Structural and elastic properties of DNA and chromatin

We investigate a chain consisting of two coupled worm-like chains withconstant distance between the strands. The effects due todouble-strandedness of the chain are studied. In a previous analyticalstudy of this system an intrinsic twist-stretch coupling and atendency of kinking is predicted. Even though a local twist structureis observed the predicted features are not recovered. A new model for DNA at the base-pair level is presented. Thebase-pairs are treated as flat rigid ellipsoids and thesugar-phosphate backbones are represented as stiff harmonic springs.The base-pair stacking interaction is modeled by a variant of theGay-Berne potential. It is shown by systematic coarse-graininghow the elastic constants of a worm-like chain are related to thelocal fluctuations of the base-pair step parameters. Even though a lotof microscopic details of the base-pair geometry is neglected themodel can be optimized to obtain a B-DNA conformation as ground stateand reasonable elastic properties. Moreover the model allows tosimulate much larger length scales than it is possible with atomisticsimulations due to the simplification of the force-field and inparticular due to the possibility of non-local Monte-Carlo moves. Asa first application the behavior under stretching is investigated. Inagreement with micromanipulation experiments on single DNA moleculesone observes a force-plateau in the force-extension curvescorresponding to an overstretching transition from B-DNA to aso-called S-DNA state. The model suggests a structure for S-DNA withhighly inclined base-pairs in order to enable at least partialbase-pair stacking. Finally a simple model for chromatin is introduced to study itsstructural and elastic properties. The underlying geometry of themodeled fiber is based on a crossed-linker model. The chromatosomesare treated as disk-like objects. Excluded volume and short rangenucleosomal interaction are taken into account by a variant of theGay-Berne potential. It is found that the bending rigidity and thestretching modulus of the fiber increase with more compact fibers. Fora reasonable parameterization of the fiber for physiologicalconditions and sufficiently high attraction between the nucleosomes aforce-extension curve is found similar to stretching experiments onsingle chromatin fibers. For very small stretching forces a kinkedfiber forming a loop is observed. If larger forces are applied theloop formation is stretched out and a decondensation of the fibertakes place.

Development of SuperEnsemble Techniques for the Mediterranean Ocean Forecasting System

This research activity studied how the uncertainties are concerned and interrelated through the multi-model approach, since it seems to be the bigger challenge of ocean and weather forecasting. Moreover, we tried to reduce model error throughout the superensemble approach. In order to provide this aim, we created different dataset and by means of proper algorithms we obtained the superensamble estimate. We studied the sensitivity of this algorithm in function of its characteristics parameters. Clearly, it is not possible to evaluate a reasonable estimation of the error neglecting the importance of the grid size of ocean model, for the large amount of all the sub grid-phenomena embedded in space discretizations that can be only roughly parametrized instead of an explicit evaluation. For this reason we also developed a high resolution model, in order to calculate for the first time the impact of grid resolution on model error.

The shaping of foreign policy: Vietnamese grand strategy after the Cold War

This study examines the case of Vietnam and uses the method of process tracing to explore the sources of foreign policy choice and change. Foreign policy is derived from grand strategy, which refers to the full package of a state’s domestic and foreign policies. I argue that a state’s grand strategy results from the interaction of four factors—its society’s historical experience, social motivation, international power, and political contest among domestic groups. Grand strategies emerge as a response to perceived shifts in the balance of international economic, political, and military power. However, this is not to say that international pressures and incentives are translated into foreign policy. Rather, pressures and incentives are given meaning by worldviews, which reflect a society’s historical experiences of its place in the international system at traumatic junctures of its encounter with the outside world. Strategic changes in foreign policy follow what I call the “strategic algorithm,” which incorporates four major mechanisms—balancing against threat, bandwagoning with power, learning, and survival by transformation. This case study generates hypotheses for a theory of strategic choice, a theory of foreign policy transformation, and a theory of grand strategy emergence.

