — 2008-03-29T18:41:41-00:00

Forest Ecology and Management, Vol. 156, No. 1-3. (1 February 2002), pp. 75-87.

The aim of this work was to investigate whether a correlation exists between maternal lineage, assessed by variation in maternally inherited chloroplast DNA (cpDNA) and nuclear controlled variation (phenotypic traits and gene markers). Variation in cpDNA and nuclear controlled traits (62 phenotypic traits, eight isozyme and 31 RAPD loci) was studied in deciduous oak trees (mostly Q. petraea) growing in 16 provenance tests. Results from two nuclear diversity studies were also included. The test for correlation was performed using two methods by: (1) comparing provenance mean values (or allele frequencies) among different lineages using ANOVA, (2) making pairwise comparisons of chloroplastic genetic distances (CGDs) with phenotypic differentiation index (DI) (or nuclear genetic distances (GD)) among all provenances using the Mantel test. Among the 62 phenotypic traits, only seven exhibited significant associations with maternal lineages when tested using ANOVA (six using Mantel test). This number decreased to two once correction for geographic distance was introduced in the calculation for Mantel test. There were stronger correlations between maternal lineage and nuclear gene markers. The existence of cytonuclear disequilibrium was shown by the significant differences in allozyme frequencies between the four maternal lineages (at least one allele for each locus). These associations were confirmed by significant correlations between CGD and GD. Finally associations were also found between levels of diversity in nuclear markers and maternal lineages. These results are discussed in the context of the glacial and postglacial history of oak populations in Europe. The analysis suggests that the processes which led to the current structure of chloroplastic diversity and variation for phenotypic traits can be subdivided into four major phases. (1) During the last long glacial period, deciduous oaks were probably confined to three major refugia which were genetically differentiated for chloroplastic and nuclear genes. (2) At the end of the glacial period, oaks migrated northwards and established a spatial pattern of distribution for chloroplastic genes which remains largely intact to this day. (3) As oaks progressively occupied the mid and northern parts of Europe, pollen flow established communication between stands originating from eastern and western refugia. This resulted in the gradual erosion of the original nuclear differentiation while conserving the chloroplastic variation installed during colonization. (4) Local selection pressures acting on the established populations eventually caused their genetic differentiation gradually to increase with time. New patterns of differentiation now exist which are totally different from those in place immediately following colonization. During this time, chloroplastic divergence remained unchanged. These processes led to the loss of any association between chloroplastic divergence and phenotypic traits, although some association with gene markers which are less affected by selection has been retained.

Relationship between inbreeding depression and inbreeding coefficient in maritime pine (Pinus pinaster)

CE Durel — 2008-03-28T03:33:24-00:00

Theoretical and Applied Genetics, Vol. 92, No. 3. (1 March 1996), pp. 347-356.

The relationship between inbreeding depression and inbreeding coefficient (F) for several important traits was investigated in an 11-year trial of maritime pine (Pinus pinaster). Five levels of inbreeding (F=0; 0.125; 0.25; 0.5; 0.75) were obtained in a mating design involving ten plus-trees, or their progenies, as parents (total of 51 families). For F=0.75, the mean inbreeding depressions were 27% for height, 37% for circumference at breast height (63% for bole volume), 23% for basal straightness (better straightness of the inbred trees), and 89% for female fertility (number of cones). Large differences were observed among inbred families for the same level of inbreeding. The evolution of depression with F was more or less linear, depending on the traits. Significant differences among F-levels appeared very early for height (from 5-years of age). Inbreeding depression was much more expressed during unfavorable years than during favorable years for yearly height growth. When compared with other Pinus species, maritime pine appears to be less affected by inbreeding, especially for the percentage of filled seeds and general vigor. A reduced genetic load in maritime pine may result from the evolutionary history of the species and its scattered distribution.

[Keeping up to date with the relevant literature: 'really simple syndication'-(RSS)-feeds within PubMed]

E Leclercq — 2008-03-07T15:01:11-00:00

Ned Tijdschr Geneeskd, Vol. 152, No. 4. (26 January 2008), pp. 221-224.

