Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis.

Competing hypotheses seek to explain the evolution of oxygenic and anoxygenic processes of photosynthesis. Since chlorophyll is less reduced and precedes bacteriochlorophyll on the modern biosynthetic pathway, it has been proposed that chlorophyll preceded bacteriochlorophyll in its evolution. However, recent analyses of nucleotide sequences that encode chlorophyll and bacteriochlorophyll biosynthetic enzymes appear to provide support for an alternative hypothesis. This is that the evolution of bacteriochlorophyll occurred earlier than the evolution of chlorophyll. Here we demonstrate that the presence of invariant sites in sequence datasets leads to inconsistency in tree building (including maximum-likelihood methods). Homologous sequences with different biological functions often share invariant sites at the same nucleotide positions. However, different constraints can also result in additional invariant sites unique to the genes, which have specific and different biological functions. Consequently, the distribution of these sites can be uneven between the different types of homologous genes. The presence of invariant sites, shared by related biosynthetic genes as well as those unique to only some of these genes, has misled the recent evolutionary analysis of oxygenic and anoxygenic photosynthetic pigments. We evaluate an alternative scheme for the evolution of chlorophyll and bacteriochlorophyll.

A maximum likelihood algorithm for genome mapping of cytogenetic loci from meiotic configuration data.

Frequencies of meiotic configurations in cytogenetic stocks are dependent on chiasma frequencies in segments defined by centromeres, breakpoints, and telomeres. The expectation maximization algorithm is proposed as a general method to perform maximum likelihood estimations of the chiasma frequencies in the intervals between such locations. The estimates can be translated via mapping functions into genetic maps of cytogenetic landmarks. One set of observational data was analyzed to exemplify application of these methods, results of which were largely concordant with other comparable data. The method was also tested by Monte Carlo simulation of frequencies of meiotic configurations from a monotelodisomic translocation heterozygote, assuming six different sample sizes. The estimate averages were always close to the values given initially to the parameters. The maximum likelihood estimation procedures can be extended readily to other kinds of cytogenetic stocks and allow the pooling of diverse cytogenetic data to collectively estimate lengths of segments, arms, and chromosomes.

Vacancy-induced magnetism in graphene and graphene ribbons

We address the electronic structure and magnetic properties of vacancies and voids both in graphene and graphene ribbons. By using a mean-field Hubbard model, we study the appearance of magnetic textures associated with removing a single atom (vacancy) and multiple adjacent atoms (voids) as well as the magnetic interactions between them. A simple set of rules, based on the Lieb theorem, link the atomic structure and the spatial arrangement of the defects to the emerging magnetic order. The total spin S of a given defect depends on its sublattice imbalance, but some defects with S=0 can still have local magnetic moments. The sublattice imbalance also determines whether the defects interact ferromagnetically or antiferromagnetically with one another and the range of these magnetic interactions is studied in some simple cases. We find that in semiconducting armchair ribbons and two-dimensional graphene without global sublattice imbalance, there is a maximum defect density above which local magnetization disappears. Interestingly, the electronic properties of semiconducting graphene ribbons with uncoupled local moments are very similar to those of diluted magnetic semiconductors, presenting giant Zeeman splitting.

Large spin splitting in the conduction band of transition metal dichalcogenide monolayers

We study the conduction band spin splitting that arises in transition metal dichalcogenide (TMD) semiconductor monolayers such as MoS2, MoSe2, WS2, and WSe2 due to the combination of spin-orbit coupling and lack of inversion symmetry. Two types of calculation are done. First, density functional theory (DFT) calculations based on plane waves that yield large splittings, between 3 and 30 meV. Second, we derive a tight-binding model that permits to address the atomic origin of the splitting. The basis set of the model is provided by the maximally localized Wannier orbitals, obtained from the DFT calculation, and formed by 11 atomiclike orbitals corresponding to d and p orbitals of the transition metal (W, Mo) and chalcogenide (S, Se) atoms respectively. In the resulting Hamiltonian, we can independently change the atomic spin-orbit coupling constant of the two atomic species at the unit cell, which permits to analyze their contribution to the spin splitting at the high symmetry points. We find that—in contrast to the valence band—both atoms give comparable contributions to the conduction band splittings. Given that these materials are most often n-doped, our findings are important for developments in TMD spintronics.