Functional characterisation of in vitro synthesised G-protein coupled receptors in polymersomes

Membrane proteins play an indispensable role in physiological processes. It is, therefore, not surprising that many diseases are based on the malfunction of membrane proteins. Hence membrane proteins and especially G-protein coupled receptors(GPCRs)- the largest subfamily- have become an important drug target. Due to their high selectivity and sensitivity membrane proteins are also feasible for the detection of small quantities of substances with biosensors. Despite this widespread interest in GPCRs due to their importance as drug targets and biosensors there is still a lack of knowledge of structure, function and endogenous ligands for quiet a few of the previously identified receptors.rnBottlenecks in over-expression, purification, reconstitution and handling of membrane proteins arise due to their hydrophobic nature. Therefore the production of reasonable amounts of functional membrane proteins for structural and functional studies is still challenging. Also the limited stability of lipid based membrane systems hampers their application as platforms forrnscreening applications and biosensors.rnIn recent years the in vitro protein synthesis became a promising alternative to gain better yields for expression of membrane proteins in bio-mimetic membrane systems. These expression systems are based on cell extracts. Therefore cellular effects on protein expression are reduced. The open nature of the cell-free expression systems easily allows for the adjustment of reactionrnconditions for the protein of interest. The cell-free expression in the presence of bio-mimetic membrane systems allows the direct incorporation of the membrane proteins and therefore skips the time-consuming purification and reconstitution processes. Amphiphilic block-copolymers emerged as promising alternative for the less stable lipid-based membrane systems. They, likernlipids, form membraneous structures in aqueous solutions but exhibit increased mechanical and chemical stability.rnThe aim of this work was the generation of a GPCR-functionalised membrane system by combining both promising alternatives: in vitro synthesis and polymeric membrane systems. This novel platform should be feasible for the characterisation of the incorporated GPCR. Immunodetection of Dopamine receptor 1 and 2 expressed in diblock- and triblock-polymersomes demonstrated the successful in vitro expression of GPCRs in polymeric membranes. Antibodyrnbinding studies suggested a favoured orientation of dopamine receptors in triblockpolymersomes.rnA dopamine-replacement assay on DRD2-functionalised immobilised triblockpolymersomes confirmed functionality of the receptor in the polymersomes. The altered binding curve suggests an effect of the altered hydrophobic environment presented by the polymer membrane on protein activity.

HCl gas gettering of 3d transition metals for crystalline silicon solar cell concepts

In order to reduce the costs of crystalline silicon solar cells, low-cost silicon materials like upgraded metallurgical grade (UMG) silicon are investigated for the application in the photovoltaic (PV) industry. Conventional high-purity silicon is made by cost-intensive methods, based on the so-called Siemens process, which uses the reaction to form chlorosilanes and subsequent several distillation steps before the deposition of high-purity silicon on slim high-purity silicon rods. UMG silicon in contrast is gained from metallurgical silicon by a rather inexpensive physicochemical purification (e.g., acid leaching and/or segregation). However, this type of silicon usually contains much higher concentrations of impurities, especially 3d transition metals like Ti, Fe, and Cu. These metals are extremely detrimental in the electrically active part of silicon solar cells, as they form recombination centers for charge carriers in the silicon band gap. This is why simple purification techniques like gettering, which can be applied between or during solar cell process steps, will play an important role for such low-cost silicon materials. Gettering in general describes a process, whereby impurities are moved to a place or turned into a state, where they are less detrimental to the solar cell. Hydrogen chloride (HCl) gas gettering in particular is a promising simple and cheap gettering technique, which is based on the reaction of HCl gas with transition metals to form volatile metal chloride species at high temperatures.rnThe aim of this thesis was to find the optimum process parameters for HCl gas gettering of 3d transition metals in low-cost silicon to improve the cell efficiency of solar cells for two different cell concepts, the standard wafer cell concept and the epitaxial wafer equivalent (EpiWE) cell concept. Whereas the former is based on a wafer which is the electrically active part of the solar cell, the latter uses an electrically inactive low-cost silicon substrate with an active layer of epitaxially grown silicon on top. Low-cost silicon materials with different impurity grades were used for HCl gas gettering experiments with the variation of process parameters like the temperature, the gettering time, and the HCl gas concentration. Subsequently, the multicrystalline silicon neighboring wafers with and without gettering were compared by element analysis techniques like neutron activation analysis (NAA). It was demonstrated that HCl gas gettering is an effective purification technique for silicon wafers, which is able to reduce some 3d transition metal concentrations by over 90%. Solar cells were processed for both concepts which could demonstrate a significant increase of the solar cell efficiency by HCl gas gettering. The efficiency of EpiWE cells could be increased by HCl gas gettering by approximately 25% relative to cells without gettering. First process simulations were performed based on a simple model for HCl gas gettering processes, which could be used to make qualitative predictions.