For clinicians, researchers and policy makers in healthcare, it is important to keep up to date with the newest medical-scientific information. The large amount of new information makes this a difficult task. There are various techniques for keeping up to date, for instance reading systematic reviews, searching the literature at regular intervals oneself, and using the e-mail alerting services of, for example, PubMed. A new possibility is to be alerted to new scientific publications, for example, via a 'really simple syndication' (RSS)-feed. This option is now also made available by PubMed. In addition to PubMed, many other websites can now be searched systematically for new information by a RSS reader. With RSS feeds the user can be alerted to new information much faster than by an e-mail alerting service, so that one can anticipate new developments more rapidly.

Forces of Interaction between DNA-Grafted Colloids: An Optical Tweezer Measurement

K Kegler — 2008-03-19T16:59:43-00:00

Physical Review Letters, Vol. 98, No. 5. (2007)

Optical tweezers are employed to measure the forces of interaction between single DNA-grafted colloids. Parameters to be varied are the length of the DNA, the grafting density, and the ion concentration of the surrounding medium. From the measured force-separation dependence an interaction length at a given force is deduced. It shows in the mushroom regime a scaling with the grafting density which levels off for brushes. For the latter the transition from an osmotic to a salted brush can be traced in detail by varying the ion concentration in accordance with mean field theories.

Tunable generic model for fluid bilayer membranes

Ira Cooke — 2008-03-18T17:53:29-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 72, No. 1. (2005)

We present a model for the efficient simulation of generic bilayer membranes. Individual lipids are represented by one head bead and two tail beads. By means of simple pair potentials these robustly self-assemble to a fluid bilayer state over a wide range of parameters, without the need for an explicit solvent. The model shows the expected elastic behavior on large length scales, and its physical properties (e.g., fluidity or bending stiffness) can be widely tuned via a single parameter. In particular, bending rigidities in the experimentally relevant range are obtained, at least within 3–30kBT. The model is naturally suited to study many physical topics, including self-assembly, fusion, bilayer melting, lipid mixtures, rafts, and protein-bilayer interactions.

Aggregation and vesiculation of membrane proteins by curvature-mediated interactions

Benedict Reynwar — 2007-05-24T01:27:29-00:00

Nature, Vol. 447, No. 7143., pp. 461-464.

The O-Ring Theory of Economic Development

Michael Kremer — 2007-02-23T02:20:20-00:00

The Quarterly Journal of Economics, Vol. 108, No. 3. (1993), pp. 551-575.

This paper proposes a production function describing processes subject to mistakes in any of several tasks. It shows that high-skill workers--those who make few mistakes--will be matched together in equilibrium, and that wages and output will rise steeply in skill. The model is consistent with large income differences between countries, the predominance of small firms in poor countries, and the positive correlation between the wages of workers in different occupations within enterprises. Imperfect observability of skill leads to imperfect matching and thus to spillovers, strategic complementarity, and multiple equilibria in education.

Using Randomization in Development Economics Research: A Toolkit

Esther Duflo — 2008-03-12T00:16:18-00:00

National Bureau of Economic Research (December 2006), 333.

Author contact info: Esther Duflo Department of Economics MIT, E52-252G 50 Memorial Drive Cambridge, MA 02142 Tel: 617/258-7013 Fax: 617/253-6915 E-Mail: eduflo@mit.edu Rachel Glennerster Abdul Latif Jameel Poverty Action Lab MIT Department of Economics E60-275 Cambridge MA 02139 Tel: 617 324 0098 E-Mail: rglenner@mit.edu Michael Kremer Harvard University Department of Economics Littauer Center M20 Cambridge, MA 02138 Tel: 617/495-9145 Fax: 617/495-7730 E-Mail: mkremer@fas.harvard.edu This paper is a practical guide (a toolkit) for researchers, students and practitioners wishing to introduce randomization as part of a research design in the field. It first covers the rationale for the use of randomization, as a solution to selection bias and a partial solution to publication biases. Second, it discusses various ways in which randomization can be practically introduced in a field settings. Third, it discusses designs issues such as sample size requirements, stratification, level of randomization and data collection methods. Fourth, it discusses how to analyze data from randomized evaluations when there are departures from the basic framework. It reviews in particular how to handle imperfect compliance and externalities. Finally, it discusses some of the issues involved in drawing general conclusions from randomized evaluations, including the necessary use of theory as a guide when designing evaluations and interpreting results.

