University of Gdańsk

All our former experience with application of quantum theory seems to say that what is predicted by quantum formalism must occur in the laboratory. But the essence of quantum formalism---entanglement, recognized by Einstein, Podolsky, Rosen, and Schr\"odinger---waited over $70\phantom{\rule{0.3em}{0ex}}\text{years}$ to enter laboratories as a new resource as real as energy. This holistic property of compound quantum systems, which involves nonclassical correlations between subsystems, has potential for many quantum processes, including canonical ones: quantum cryptography, quantum teleportation, and dense coding. However, it appears that this new resource is complex and difficult to detect. Although it is usually fragile to the environment, it is robust against conceptual and mathematical tools, the task of which is to decipher its rich structure. This article reviews basic aspects of entanglement including its characterization, detection, distillation, and quantification. In particular, various manifestations of entanglement via Bell inequalities, entropic inequalities, entanglement witnesses, and quantum cryptography are discussed, and some interrelations are pointed out. The basic role of entanglement in quantum communication within a distant laboratory paradigm is stressed, and some peculiarities such as the irreversibility of entanglement manipulations are also discussed including its extremal form---the bound entanglement phenomenon. The basic role of entanglement witnesses in detection of entanglement is emphasized.

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are 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 multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

We provide necessary and sufficient conditions for the separability of mixed states. As a result we obtain a simple criterion of the separability for 2 x 2 and 2 x 3 systems. Here, the positivity of the partial transposition of a state is necessary and sufficient for its separability. However, this is not the case in general. Some examples of mixtures which demonstrate the utility of the criterion are considered.

Using independent sources one can realize an ``event-ready'' Bell--Einstein-Podolsky-Rosen experiment in which one can measure directly the probabilities of the various outcomes including nondetection of both particles. Our proposal involves two parametric down-converters. Subcoherence-time monitoring of the idlers provides a noninteractive quantum measurement entangling and preselecting the independent signals without touching them. We give the conditions for high fringe visibility and particle collection efficiency as required for a Bell test.

Multiphoton interference reveals strictly nonclassical phenomena. Its applications range from fundamental tests of quantum mechanics to photonic quantum information processing, where a significant fraction of key experiments achieved so far comes from multiphoton state manipulation. The progress, both theoretical and experimental, of this rapidly advancing research is reviewed. The emphasis is given to the creation of photonic entanglement of various forms, tests of the completeness of quantum mechanics (in particular, violations of local realism), quantum information protocols for quantum communication (e.g., quantum teleportation, entanglement purification, and quantum repeater), and quantum computation with linear optics. The scope of the review is limited to ``few-photon'' phenomena involving measurements of discrete observables.

It is shown that if a mixed state can be distilled to the singlet form it must violate partial transposition criterion [A. Peres, Phys. Rev. Lett. 76, 1413 (1996)]. It implies that there are two qualitatively different types of entanglement: ``free'' entanglement which is distillable, and ``bound'' entanglement which cannot be brought to the singlet form useful for quantum communication purposes. A possible physical meaning of the result is discussed.

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds.

Amyloid beta peptide (Abeta), the principal proteinaceous component of amyloid plaques in brains of Alzheimer's disease patients, is derived by proteolytic cleavage of the amyloid precursor protein (APP). Proteolytic cleavage of APP by a putative alpha-secretase within the Abeta sequence precludes the formation of the amyloidogenic peptides and leads to the release of soluble APPsalpha into the medium. By overexpression of a disintegrin and metalloprotease (ADAM), classified as ADAM 10, in HEK 293 cells, basal and protein kinase C-stimulated alpha-secretase activity was increased severalfold. The proteolytically activated form of ADAM 10 was localized by cell surface biotinylation in the plasma membrane, but the majority of the proenzyme was found in the Golgi. These results support the view that APP is cleaved both at the cell surface and along the secretory pathway. Endogenous alpha-secretase activity was inhibited by a dominant negative form of ADAM 10 with a point mutation in the zinc binding site. Studies with purified ADAM 10 and Abeta fragments confirm the correct alpha-secretase cleavage site and demonstrate a dependence on the substrate's conformation. Our results provide evidence that ADAM 10 has alpha-secretase activity and many properties expected for the proteolytic processing of APP. Increases of its expression and activity might be beneficial for the treatment of Alzheimer's disease.