Chemical Compatibility of Model Soil-Bentonite Backfill Containing Multiswellable Bentonite

The objective of this study was to evaluate the chemical compatibility of model soil-bentonite backfills containing multiswellable bentonite (MSB) relative to that of similar backfills containing untreated sodium (Na) bentonite or a commercially available, contaminant resistant bentonite (SW101). Flexible-wall tests were conducted on consolidated backfill specimens (effective stress =34.5 kPa) containing clean sand and 4.5–5.7% bentonite (by dry weight) using tap water and calcium chloride (CaCl2) solutions (10–1,000 mM) as the permeant liquids. Final values of hydraulic conductivity (k) and intrinsic permeability (K) to the CaCl2 solutions were determined after achieving both short-term termination criteria as defined by ASTM D5084 and long-term termination criteria for chemical equilibrium between the influent and effluent. Specimens containing MSB exhibited the smallest increases in k and K upon permeation with a given CaCl2 solution relative to specimens containing untreated Na bentonite or SW101. However, none of the specimens exhibited more than a five-fold increase in k or K, regardless of CaCl2 concentration or bentonite type. Final k values for specimens permeated with a given CaCl2 solution after permeation with tap water were similar to those for specimens of the same backfill permeated with only the CaCl2 solution, indicating that the order of permeation had no significant effect on k. Also, final k values for all specimens were within a factor of two of the k measured after achieving the ASTM D5084 termination criteria. Thus, use of only the ASTM D5084 criteria would have been sufficient to obtain reasonable estimates of long-term hydraulic conductivity for the specimens in this study.

Mapping the Operation of the Miniature Combustion Aerosol Standard (Mini-CAST) Soot Generator

The Jing Ltd. miniature combustion aerosol standard (Mini-CAST) soot generator is a portable, commercially available burner that is widely used for laboratory measurements of soot processes. While many studies have used the Mini-CAST to generate soot with known size, concentration, and organic carbon fraction under a single or few conditions, there has been no systematic study of the burner operation over a wide range of operating conditions. Here, we present a comprehensive characterization of the microphysical, chemical, morphological, and hygroscopic properties of Mini-CAST soot over the full range of oxidation air and mixing N-2 flow rates. Very fuel-rich and fuel-lean flame conditions are found to produce organic-dominated soot with mode diameters of 10-60nm, and the highest particle number concentrations are produced under fuel-rich conditions. The lowest organic fraction and largest diameter soot (70-130nm) occur under slightly fuel-lean conditions. Moving from fuel-rich to fuel-lean conditions also increases the O:C ratio of the soot coatings from similar to 0.05 to similar to 0.25, which causes a small fraction of the particles to act as cloud condensation nuclei near the Kelvin limit (kappa similar to 0-10(-3)). Comparison of these property ranges to those reported in the literature for aircraft and diesel engine soots indicates that the Mini-CAST soot is similar to real-world primary soot particles, which lends itself to a variety of process-based soot studies. The trends in soot properties uncovered here will guide selection of burner operating conditions to achieve optimum soot properties that are most relevant to such studies.

