Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Anomalin. A Dihydropyranocoumarin Derivative from the Plant Lingusticum elatum

The title compound, 9,10-dihydro-8,8-dimethyl-2-oxo-2H,8H-benzo[1,2-b:3,4-b']dipyran-9,10-diyl 2-methyl-2-butenoate, C24H26O7, contains a highly planar coumarin nucleus and a substituted dihydropyran ring (C), which has a distorted half-chair conformation, with an 8 alpha,9 beta orientation. The conformation of ring C is further supported by the two angelyloxy (2-methyl-2-butenoyloxy) substituents at positions C9 and C10, which are cis oriented and thus cannot both occupy equatorial positions with respect to the plane of ring C. The conformations of the two angelyloxy substituents are different, as indicated by their endocyclic torsion angles. The most striking of these angles are O1'-C2'-C4'=C6' and O1'-C2'-C4'-C5' [-137.7 (5) and 43.7 (5)degrees, respectively, in the chain at C10 and 155.8 (5) and -24.7 (9)degrees, respectively in the chain at C9]. These variations are due to two intramolecular hydrogen bonds, namely, C16-H161 ... O1' [C16 ... O1' 3.056 (7) Angstrom] and C7''-H7Y ... O3'' [C7'' ... O3'' 2.955 (12) Angstrom]. The methyl substituents, C15 and C16, at position C8 are alpha and beta oriented, respectively. The crystal structure is stabilized by a weak C4-H41 ... O3' hydrogen bond [C4 ... O3' 3.297 (6) Angstrom] between the screw-related molecules.

Indexed Regulation

Seminal work by Weitzman (1974) revealed prices are preferred to quantities when marginal benefits are relatively flat compared to marginal costs. We extend this comparison to indexed policies, where quantities are proportional to an index, such as output. We find that policy preferences hinge on additional parameters describing the first and second moments of the index and the ex post optimal quantity level. When the ratio of these variables' coefficients of variation divided by their correlation is less than approximately two, indexed quantities are preferred to fixed quantities. A slightly more complex condition determines when indexed quantities are preferred to prices. Applied to climate change policy, we find that the range of variation and correlation in country-level carbon dioxide emissions and GDP suggests the ranking of an emissions intensity cap (indexed to GDP) compared to a fixed emission cap is not uniform across countries; neither policy clearly dominates the other.

Equal Factor Equivalence in Economies with Multiple Public Goods.

We consider the problem of provisioon and cost-sharing of multiple public goods. the efficient equal factor equivalent allocation rule makes every agent indifferent between what he receives and the opportunity of choosing the bundle of public goods subject to the constraint of paying r times its cost, where r is set as low as possible.

Sharing the Cost of a Public Good without Subsidies

We study the construction of a social ordering function for the case of a public good financed by contributions from the population, and we extend the analysis of Maniquet and Sprumont (2004) to the case when contributions cannot be negative, i.e. agents cannot receive subsidies from others.

Priorities in the Location of Multiple Public Facilities

A collective decision problem is described by a set of agents, a profile of single-peaked preferences over the real line and a number k of public facilities to be located. We consider public facilities that do not su¤er from congestion and are non-excludable. We provide a characterization of the class of rules satisfying Pareto-efficiency, object-population monotonicity and sovereignty. Each rule in the class is a priority rule that selects locations according to a predetermined priority ordering among interest groups. We characterize each of the subclasses of priority rules that respectively satisfy anonymity, hiding-proofness and strategy-proofness. In particular, we prove that a priority rule is strategy-proof if and only if it partitions the set of agents into a fixed hierarchy. Alternatively, any such rule can be viewed as a collection of fixed-populations generalized peak-selection median rules (Moulin, 1980), that are linked across populations, in a way that we describe.

Individuals' (re-)action in the face of global warming

Climate change remains a major challenge for today’s and future societies due to its immense impacts on human lives and the natural environment. This thesis investigates the extent to which individuals are willing and prepared to voluntarily contribute to climate protection and to adjust to new climatic conditions in order to cope with the consequences of climate change and reduce the severity of potential negative impacts. The thesis thereby combines research in the fields of the private provision of environmental public goods and adaptation to climate change, which is still widely unconnected in the existing literature. The six contributions of this thesis mainly focus on microeconometric analyses using data from international surveys in China, Germany, and the USA. The main findings are: (i) A substantial share of individuals is willing to voluntarily contribute to climate protection and to adapt to climatic change. The engagement in both strategies is positively interrelated at the individual level and the analyses reveal hardly any evidence that adaptation activities crowd out individuals’ incentives to engage in climate protection. (ii) The main determinants of individuals’ adaptation activities seem to be the subjective risk perception as well as socio-economic and socio-demographic characteristics like age, gender, education, and income, while their climate protection efforts are found to be broadly motivated by financial advantages from these activities and additional immaterial benefits. (iii) The empirical findings also suggest a significantly positive relationship between certain climate protection activities. Substitutions are found to occur merely if one measure is perceived to be more effective in providing climate protection or if individuals have high environmental preferences. (iv) This thesis further reveals a common understanding of a (normatively) fair burden-sharing in international climate policy across citizens in China, Germany, and the USA. The highest preferences are found for the accountability principle.

