Crystallization and preliminary X-ray analysis of monalysin, a novel β-pore-forming toxin from the entomopathogen Pseudomonas entomophila.

Monalysin was recently described as a novel pore-forming toxin (PFT) secreted by the Drosophila pathogen Pseudomonas entomophila. Recombinant monalysin is multimeric in solution, whereas PFTs are supposed to be monomeric until target membrane association. Monalysin crystals were obtained by the hanging-drop vapour-diffusion method using PEG 8000 as precipitant. Preliminary X-ray diffraction analysis revealed that monalysin crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 162.4, b = 146.2, c = 144.4 Å, β = 122.8°, and diffracted to 2.85 Å resolution using synchrotron radiation. Patterson self-rotation analysis and Matthews coefficient calculation indicate that the asymmetric unit contains nine copies of monalysin. Heavy-atom derivative data were collected and a Ta6Br14 cluster derivative data set confirmed the presence of ninefold noncrystallographic symmetry.

FastEpistasis: a high performance computing solution for quantitative trait epistasis.

Motivation: Genome-wide association studies have become widely used tools to study effects of genetic variants on complex diseases. While it is of great interest to extend existing analysis methods by considering interaction effects between pairs of loci, the large number of possible tests presents a significant computational challenge. The number of computations is further multiplied in the study of gene expression quantitative trait mapping, in which tests are performed for thousands of gene phenotypes simultaneously. Results: We present FastEpistasis, an efficient parallel solution extending the PLINK epistasis module, designed to test for epistasis effects when analyzing continuous phenotypes. Our results show that the algorithm scales with the number of processors and offers a reduction in computation time when several phenotypes are analyzed simultaneously. FastEpistasis is capable of testing the association of a continuous trait with all single nucleotide polymorphism ( SNP) pairs from 500 000 SNPs, totaling 125 billion tests, in a population of 5000 individuals in 29, 4 or 0.5 days using 8, 64 or 512 processors.

Release of vancomycin and teicoplanin from a plasticized and resorbable gelatin sponge: in vitro investigation of a new antibiotic delivery system with glycopeptides.

BACKGROUND: The aim of this study was to evaluate the efficacy of sustained release of vancomycin and teicoplanin from a resorbable gelatin glycerol sponge, in order to establish a new delivery system for local anti-infective therapy. MATERIALS AND METHODS: 60 plasticized glycerol gelatin sponges containing either 10 or 20% gelatin (w/v) were incubated in vancomycin or teicoplanin solution at 20 degrees C for either 1 or 24 h. In vitro release properties of the sponges were investigated over a period of 1 week by determining the levels of vancomycin and teicoplanin eluted in plasma using fluorescent polarization immunoassay. The rate constant and the half-life for the antibiotic release of each group were calculated by linear regression assuming first order kinetics. RESULTS: Presoaking for 24 h was associated with a significant increase in the total antibiotic release in all groups opposed to 1 h of incubation, except for the 10% sponges presoaked in teicoplanin. Doubling the gelatin content of the sponges from 10 to 20% significantly increased the total release of antibiotic load only in teicoplanin-containing sponges after 24 h incubation. In all corresponding groups investigated, release of vancomycin was more prolonged compared to teicoplanin, which allowed a gradual release beyond 5 days. The half-life (h +/- SEM) of both types of vancomycin-containing sponges was significantly prolonged by 24 h incubation in comparison to 1 h incubation (29.1 +/- 5.9 vs 5.9 +/- 1.0; p < 0.001, 30.0 +/- 2.1 vs 11.1 +/- 1.9; p < 0.001). However, neither doubling the gelatin content of the sponges nor a prolonged incubation was associated with a significantly prolonged delivery of teicoplanin. CONCLUSION: This study demonstrated a better diffusion-controlled release of vancomycin-impregnated glycerol gelatin sponges compared to those pretreated with teicoplanin. The plasticized glycerol gelatin sponge may be a promising carrier for the application of vancomycin to infected wounds for local anti-infective therapy.