Transport of Hydraulic Fracturing Water and Wastes in the Susquehanna River Basin, Pennsylvania

The development of the Marcellus Shale gas play in Pennsylvania and the northeastern United States has resulted in significant amounts of water and wastes transported by truck over roadways. This study used geographic information systems (GIS) to quantify truck travel distances via both the preferred routes (minimum distance while also favoring higher-order roads) as well as, where available, the likely actual distances for freshwater and waste transport between pertinent locations (e. g., gas wells, treatment facilities, freshwater sources). Results show that truck travel distances in the Susquehanna River Basin are greater than those used in prior life-cycle assessments of tight shale gas. When compared to likely actual transport distances, if policies were instituted to constrain truck travel to the closest destination and higher-order roads, transport mileage reductions of 40-80% could be realized. Using reasonable assumptions of current practices, greenhouse gas (GHG) emissions associated with water and waste hauling were calculated to be 70-157 MT CO2 eq per gas well. Furthermore, empty so-called backhaul trips, such as to freshwater withdrawal sites or returning from deep well injection sites, were found to increase emissions by an additional 30%, underscoring the importance of including return trips in the analysis. The results should inform future life-cycle assessments of tight shale gases in managed watersheds and help local and regional governments plan for impacts of transportation on local infrastructure. (C) 2013 American Society of Civil Engineers.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Improving the sustainability of an appropriate technology solution; bone char defluoridation filters in Arusha, Tanzania

High concentrations of fluoride naturally occurring in the ground water in the Arusha region of Tanzania cause dental, skeletal and non-skeletal fluorosis in up to 90% of the region’s population [1]. Symptoms of this incurable but completely preventable disease include brittle, discolored teeth, malformed bones and stiff and swollen joints. The consumption of high fluoride water has also been proven to cause headaches and insomnia [2] and adversely affect the development of children’s intelligence [3, 4]. Despite the fact that this array of symptoms may significantly impact a society’s development and the citizens’ ability to perform work and enjoy a reasonable quality of life, little is offered in the Arusha region in the form of solutions for the poor, those hardest hit by the problem. Multiple defluoridation technologies do exist, yet none are successfully reaching the Tanzanian public. This report takes a closer look at the efforts of one local organization, the Defluoridation Technology Project (DTP), to address the region’s fluorosis problem through the production and dissemination of bone char defluoridation filters, an appropriate technology solution that is proven to work. The goal of this research is to improve the sustainability of DTP’s operations and help them reach a wider range of clients so that they may reduce the occurrence of fluorosis more effectively. This was done first through laboratory testing of current products. Results of this testing show a wide range in uptake capacity across batches of bone char emphasizing the need to modify kiln design in order to produce a more consistent and high quality product. The issue of filter dissemination was addressed through the development of a multi-level, customerfunded business model promoting the availability of filters to Tanzanians of all socioeconomic levels. Central to this model is the recommendation to focus on community managed, institutional sized filters in order to make fluoride free water available to lower income clients and to increase Tanzanian involvement at the management level.

When do combinations of diuretics make sense?

Diuretics are commonly prescribed by physicians to contract the ECF volume. In two clinical situations combining different classes of diuretics make sense: First, if a loop diuretic at maximal dose alone does not lead to sufficient diuresis or second, if the side effect of a diuretic needs to be corrected by adding a diuretic of another class. The latter is clinically often used to counteract loop or thiazide diuretic-induced hypokalemia by the addition of a potassium sparing diuretic. Key to a reasonable combination of diuretics is understanding of the pharmaco-kinetics and knowledge of the molecular targets of the diuretics involved.

Controversies of fetal cardiac intervention

Remarkable advances in ultrasound imaging technology have made it possible to diagnose fetal cardiovascular lesions as early as 12-14 weeks of gestation and to assess their physiological relevance by echocardiography. Moreover, invasive techniques have been developed and refined to relieve significant congenital heart disease (CHD), such as critical aortic and pulmonary stenoses in the pediatric population including neonates. Recognition of the fact that certain CHDs can evolve in utero, and early intervention may improve the outcome by altering the natural history of such conditions has led to the evolution of a new fetal therapy, i.e. fetal cardiac intervention. Two entities, pulmonary valvar atresia and intact ventricular septum (PA/IVS) and hypoplastic left heart syndrome (HLHS), are associated with significant morbidity and mortality even with postnatal surgical therapy. These cases are believed to occur due to restricted blood flow, leading to impaired growth and function of the right or left ventricle. Therefore, several centers started the approach of antenatal intervention with the primary goal of improving the blood flow through the stenotic/atretic valve orifices to allow growth of cardiac structures. Even though centers with a reasonable number of cases seem to have improved the technique and the immediate outcome of fetal interventions, the field is challenged by ethical issues as the intervention puts both the mother and the fetus at risk. Moreover, the perceived benefits of prenatal treatment have to be weighed against steadily improving postnatal surgical and hybrid procedures, which have been shown to reduce morbidity and mortality for these complex heart defects. This review is an attempt to provide a balanced opinion and an update on fetal cardiac intervention.