Dynamics of polymer solutions and melts. Reptation predictions and scaling of relaxation times

Wolfgang Paul — 2006-08-18T15:51:49-00:00

The Journal of Chemical Physics, Vol. 95, No. 10. (1991), pp. 7726-7740.

The bond fluctuation model on the simple cubic lattice is studied by Monte Carlo simulations on a multitransputer array, for polymer volume fractions in the range 0.0250.500 and chain lengths N in the range 20N200. Extensive data are presented on the dynamics of monomer displacements, center-of-gravity displacements, and relaxation times. This study is complementary to previous work, in which the crossover scaling properties of the chain linear dimensions, structure factor, and self-diffusion constant were tested for the same athermal model. The simulation technique takes both excluded volume interactions and entanglement constraints into account, but ignores hydrodynamic forces. Our results describe the crossover from Rouse behavior of swollen chains (~N1 + 2, being the exponent describing the radius R of the chains, R~N ) to reptation, ~N3. Since the excluded volume screening length is found to be smaller than the tube diameter by a factor of about 3, the rescaled times W/N1 + 2 decrease first as a function of the scaled chain length ~N1/(3–1), before they increase due to the onset of reptation. Additional evidence for reptative behavior is found by identifying the several successive crossovers in the time-dependent displacements predicted by de Gennes. The Journal of Chemical Physics is copyrighted by The American Institute of Physics.

famoz: a software for parentage analysis using dominant, codominant and uniparentally inherited markers

S Gerber — 2008-03-04T17:09:31-00:00

Molecular Ecology Notes, Vol. 3, No. 3. (2003), pp. 479-481.

Abstract famoz (an acronym for father/mother) is a software useful in reconstructing parentage for dominant, codominant and uniparentally inherited markers. It is written in C and TclTk languages and is available for Unix, Linux and Windows systems at http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html . Parameters and assumptions used in the calculations are few and simple. Exclusion and identity probabilities, log-likelihoods of any genetic relationship, potential father and parent or parent pair, half- and full-sibship are calculated based on real or simulated data. Error rates for genotypic mistyping can be introduced. Simulations can be done to build statistical tests for parentage assignment.

Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis

S Gerber — 2008-03-04T17:08:20-00:00

Molecular Ecology, Vol. 9, No. 8. (2000), pp. 1037-1048.

Abstract This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1-0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.

Programming ad-hoc networks of mobile and resource-constrained devices

Yang Ni — 2005-11-27T23:49:56-00:00

Vol. 40, No. 6. (June 2005), pp. 249-260.

Clinical characteristics of a Dutch DFNA9 family with a novel COCH mutation, G87W.

RJ Pauw — 2008-02-22T12:24:27-00:00

Audiol Neurootol, Vol. 12, No. 2. (2007), pp. 77-84.

The present study aims to report audiological and vestibular characteristics of a Dutch DFNA9 family with a novel mutation, G87W, in the LCCL domain of COCH. From the family with the novel G87W COCH mutation audiometric data were collected and analyzed longitudinally. Results were compared with those obtained in previously identified P51S COCH mutation carriers (n = 74) and with those obtained in G88E mutation carriers. Special attention was also given to a comparison of age-related features, such as progressive hearing loss and vestibular impairment. A novel mutation (G87W) in COCH is indicative of hearing impairment and vestibular dysfunction in the present family. Pure-tone thresholds, phoneme recognition scores, and vestibular responses of the G87W mutation carriers were essentially similar to those previously established in the P51S and G88E mutation carriers. Deterioration of hearing and vestibular function in the G87W mutation carriers started at the age of 43 years. Remarkably, similar to G88E mutation carriers, the proportion of patients over 40 years of age who developed complete vestibular areflexia was significantly lower for the G87W mutation carriers than for the P51S mutation carriers. In conclusion, the phenotype associated with the novel COCH (G87W) mutation is largely similar to that associated with the P51S and G88E mutation carriers. However, subtle differences in terms of onset age and rate of progression seem to exist.