Archaeological and archaeomagnetic dating at a site from the ager Tarraconensis (Tarragona, Spain): El Vila-sec Roman pottery

A very accurate archaeological dating of a Roman site in NE Spain (El Vila-sec) was made based on the typology of pottery artifacts. Three different phases were identifi ed with activity ranging from the mid- 1st century BC to the early-3rd century AD. Analyses of bricks from kilns at El Vila-sec produced data on their stored archaeomagnetic vector. These data were compared with the secular variation curve for the Iberian Peninsula and the SCHA.DIF.3K regional archaeomagnetic model. Both, the reference curve and the model, produced probability distributions for the final period of use for two kilns from the second archaeological phase that were not used during the third phase. At a 95% con fidence level, both time distributions cover a wide chronological range including the presumed archaeological age. Both the Iberian secular variation curve and the SCHA.DIF.3K regional model proved to be suitable models for dating the site, although on their own they do not produce a single unambiguous solution. This archaeomagnetic approach could also be applied to neighbouring archaeological sites that have an imprecise archaeological age.

Exotic terrains in the Alps - A solution for a single Jurassic ocean

The Brianconnais area is explained as a large scale exotic terrain separating from Europe during the opening of the Valais ocean. It's displacement history during the Alpine evolution allows to replace older concepts of multiple oceans separating narrow strips of continental crust.

From caging to rouse dynamics in polymer melts with intramolecular barriers: a critical test of the mode coupling theory

By means of computer simulations and solution of the equations of the mode coupling theory (MCT),we investigate the role of the intramolecular barriers on several dynamic aspects of nonentangled polymers. The investigated dynamic range extends from the caging regime characteristic of glass-formers to the relaxation of the chain Rouse modes. We review our recent work on this question,provide new results, and critically discuss the limitations of the theory. Solutions of the MCT for the structural relaxation reproduce qualitative trends of simulations for weak and moderate barriers. However, a progressive discrepancy is revealed as the limit of stiff chains is approached. This dis-agreement does not seem related with dynamic heterogeneities, which indeed are not enhanced by increasing barrier strength. It is not connected either with the breakdown of the convolution approximation for three-point static correlations, which retains its validity for stiff chains. These findings suggest the need of an improvement of the MCT equations for polymer melts. Concerning the relaxation of the chain degrees of freedom, MCT provides a microscopic basis for time scales from chain reorientation down to the caging regime. It rationalizes, from first principles, the observed deviations from the Rouse model on increasing the barrier strength. These include anomalous scaling of relaxation times, long-time plateaux, and nonmonotonous wavelength dependence of the mode correlators.

Cadmium-free quantum dots in aqueous solution: potential for fingermark detection, synthesis and an application to the detection of fingermarks in blood on non-porous surfaces

The use of quantum dots (QDs) in the area of fingermark detection is currently receiving a lot of attention in the forensic literature. Most of the research efforts have been devoted to cadmium telluride (CdTe) quantum dots often applied as powders to the surfaces of interests. Both the use of cadmium and the nano size of these particles raise important issues in terms of health and safety. This paper proposes to replace CdTe QDs by zinc sulphide QDs doped with copper (ZnS:Cu) to address these issues. Zinc sulphide-copper doped QDs were successfully synthesized, characterized in terms of size and optical properties and optimized to be applied for the detection of impressions left in blood, where CdTe QDs proved to be efficient. Effectiveness of detection was assessed in comparison with CdTe QDs and Acid Yellow 7 (AY7, an effective blood reagent), using two series of depletive blood fingermarks from four donors prepared on four non-porous substrates, i.e. glass, transparent polypropylene, black polyethylene and aluminium foil. The marks were cut in half and processed separately with both reagents, leading to two comparison series (ZnS:Cu vs. CdTe, and ZnS:Cu vs. AY7). ZnS:Cu proved to be better than AY7 and at least as efficient as CdTe on most substrates. Consequently, copper-doped ZnS QDs constitute a valid substitute for cadmium-based QDs to detect blood marks on non-porous substrates and offer a safer alternative for routine use.