Virulence properties and antimicrobial susceptibility of Shiga toxin-producing Escherichia coli strains isolated from healthy cattle from Parana State, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

国際公共財としての感染症対策

HIV/AIDS、SARS、鳥インフルエンザといった新興感染症、薬剤耐性を持った病原体の出現によって問題が深刻化している結核、マラリア等再興感染症への関心が世界で高まっている。感染症の予防や治療はそれを個人に施すことのプラスの効果が国境を超えてスピル・オーバーすることが多く、国際公共財としての性質を持っている。また、新薬・ワクチンの成分・製法に関する情報および、感染症の流行に関する情報は典型的な公共財であり、誰しもがフリー・ライドするインセンティブを持っている。したがって、これら公共財の過少供給の問題を解決するためには国際的な協調行動が必要である。 　世界の感染症対策は、感染がより大規模に広まっている発展途上国を中心としたものにならざるを得ない。現在これをリードしているのはアメリカであり、日本はWHOへの出資については存在感を示しているものの、それ以外の機関への出資や二国間協力の面において、少なくとも今現在においては貢献度が大きいと見られていない。また、新薬・ワクチン開発については日本の財政的な面での貢献は全く目立たない。 　国際的な感染症対策に関する日本の印象を高めるためには、沖縄感染症イニシアティブの際になされたような形で金銭的貢献度を再び高める、あるいは、国際的に必要と考えられているものの他国が協力を決めていない分野への貢献をいち早く宣言する、等の対応が考えられる。

The determinants of rural electrification in Bihar, India

This paper explores intra-state disparity in access to electricity and examines the determinants of electrification at the village level in Bihar, one of the underdeveloped states in India. Our field survey of 80 villages in 5 districts conducted in 2008-09 found that 48 villages (60%) are electrified when using the definition of electrification that a village is electrified if any one household in the village is connected to electricity. The degrees of “electrification” in terms of the proportion of household connection and available hours of electricity remain by and large low, and at the same time differ across districts, villages and seasons. In the processes of electrification, approximately 40% of villages have been electrified in recent years. Based on the basic findings of the survey, this paper examines the electrification processes and how it has changed in recent years. The econometric analyses demonstrate that location is the most important determinant of a village’s electricity connection. Another important finding is that with the rapid progress of rural electrificationunder the recent government programme and the tendency to connect the villages which are easily accessible, the collective bargaining power of the village, which used to significantly affect the process of electrification, has lost influence. This adversely affects remote villages. In order to extend electricity supplies to remote and geographically disadvantaged villages, the government needs to consider seriously other options for sustainable electricity supply, such as decentralized distribution of electricity rather than the conventional connection through the national/local grids.

Progress and issues in rural electrification in Bihar, India : a preliminary analysis

Rural electrification has been an important part of government policy since India gained independence. However, despite the number of electrified villages expanding rapidly in recent years, there are many that still remain un-electrified. This paper addresses the issue of intra-state disparity in access to electricity and examines the determinants of electrification at the village level using data from a survey conducted in rural Bihar, one of the underdeveloped states in India. An econometric analysis demonstrates that small villages in remote locations tend to be considered a low priority in the process of electrification. Electrification at the village level in the more advanced states is no longer an issue, though the challenge of access to electrification at the household level remains. This paper also discusses issues that emerged from interviewing villagers and visiting rural areas, and shows that the actual progress of rural electrification may not be as advanced as government statistics indicate.

Stomach content records for pelagic fish (herring, mackerel, blue whiting, albacore and bluefin tuna) in the northeast Atlantic

Fish stomach content records extracted from the DAPSTOM 4.5 database (held at the UK Centre for Environment, Fisheries and Aquaculture Science - CEFAS). Data collated as part of the EU Euro-Basin project and specifically concerning herring (Clupea harengus), mackerel (Scomber scombrus), blue whiting (Micromesistius poutassou), albacore (Thunnus alalunga) and bluefin tuna (Thunnus thynnus). The data set consist of 20720 records - collected throughout the northeast Atlantic, between 1906 and 2011 - mostly during routine fisheries monitoring research cruises.

Sequence type 131 fimH30 and fimH41 subclones amongst escherichia coli isolates in Australia and New Zealand

The clonal composition of Escherichia coli causing extra-intestinal infections includes ST131 and other common uropathogenic clones. Drivers for the spread of these clones and risks for their acquisition have been difficult to define. In this study, molecular epidemiology was combined with clinical data from 182 patients enrolled in a case-control study of community-onset expanded-spectrum cephalosporin-resistant E. coli (ESC-R-EC) in Australia and New Zealand. Genetic analysis included antimicrobial resistance mechanisms, clonality by DiversiLab (rep-PCR) and multilocus sequence typing (MLST), and subtyping of ST131 by identification of polymorphisms in the fimH gene. The clonal composition of expanded-spectrum cephalosporin-susceptible E. coli and ESC-R-EC isolates differed, with six MLST clusters amongst susceptible isolates (median 7 isolates/cluster) and three clusters amongst resistant isolates, including 40 (45%) ST131 isolates. Population estimates indicate that ST131 comprises 8% of all E. coli within our population; the fluoroquinolone-susceptible H41 subclone comprised 4.5% and the H30 subclone comprised 3.5%. The H30 subclone comprised 39% of all ESC-R-EC and 41% of all fluoroquinolone-resistant E. coli within our population. Patients with ST131 were also more likely than those with non-ST131 isolates to present with an upper than lower urinary tract infection (RR=1.8, 95% CI 1.01-3.1). ST131 and the H30 subclone were predominant amongst ESC-R-EC but were infrequent amongst susceptible isolates where the H41 subclone was more prevalent. Within our population, the proportional contribution of ST131 to fluoroquinolone resistance is comparable with that of other regions. In contrast, the overall burden of ST131 is low by global standards.