Quantitative trait dissection analysis in Eucalyptus using RAPD markers: 1. Detection of QTL in interspecific hybrid progeny, stability of QTL expression across different ages

D Verhaegen — 2008-02-19T10:39:33-00:00

TAG Theoretical and Applied Genetics, Vol. 95, No. 4. (1997), pp. 597-608.

Abstract The objective of this study was to use random amplified polymorphic DNA (RAPD) to determine the genetic location and effects of genomic regions controlling wood density, stem growth and stem form in two species of Eucalyptus. Two hundred F1 trees generated from an interspecific cross E. urophylla�E. grandis between two elite trees were used. Genetic maps were constructed for each parent with markers segregating in the 1:1 ratio in FS progeny. A total of 86 and 92 markers distributed among 11 linkage groups covered 1295 cM and 1312 cM for the E. urophylla and E. grandis parent, respectively. Traits were measured three times up to selection age (38 months). The magnitude of the phenotypic variation explained by the joint action of the segregating quantitative trait alleles indicated that genetic factors of large effect were involved in the control of the studied characters. Several regions controlling part of the variation for the studied traits were identified by interval mapping. Some regions of the genome exerted effects on more than one trait, providing a genetic explanation for at least some of the correlation between the traits. On the basis of an age-by-age analysis, a partial stability of QTL expression was observed with 68% of the QTL being expressed at two ages and 32% being age-specific. No QTL were significant for all three ages. Taking advantage of repeated measurements on the same material across different ages, we investigated with a maximum statistical power, the effect of marker genotype on traits, with age and QTL�age interaction effects being removed. A two-way analysis of variance made it possible to detect significant marker-trait associations over the period studied. Most of them had already been detected in the annual analysis. This result is very encouraging for the application of marker information to the early selection of hybrid trees to be vegetatively propagated for the production of clonal varieties.

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

Silvina Matysiak — 2008-02-18T12:34:22-00:00

The Journal of Chemical Physics, Vol. 128, No. 2. (2008)

Many Children Left Behind? Textbooks and Test Scores in Kenya

Paul Glewwe — 2008-02-13T09:09:45-00:00

National Bureau of Economic Research Working Paper Series (August 2007), 13300.

Author contact info: Paul W. Glewwe Dept of Applied Economics, U of MN 1994 Buford Ave. St. Paul MN 55108 E-Mail: pglewwe@umn.edu Michael Kremer Harvard University Department of Economics Littauer Center M20 Cambridge, MA 02138 Tel: 617/495-9145 Fax: 617/495-7730 E-Mail: mkremer@fas.harvard.edu Sylvie Moulin World Bank 1818 H Street, N.W. Washington, DC 20433 A randomized evaluation suggests that a program which provided official textbooks to randomly selected rural Kenyan primary schools did not increase test scores for the average student. In contrast, the previous literature suggests that textbook provision has a large impact on test scores. Disaggregating the results by students? initial academic achievement suggests a potential explanation for the lack of an overall impact. Textbooks increased scores for students with high initial academic achievement and increased the probability that the students who had made it to the selective final year of primary school would go on to secondary school. However, students with weaker academic backgrounds did not benefit from the textbooks. Many pupils could not read the textbooks, which are written in English, most students? third language. The results are consistent with the hypothesis that the Kenyan education system and curricular materials are oriented to the academically strongest students rather than to typical students. More generally, many students may be left behind in societies that combine 1) a centralized, unified education system; 2) the heterogeneity in student preparation associated with rapid expansion of education; and 3) disproportionate elite power.

A simple and inexpensive screening test for low protein levels in urine.

D Kutter — 2008-02-13T07:43:49-00:00

Clin Chim Acta, Vol. 258, No. 2. (17 February 1997), pp. 231-239.

Nigrosin binds to proteins yielding a dark blue complex. This reaction is used for detecting low protein concentrations in urine by applying spots of urine to cellulose acetate strips which are coloured by nigrosin. The intensity of coloured spots remaining after washing of the strips indicates protein concentration. With a cut-off at 50 mg protein/l, the test offers an excellent possibility for first line screening for microalbuminuria at lowest cost.