We prove a theorem on direct relation between the optimal fidelity ${f}_{\mathrm{max}}$ of teleportation and the maximal singlet fraction ${F}_{\mathrm{max}}$ attainable by means of trace-preserving local quantum and classical communication (LQCC) action. For a given bipartite state acting on ${C}^{d}\ensuremath{\bigotimes}{C}^{d}$ we have ${f}_{\mathrm{max}}{=(F}_{\mathrm{max}}d+1)/(d+1)$. We assume completely general teleportation scheme (trace preserving LQCC action over the pair and the third particle in unknown state). The proof involves the isomorphism between quantum channels and a class of bipartite states. We also exploit the technique of $U\ensuremath{\bigotimes}{U}^{*}$ twirling states (random application of unitary transformation of the above form) and the introduced analogous twirling of channels. We illustrate the power of the theorem by showing that any bound entangled state does not provide better fidelity of teleportation than for the purely classical channel. Subsequently, we apply our tools to the problem of the so-called conclusive teleportation, then reduced to the question of optimal conclusive increasing of singlet fraction. We provide an example of state for which Alice and Bob have no chance to obtain perfect singlet by LQCC action, but still singlet fraction arbitrarily close to unity can be obtained with nonzero probability. We show that a slight modification of the state has a threshold for singlet fraction, which cannot be exceeded anymore.

Here, palaeobotanical and genetic data for common beech (Fagus sylvatica) in Europe are used to evaluate the genetic consequences of long-term survival in refuge areas and postglacial spread. Four large datasets are presented, including over 400 fossil-pollen sites, 80 plant-macrofossil sites, and 450 and 600 modern beech populations for chloroplast and nuclear markers, respectively. The largely complementary palaeobotanical and genetic data indicate that: (i) beech survived the last glacial period in multiple refuge areas; (ii) the central European refugia were separated from the Mediterranean refugia; (iii) the Mediterranean refuges did not contribute to the colonization of central and northern Europe; (iv) some populations expanded considerably during the postglacial period, while others experienced only a limited expansion; (v) the mountain chains were not geographical barriers for beech but rather facilitated its diffusion; and (vi) the modern genetic diversity was shaped over multiple glacial-interglacial cycles. This scenario differs from many recent treatments of tree phylogeography in Europe that largely focus on the last ice age and the postglacial period to interpret genetic structure and argue that the southern peninsulas (Iberian, Italian and Balkan) were the main source areas for trees in central and northern Europe.

We analyze the problem of distillation of entanglement of mixed states in higher-dimensional compound systems. Employing the positive maps method [M. Horodecki et al., Phys. Lett. A 223, 1 (1996)] we introduce and analyze a criterion of separability that relates the structures of the total density matrix and its reductions. We show that any state violating the criterion can be distilled by suitable generalization of the two-qubit protocol that distills any inseparable two-qubit state. In particular, this means that any state $\ensuremath{\varrho}$ of two N-level systems with $〈{\ensuremath{\psi}}_{+}|\ensuremath{\varrho}|{\ensuremath{\psi}}_{+}〉>1/N$ can be distilled $({\ensuremath{\psi}}_{+}$ is the singlet state generalized to higher dimension). The criterion also singles out all the states that can be distilled by a class of protocols. The proof involves construction of the family of states that are invariant under transformation $\stackrel{\ensuremath{\rightarrow}}{\ensuremath{\varrho}}U\ensuremath{\bigotimes}{U}^{*}\ensuremath{\varrho}{U}^{\ifmmode\dagger\else\textdagger\fi{}}\ensuremath{\bigotimes}{U}^{*\ifmmode\dagger\else\textdagger\fi{}},$ where U is a unitary transformation and the asterisk denotes complex conjugation. The states are related to the depolarizing channel generalized to the nonbinary case.