Global behavior of the Douglas–Rachford method for a nonconvex feasibility problem

In recent times the Douglas–Rachford algorithm has been observed empirically to solve a variety of nonconvex feasibility problems including those of a combinatorial nature. For many of these problems current theory is not sufficient to explain this observed success and is mainly concerned with questions of local convergence. In this paper we analyze global behavior of the method for finding a point in the intersection of a half-space and a potentially non-convex set which is assumed to satisfy a well-quasi-ordering property or a property weaker than compactness. In particular, the special case in which the second set is finite is covered by our framework and provides a prototypical setting for combinatorial optimization problems.

A summary of the politico-economic changes taking place during Vladimir Putin's first term in office; Chechnya and Russia: The significance of the Chechen problem for contemporary Russia. OSW Study 11/2003

Putin's first term in office: The most significant achievement of Vladimir Putin's team over the three years of his term of office is the realisation of legislative changes, which may constitute a base for further - more detailed - political and economic reforms. This is, to a certain degree, a return to the economic tasks set out by a team of reformists in the early 1990s, which were impossible to realise at the time due to conflicts between the Kremlin and legislative powers. Chechnya and Russia: The purpose of this analysis is to examine the significance of the Chechen issue for contemporary Russia. Part I discusses the history of the conflict from 1991 to date and the impact of developments in the republic on Russia as a whole. Part II is an attempt to indicate the areas of Russian reality that are most deeply affected by the Chechen problem.

Germany’s ‘refugee’ problem. The most important test for Chancellor Merkel and the grand coalition. OSW COMMENTARY NUMBER 182/11.09.2015 2015-09-11

The rapid increase in the number of immigrants from outside of the EU coming to Germany has become the paramount political issue. According to new estimates, the number of individuals expected arrive in Germany in 2015 and apply for asylum there is 800,000, which is nearly twice as many as estimated in earlier forecasts. Various administrative, financial and social problems related to the influx of migrants are becoming increasingly apparent. The problem of ‘refugees’ (in public debate, the terms ‘immigrants’, ‘refugees’, ‘illegal immigrants’, ‘economic immigrants’ have not been clearly defined and have often been used interchangeably) has been culminating for over a year. Despite this, it was being disregarded by Angela Merkel’s government which was preoccupied with debates on how to rescue Greece. It was only daily reports of cases of refugee centres being set on fire that convinced Chancellor Merkel to speak and to make immigration problem a priority issue (Chefsache). Neither the ruling coalition nor the opposition parties have a consistent idea of how Germany should react to the growing number of refugees. In this matter, divisions run across parties. Various solutions have been proposed, from liberalisation of laws on the right to stay in Germany to combating illegal immigration more effectively, which would be possible if asylum granting procedures were accelerated. The proposed solutions have not been properly thought through, instead they are reactive measures inspired by the results of opinion polls. This is why their assumptions are often contradictory. The situation is similar regarding the actions proposed by Chancellor Merkel which involve faster procedures to expel individuals with no right to stay in Germany and a plan to convince other EU states to accept ‘refugees’. None of these ideas is new – they were already present in the German internal debate.

Migration and Asylum Data for Policy-making in the European Union – The problem with numbers. CEPS Liberty and Security in Europe No. 89/March 2016

Among many other problems, the migration, humanitarian and policy crises in the European Union in 2015 and early 2016 have highlighted a pressing need for reliable, timely and comparable statistical data on migration, asylum and arrivals at national borders. In this fast-moving policy field, data production and the timeliness of dissemination have seen some improvements but the sources of data remain largely unchanged at national level. In this paper the author examines the reasons for some of the problems with the data for policy and for public discussion, and makes a set of recommendations that call for a complete and updated inventory of data sources and for an evaluation of the quality of data used for policy-making.

Stricter regulation boosts exports: the case of Maximum Residue Levels in pesticides

Constructing an original panel on Maximum Residue Levels (MRLs) in pesticides for 50 countries over 2006-2012, this paper studies the effect of heterogeneity in MRL regulation on bilateral trade. We find evidence of regulatory heterogeneity diminishing trade at the extensive margin when the exporter faces more stringent regulation abroad, suggesting compliance costs in entering the destination market. Significantly, however, we also find strong evidence of regulatory heterogeneity increasing trade at the intensive margin for exports coming from countries that set the strictest standards, alluding to the positive informative effect of such regulation.

Handling the Problem of Unbalanced Data Sets in the Classification of Technical Equipment States

Questions of handling unbalanced data considered in this article. As models for classification, PNN and MLP are used. Problem of estimation of model performance in case of unbalanced training set is solved. Several methods (clustering approach and boosting approach) considered as useful to deal with the problem of input data.