Scheduling of continuous and discontinuous material flows with intermediate storage restrictions

This paper deals with scheduling batch (i.e., discontinuous), continuous, and semicontinuous production in process industries (e.g., chemical, pharmaceutical, or metal casting industries) where intermediate storage facilities and renewable resources (processing units and manpower) of limited capacity have to be observed. First, different storage configurations typical of process industries are discussed. Second, a basic scheduling problem covering the three above production modes is presented. Third, (exact and truncated) branch-and-bound methods for the basic scheduling problem and the special case of batch scheduling are proposed and subjected to an experimental performance analysis. The solution approach presented is flexible and in principle simple, and it can (approximately) solve relatively large problem instances with sufficient accuracy.

Advanced production scheduling for batch plants in process industries

An Advanced Planning System (APS) offers support at all planning levels along the supply chain while observing limited resources. We consider an APS for process industries (e.g. chemical and pharmaceutical industries) consisting of the modules network design (for long–term decisions), supply network planning (for medium–term decisions), and detailed production scheduling (for short–term decisions). For each module, we outline the decision problem, discuss the specifi cs of process industries, and review state–of–the–art solution approaches. For the module detailed production scheduling, a new solution approach is proposed in the case of batch production, which can solve much larger practical problems than the methods known thus far. The new approach decomposes detailed production scheduling for batch production into batching and batch scheduling. The batching problem converts the primary requirements for products into individual batches, where the work load is to be minimized. We formulate the batching problem as a nonlinear mixed–integer program and transform it into a linear mixed–binary program of moderate size, which can be solved by standard software. The batch scheduling problem allocates the batches to scarce resources such as processing units, workers, and intermediate storage facilities, where some regular objective function like the makespan is to be minimized. The batch scheduling problem is modelled as a resource–constrained project scheduling problem, which can be solved by an efficient truncated branch–and–bound algorithm developed recently. The performance of the new solution procedures for batching and batch scheduling is demonstrated by solving several instances of a case study from process industries.

Estimation of heart weight by post-mortem cardiac magnetic resonance imaging

Introduction The aim of this study was to determine which single measurement on post-mortem cardiac MR reflects actual heart weight as measured at autopsy, assess the intra- and inter-observer reliability of MR measurements, derive a formula to predict heart weight from MR measurements and test the accuracy of the formula to prospectively predict heart weight. Materials and methods 53 human cadavers underwent post-mortem cardiac MR and forensic autopsy. In Phase 1, left ventricular area and wall thickness were measured on short axis and four chamber view images of 29 cases. All measurements were correlated to heart weight at autopsy using linear regression analysis. In Phase 2, single left ventricular area measurements on four chamber view images (LVA_4C) from 24 cases were used to predict heart weight at autopsy based on equations derived during Phase 1. Intra-class correlation coefficient (ICC) was used to determine inter- and intra-reader agreement. Results Heart weight strongly correlates with LVA_4C (r=0.78 M; p<0.001). Intra-reader and inter-reader reliability was excellent for LVA_4C (ICC=0.81–0.91; p<0.001 and ICC=0.90; p<0.001 respectively). A simplified formula for heart weight ([g]≈LVA_4C [mm2]×0.11) was derived based on linear regression analysis. Conclusions This study shows that single circumferential area measurements of the left ventricle in the four chamber view on post-mortem cardiac MR reflect actual heart weight as measured at autopsy. These measurements yield an excellent intra- and inter-reader reliability and can be used to predict heart weight prior to autopsy or to give a reasonable estimate of heart weight in cases where autopsy is not performed.