Spatial visualization of DNA in solution.

An image analysis method is presented which allows for the reconstruction of the three-dimensional path of filamentous objects from two of their projections. Starting with stereo pairs, this method is used to trace the trajectory of DNA molecules embedded in vitreous ice and leads to a faithful representation of their three-dimensional shape in solution. This computer-aided reconstruction is superior to the subjective three-dimensional impression generated by observation of stereo pairs of micrographs because it enables one to look at the reconstructed molecules from any chosen direction and distance and allows quantitative analysis such as determination of distances, curvature, persistence length, and writhe of DNA molecules in solution.

Modeling morphogen gradient formation from arbitrary realistically shaped sources.

Much of the analytical modeling of morphogen profiles is based on simplistic scenarios, where the source is abstracted to be point-like and fixed in time, and where only the steady state solution of the morphogen gradient in one dimension is considered. Here we develop a general formalism allowing to model diffusive gradient formation from an arbitrary source. This mathematical framework, based on the Green's function method, applies to various diffusion problems. In this paper, we illustrate our theory with the explicit example of the Bicoid gradient establishment in Drosophila embryos. The gradient formation arises by protein translation from a mRNA distribution followed by morphogen diffusion with linear degradation. We investigate quantitatively the influence of spatial extension and time evolution of the source on the morphogen profile. For different biologically meaningful cases, we obtain explicit analytical expressions for both the steady state and time-dependent 1D problems. We show that extended sources, whether of finite size or normally distributed, give rise to more realistic gradients compared to a single point-source at the origin. Furthermore, the steady state solutions are fully compatible with a decreasing exponential behavior of the profile. We also consider the case of a dynamic source (e.g. bicoid mRNA diffusion) for which a protein profile similar to the ones obtained from static sources can be achieved.

Protecting mobile agents from external replay attacks

Peer-reviewed

The continuous wavelet transform as a maximum entropy solution of the corresponding inverse problem

The continuous wavelet transform is obtained as a maximumentropy solution of the corresponding inverse problem. It is well knownthat although a signal can be reconstructed from its wavelet transform,the expansion is not unique due to the redundancy of continuous wavelets.Hence, the inverse problem has no unique solution. If we want to recognizeone solution as "optimal", then an appropriate decision criterion hasto be adopted. We show here that the continuous wavelet transform is an"optimal" solution in a maximum entropy sense.

Unlicensed Mobile Access Concept from Testing Point of View

Viime vuosikymmenien aikana kommunikaatioteknologiat ovat kehittyneet erittäin paljon. Uusia verkkoja, liityntätekniikoita, protokollia ja päätelaitteita on luotu alati kehittyvällä vauhdilla, eikä hidastumisen merkkejä ole näkyvissä. Varsinkin mobiilisovellukset ovat kasvattaneet markkinaosuuksiaan viime aikoina. Unlicensed MobileAccess (UMA) on uusi liityntätekniikka mobiilipäätelaitteille, joka mahdollistaa liitynnän GSM- runkoverkkoon WLAN- tai Bluetooth - tekniikoiden avulla. Tämä diplomityö keskittyy UMAan liittyviin teknologioihin, joita tarkastellaan lähemmin ensimmäisissä kappaleissa. Tavoitteena on esitellä, mitä UMA merkitsee, ja kuinka eri tekniikoita voidaan soveltaa sen toteutuksissa. Ennenkuin uusia teknologioita voidaan soveltaa kaupallisesti, täytyy niiden olla kokonaisvaltaisesti testattuja. Erilaisia testausmenetelmiä sovelletaan laitteistonja ohjelmiston testaukseen, mutta tavoite on kuitenkin sama, eli vähentää testattavan tuotteen epäluotettavuutta ja lisätä sen laatua. Vaikka UMA käsittääkin pääasiassa jo olemassa olevia tekniikoita, tuo se silti mukanaan uuden verkkoelementin ja kaksi uutta kommunikaatioprotokollaa. Ennen kuin mitään UMAa tukevia ratkaisuja voidaan tuoda markkinoille, monia erilaisia testausmenetelmiä on suoritettava, jotta varmistutaan uuden tuotteen oikeasta toiminnallisuudesta. Koska tämä diplomityö käsittelee uutta tekniikkaa, on myös testausmenetelmien yleisen testausteorian käsittelemiselle varattu oma kappale. Kappale esittelee erilaisia testauksen näkökulmia ja niihin perustuen rakennetaan myös testausohjelmisto. Tavoitteena on luoda ohjelmisto, jota voidaan käyttää UMA-RR protokollan toiminnan varmentamiseen kohdeympäristössä.

Logistics Development in Finnish and Swedish Companies with Respect of Russia and Four Asian Countries: Traffic Flow and Warehousing Analysis from Current Situation and Likely Development Trends

On selvää, että tänä päivänä maailmankaupan painopiste on hiljalleen siirtymässä Aasiaan ja varsinkin Kiina on ollut huomion keskipisteessä. Erityisesti valmistavien yritysten perspektiivistä muutos on ollut merkittävä ja tämä tosiasia kasvattaa yrityksissä paineita luoda kustannustehokkaita toimitusketjuratkaisuja,joiden vasteaika on mahdollisimman lyhyt. Samaan aikaan kun tarkastellaan kuljetusvirtoja, huomattaan että maanosien välillä on suuri epätasapaino. Tämä on enimmäkseen seurausta suurten globaalisti toimivien yritysten toimitusketjustrategioista. Useimmat näistä toimijoista optimoivat verkostonsa turvautumalla 'paikalliseen hankintaan', jotta he voisivat paremmin hallita toimitusketjujaan ja saada näitä reagointiherkimmiksi. Valmistusyksiköillä onkin monesti Euroopassa pakko käyttää kalliita raaka-aineita ja puolivalmisteita. Kriittisiksi tekijöiksi osoittautuvat kuljetus- ja varastointikustannukset sekä näiden seurauksena hukka-aika, joka aiheutuu viivästyksistä. Voidakseen saavuttaa optimiratkaisun, on tehtävä päätös miten tuotteet varastoidaan: keskitetysti tai hajautetusti ja integroida tämä valinta sopivien kuljetusmuotojen kanssa. Aasiasta Pohjois-Eurooppaan on halpaa käyttää merikuljetusta, mutta operaatio kestää hyvin pitkään - joissain tapauksessa jopa kahdeksan viikkoa. Toisaalta lentokuljetus on sekä kallis että rajoittaa siirrettävien tuotteiden eräkokoa.On olemassa kolmaskin vaihtoehto, josta voisi olla ratkaisuksi: rautatiekuljetus on halvempi kuin lentokuljetus ja vasteajat ovat lyhyemmät kuin merikuljetuksissa. Tässä tutkimuksessa tilannetta selvitetään kyselyllä, joka suunnattiin Suomessa ja Ruotsissa toimiville yrityksille. Tuloksien perusteella teemme johtopäätökset siitä, mitkä kuljetusmuotojen markkinaosuudet tulevat olemaan tulevaisuudessa sekä luomme kuvan kuljetusvirroista Euroopan, Venäjän, Etelä-Korea, Intian, Kiinan ja Japanin välillä. Samalla on tarkoitus ennakoida sitä, miten tarkastelun kohteena olevat yritykset aikovat kehittää kuljetuksiaan ja varastointiaan tulevien vuosien aikana. Tulosten perusteella näyttää siltä, että seuraavan viiden vuoden kuluessa kuljetuskustannukset eivät merkittävissä määrin tule muuttuman ja meri- sekä kumipyöräkuljetukset pysyvät suosituimpina vaihtoehtoina.Kuitenkin lentokuljetusten osuus laskee hiukan, kun taas rautatiekuljetusten painotus kasvaa. Tulokset paljastavat, että Kiinassa ja Venäjällä kuljetettava konttimäärä kasvaa; Intiassa tulos on saman suuntainen, joskaan ei niin voimakas. Analyysimme mukaan kuljetusvirtoihin liittyvä epätasapaino säilyy Venäjän kuljetusten suhteen: yritykset jatkavat tulevaisuudessakin vientiperusteista strategiaansa. Varastoinnin puolella tunnistamme pienemmän muutoksen, jonka mukaan pienikokoisten varastojen määrät todennäköisesti vähenevät tulevaisuudessa ja kiinnostus isoja varastoja kohtaan lisääntyy. Tässä kohtaa on mainittava, että suomalaisilla yrityksillä on enemmän varastoja Keski- ja Itä-Euroopassa verrattuna ruotsalaisiin toimijoihin, jotka keskittyvät selkeämmin Länsi-Euroopan maihin. Varastoja yrityksillä on molemmissa tapaukissa paljolti kotimaassaan. Valitessaan varastojensa sijoituskohteita yritykset painottavat seuraavia kriteereitä: alhaiset jakelukustannukset, kokoamispaikan/valmistustehtaan läheisyys, saapuvan logistiikan integroitavuus ja saatavilla olevat logistiikkapalvelut. Tutkimuksemme lopussa päädymme siihen, että varastojen sijoituspaikat eivät muutu satamien rakenteen ja liikenneyhteyksien takia kovinkaan nopeasti.

Solution scanning as a key policy tool: identifying management interventions to help maintain and enhance regulating ecosystem services

The major task of policy makers and practitioners when confronted with a resource management problem is to decide on the potential solution(s) to adopt from a range of available options. However, this process is unlikely to be successful and cost effective without access to an independently verified and comprehensive available list of options. There is currently burgeoning interest in ecosystem services and quantitative assessments of their importance and value. Recognition of the value of ecosystem services to human well-being represents an increasingly important argument for protecting and restoring the natural environment, alongside the moral and ethical justifications for conservation. As well as understanding the benefits of ecosystem services, it is also important to synthesize the practical interventions that are capable of maintaining and/or enhancing these services. Apart from pest regulation, pollination, and global climate regulation, this type of exercise has attracted relatively little attention. Through a systematic consultation exercise, we identify a candidate list of 296 possible interventions across the main regulating services of air quality regulation, climate regulation, water flow regulation, erosion regulation, water purification and waste treatment, disease regulation, pest regulation, pollination and natural hazard regulation. The range of interventions differs greatly between habitats and services depending upon the ease of manipulation and the level of research intensity. Some interventions have the potential to deliver benefits across a range of regulating services, especially those that reduce soil loss and maintain forest cover. Synthesis and applications: Solution scanning is important for questioning existing knowledge and identifying the range of options available to researchers and practitioners, as well as serving as the necessary basis for assessing cost effectiveness and guiding implementation strategies. We recommend that it become a routine part of decision making in all environmental policy areas.

N=1 SQCD-like theories with N_f massive flavors from AdS/CFT and beta functions

We study new supergravity solutions related to large-N c N=1 supersymmetric gauge field theories with a large number N f of massive flavors. We use a recently proposed framework based on configurations with N c color D5 branes and a distribution of N f flavor D5 branes, governed by a function N f S(r). Although the system admits many solutions, under plausible physical assumptions the relevant solution is uniquely determined for each value of x ≡ N f /N c . In the IR region, the solution smoothly approaches the deformed Maldacena-Núñez solution. In the UV region it approaches a linear dilaton solution. For x < 2 the gauge coupling β g function computed holographically is negative definite, in the UV approaching the NSVZ β function with anomalous dimension γ 0 = −1/2 (approaching − 3/(32π 2)(2N c  − N f )g 3)), and with β g  → −∞ in the IR. For x = 2, β g has a UV fixed point at strong coupling, suggesting the existence of an IR fixed point at a lower value of the coupling. We argue that the solutions with x > 2 describe a"Seiberg dual" picture where N f  − 2N c flips sign.