DAPI (4',6-diamidino-2-phenylindole) is a DNA-specific probe which forms a fluorescent complex by attaching in the minor grove of A-T rich sequences of DNA. It also forms nonfluorescent intercalative complexes with double-stranded nucleic acids. The physicochemical properties of the dye and its complexes with nucleic acids and history of the development of this dye as a biological stain are described. The application of DAPI as a DNA-specific probe for flow cytometry, chromosome staining, DNA visualization and quantitation in histochemistry and biochemistry is reviewed. The mechanisms of DAPI-nucleic acid complex formation including minor groove binding, intercalation and condensation are discussed.

The products of the Escherichia coli dnaK, dnaJ, and grpE heat shock genes have been previously shown to be essential for bacteriophage lambda DNA replication at all temperatures and for bacterial survival under certain conditions. DnaK, the bacterial heat shock protein hsp70 analogue and putative chaperonin, possesses a weak ATPase activity. Previous work has shown that ATP hydrolysis allows the release of various polypeptides complexed with DnaK. Here we demonstrate that the ATPase activity of DnaK can be greatly stimulated, up to 50-fold, in the simultaneous presence of the DnaJ and GrpE heat shock proteins. The presence of either DnaJ or GrpE alone results in a slight stimulation of the ATPase activity of DnaK. The action of the DnaJ and GrpE proteins may be sequential, since the presence of DnaJ alone leads to an acceleration in the rate of hydrolysis of the DnaK-bound ATP. The presence of GrpE alone increases the rate of release of bound ATP or ADP without affecting the rate of hydrolysis. The stimulation of the ATPase activity of DnaK may contribute to its more efficient recycling, and it helps explain why mutations in dnaK, dnaJ, or grpE genes often exhibit similar pleiotropic phenotypes.

In order to eliminate ratcheting a so-called intergranular strain has been added to a hypoplastic constitutive model. This additional state variable represents the deformation of the interface layer between the grains. The new concept is outlined and comparisons with and without intergranular strain are presented. Some comments on numerical implementation and determination of material constants are made. A discussion on the uniqueness of the solution and objectivity of the rate of intergranular strain is added. © 1997 John Wiley & Sons, Ltd.

Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

Based on the notion that approach-avoidance underlies impression formation processes and that approach-avoidance is more directly based on appraisals of others' morality (M) than competence (C), we hypothesized that M-related information played a more important role at various phases of global impression formation than C-related information on target persons. In four studies (N = 342 university students), we predicted and found that (a) M traits showed a higher chronic accessibility than C traits; (b) when gathering information to formulate a global impression, perceivers were more interested in M traits than C traits; (c) global impressions of real persons were better predicted from M trait ascriptions than C trait ascriptions, and (d) positivity-negativity of impressions of fictitious persons was decided mainly by the M content of their behavior, whereas C information served as a weak modifier of impression intensity. The dominance of M traits over C traits was more pronounced for female perceivers than for male perceivers.

The quantum open system weakly coupled to thermal reservoirs at different temperatures and under the influence of slowly varying external conditions is studied. The famous Carnot inequality for the efficiency of any heat engine is obtained.

During the last five years, several methods have been proposed for handling nonlinear constraints using evolutionary algorithms (EAs) for numerical optimization problems. Recent survey papers classify these methods into four categories: preservation of feasibility, penalty functions, searching for feasibility, and other hybrids. In this paper we investigate a new approach for solving constrained numerical optimization problems which incorporates a homomorphous mapping between n-dimensional cube and a feasible search space. This approach constitutes an example of the fifth decoder-based category of constraint handling techniques. We demonstrate the power of this new approach on several test cases and discuss its further potential.

The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies.