Correlative microscopy: a powerful tool for exploring neurological cells and tissues

Imaging tools for exploring the neurological samples have seen a rapid transformation over the last decade. Approaches that allow clear and specific delineation of targeted tissues, individual neurons, and their cell–cell connections as well as subcellular constituents have been especially valuable. Considering the significant complexity and extent to which the nervous system interacts with every organ system in the body, one non-trivial challenge has been how to identify and target specific structures and pathologies by microscopy. To this end, correlative methods enable one to view the same exact structure of interest utilizing the capabilities of typically separate, but powerful, microscopy platforms. As such, correlative microscopy is well-positioned to address the three critical problems of identification, scale, and resolution inherent to neurological systems. Furthermore, the application of multiple imaging platforms to the study of singular biological events enables more detailed investigations of structure–function relationships to be conducted, greatly facilitating our understanding of relevant phenomenon. This comprehensive review provides an overview of methods for correlative microscopy, including histochemistry, transgenic markers, immunocytochemistry, photo-oxidation as well as various probes and tracers. An emphasis is placed on correlative light and electron microscopic strategies used to facilitate relocation of neurological structures. Correlative microscopy is an invaluable tool for neurological research, and we fully anticipate developments in automation of the process, and the increasing availability of genomic and transgenic tools will facilitate the adoption of correlative microscopy as the method of choice for many imaging experiments.     

C++QED: an object-oriented framework for wave-function simulations of cavity QED systems

We present a framework for efficiently performing Monte Carlo wave-function simulations in cavity QED with moving particles. It relies heavily on the object-oriented programming paradigm as realised in C++, and is extensible and applicable for simulating open interacting qua ntum dynamics in general. The user is provided with a number of “elements”, e.g. pumped moving particles, pumped lossy cavity modes, and various interactions to compose complex interacting systems, which contain several particles moving in electromagnetic fields of various configurations, and perform wave-function simulations on such systems. A number of tools are provided to facilitate the implementation of new elements.     

Mathematical modeling in biology: A critical assessment

Summary  The molecular revolution and the development of biology-derived industry have led in the last fifty years to an unprecedented “leap forward” of life sciences in terms of experimental data. Less success has been achieved in the organisation of such data and in the consequent development of adequate explanatory and predictive theories and models. After a brief historical excursus inborn difficulties of mathematisation of biological objects and processes derived from the complex dynamics of life are discussed along with the logical tools (simplification, choice of observation points etc.) used to overcome them. “Autistic”, monodisciplinary attitudes towards biological modeling of mathematicians, physicists, biologists aimed in each case at the use of the tools of other disciplines to solve “selfish” problems are also taken into account and a warning against derived dangers (reification of monodisciplinary metaphors, lack of falsification etc.) is given. Finally “top-down” (deductive) and “bottom up” (inductive) heuristic interactive approaches to mathematisation are critically discussed with the help of a serie of examples.     

Knowledge Discovery from Medical Data and Development of an Expert System in Immunology

Artificial intelligence is one of the fastest-developing areas of science that covers a remarkably wide range of problems to be solved. It has found practical application in many areas of human activity, also in medicine. One of the directions of cooperation between computer science and medicine is to assist in diagnosing and proposing treatment methods with the use of IT tools. This study is the result of collaboration with the Children’s Memorial Health Institute in Warsaw, from where a database containing information about patients suffering from Bruton’s disease was made available. This is a rare disorder, difficult to detect in the first months of life. It is estimated that one in 70,000 to 90,000 children will develop Bruton’s disease. But even these few cases need detailed attention from doctors. Based on the data contained in the database, data mining was performed. During this process, knowledge was discovered that was presented in a way that is understandable to the user, in the form of decision trees. The best models obtained were used for the implementation of expert systems. Based on the data introduced by the user, the system conducts expertise and determines the severity of the course of the disease or the severity of the mutation. The CLIPS language was used for developing the expert system. Then, using this language, software was developed producing six expert systems. In the next step, experimental verification was performed, which confirmed the correctness of the developed systems.     

LSDA+U方法对富勒烯内掺稀土原子的结构和电子结构的理论研究

在密度泛函理论框架下的局域密度近似方法 (LDA)能够准确地给出广延态电子体系的基态电子结构 ,是研究复杂体系的电子结构的一种非常成功的方法。由于这种方法不含参数 ,被广泛地用于微观体系的研究。但是 ,在处理的体系中含有局域电子时 ,由于方法的局限 ,给出的结果与光电子谱等试验结果符合得并不好。LSDA U方法是在局域自旋密度近似的框架下 ,结合模型哈密顿方法 ,对局域电子采用哈伯德模型描述 ,用以改进局域密度近似计算的一种方法。本文利用局域密度近似下的离散变分团簇方法 (DVM )对于内嵌稀土原子的富勒烯Er2 @C82 、Tm @C82 的电子结构进行了第一性原理的计算。对于体系中所含的稀土原子存在强关联的 4f电子 ,在LDA方法计算的基础上 ,考虑 4f电子在位库仑作用 ,用LSDA U方法研究了上述体系 ,得到了可以和XPS和吸收谱相比较的结果。     

Reducing Cognitive Effort in Scoring Negotiation Space Using the Fuzzy Clustering Model

Negotiation scoring systems are fundamental tools used in negotiation support to facilitate parties searching for negotiation agreement and analyzing its efficiency and fairness. Such a scoring system is obtained in prenegotiation by implementing selected multiple criteria decision-aiding methods to elicit the negotiator’s preferences precisely and ensure that the support is reliable. However, the methods classically used in the preference elicitation require much cognitive effort from the negotiators, and hence, do not prevent them from using heuristics and making simple errors that result in inaccurate scoring systems. This paper aims to develop an alternative tool that allows scoring the negotiation offers by implementing a sorting approach and the reference set of limiting profiles defined individually by the negotiators in the form of complete packages. These limiting profiles are evaluated holistically and verbally by the negotiator. Then the fuzzy decision model is built that uses the notion of increasing the preference granularity by introducing a series of limiting sub-profiles for corresponding sub-categories of offers. This process is performed automatically by the support algorithm and does not require any additional preferential information from the negotiator. A new method of generating reference fuzzy scores to allow a detailed assignment of any negotiation offer from feasible negotiation space to clusters and sub-clusters is proposed. Finally, the efficient frontier and Nash’s fair division are used to identify the recommended packages for negotiation in the bargaining phase. This new approach allows negotiators to obtain economically efficient, fair, balanced, and reciprocated agreements while minimizing information needs and effort.     

Phase diagram of a Schelling segregation model

The collective behavior in a variant of Schelling’s segregation model is characterized with methods borrowed from statistical physics, in a context where their relevance was not conspicuous. A measure of segregation based on cluster geometry is defined and several quantities analogous to those used to describe physical lattice models at equilibrium are introduced. This physical approach allows to distinguish quantitatively several regimes and to characterize the transitions between them, leading to the building of a phase diagram. Some of the transitions evoke empirical sudden ethnic turnovers. We also establish links with ‘spin-1’ models in physics. Our approach provides generic tools to analyze the dynamics of other socio-economic systems.     

Functionalized single-walled carbon nanotubes interacting with glycine amino acid: DFT study

We have investigated the adsorption of glycine on carbon nanotubes (CNTs) functionalized by various functional groups using density functional theory calculations. Compared with the pristine CNTs, the functionalized CNTs system has significantly higher binding energy value and shorter distance between the glycine and the nanotube surface. The calculations of electronic structures and charge Mulliken population indicate a strong physisorption process for the glycine adsorption on the functionalized CNTs. Therefore, functionalized CNT is expected to be a novel material for designing life science-related tools employing biological systems.     

Dynamics of Coordinate Ascent Variational Inference: A Case Study in 2D Ising Models

Variational algorithms have gained prominence over the past two decades as a scalable computational environment for Bayesian inference. In this article, we explore tools from the dynamical systems literature to study the convergence of coordinate ascent algorithms for mean field variational inference. Focusing on the Ising model defined on two nodes, we fully characterize the dynamics of the sequential coordinate ascent algorithm and its parallel version. We observe that in the regime where the objective function is convex, both the algorithms are stable and exhibit convergence to the unique fixed point. Our analyses reveal interesting discordances between these two versions of the algorithm in the region when the objective function is non-convex. In fact, the parallel version exhibits a periodic oscillatory behavior which is absent in the sequential version. Drawing intuition from the Markov chain Monte Carlo literature, we empirically show that a parameter expansion of the Ising model, popularly called the Edward–Sokal coupling, leads to an enlargement of the regime of convergence to the global optima.     

Construction and solution of a Wannier-functions based Hamiltonian in the pseudopotential plane-wave framework for strongly correlated materials

Ab initio determination of model Hamiltonian parameters for strongly correlated materials is a key issue in applying many-particle theoretical tools to real narrow-band materials. We propose a selfcontained calculation scheme to construct, with an ab initio approach, and solve such a Hamiltonian. The scheme uses a Wannier-function-basis set, with the Coulomb interaction parameter U obtained specifically for theseWannier functions via constrained Density functional theory (DFT) calculations. The Hamiltonian is solved by Dynamical Mean-Field Theory (DMFT) with the effective impurity problem treated by the Quantum Monte Carlo (QMC) method. Our scheme is based on the pseudopotential plane-wave method, which makes it suitable for developments addressing the challenging problem of crystal structural relaxations and transformations due to correlation effects. We have applied our scheme to the “charge transfer insulator” material nickel oxide and demonstrate a good agreement with the experimental photoemission spectra.     

Toy models and stylized realities

I discuss the role of toy models as theoretical tools for understanding complex systems of interacting agents. I review some concrete examples, in order to illustrate how this approach is able to capture, though in an admittedly stylized way, the interactions and non-linearities which are responsible for the rich phenomenology observed in reality. This allows one to interpret the system's behavior in terms of phase transitions and critical phenomena.     

On the interplay between mathematics and biology: Hallmarks toward a new systems biology

This paper proposes a critical analysis of the existing literature on mathematical tools developed toward systems biology approaches and, out of this overview, develops a new approach whose main features can be briefly summarized as follows: derivation of mathematical structures suitable to capture the complexity of biological, hence living, systems, modeling, by appropriate mathematical tools, Darwinian type dynamics, namely mutations followed by selection and evolution. Moreover, multiscale methods to move from genes to cells, and from cells to tissue are analyzed in view of a new systems biology approach.     

Instruments of scientific visual representation in atomic databases

Graphic tools of spectral data representation provided by operating information systems on atomic spectroscopy—ASD NIST, VAMDC, SPECTR-W3, and Electronic Structure of Atoms—for the support of scientific-research and human-resource development are presented. Such tools of visual representation of scientific data as those of the spectrogram and Grotrian diagram plotting are considered. The possibility of comparative analysis of the experimentally obtained spectra and reference spectra of atomic systems formed according to the database of a resource is described. The access techniques to the mentioned graphic tools are presented.     

Kaonic nuclear systems KN and KNN as decaying states

The formation spectra of model KN and KNN systems formed by (K(-),n) reactions are investigated in order to obtain a theoretical basis for a proper interpretation of experimental data concerning kaonic nuclear quasi-bound states. It has been clarified that the experimentally observable kaonic nuclear state K(-)pp should be regarded as the decaying state introduced by Kapur-Peierls, which is different from the pole state solution of the Faddeev equation.     

Determination of NMR cogwheel phase cycle with XML

The selection of correct coherence transfer pathways is an essential component of an NMR pulse sequence. This article describes a new method based on the use of web tools (eXtensible Markup Language and eXtensible Stylesheet Language Transformation) to generate a cogwheel phase cycle for selecting coherence transfer pathways. We illustrate this method with the three-pulse phase-modulated shifted-echo or split-t₁ MQMAS sequences for triple-quantum spin-3/2 systems. After generalization to the different half-integer quadrupole spins, we use the SIMPSON program to confirm our results. Finally, we apply our method to the case of the z-filter 3QMAS sequence for I=3/2 systems.     

TiN/SiO2纳米多层膜的晶体生长与超硬效应

高硬度的含氧化物纳米多层膜在工具涂层上具有重要的应用价值.研究了TiN/SiO2_{2纳米多 层膜的晶体生长特征和超硬效应.一系列具有不同SiO22和TiN调制层厚的纳米多 层膜采用多 靶磁控溅射法制备；采用x射线衍射、x射线能量色散谱、高分辨电子显微镜和微力学探针表 征了多层膜的微结构和力学性能.结果表明，虽然以单层膜形式存在的TiN和SiO22分别形成 纳米晶和非晶结构，它们组成多层膜时会因晶体生长的互促效应而呈现共格外延生长的结构 特 关键词： 2纳米多层膜')" href="#">TiN/SiO22纳米多层膜 外延生长 非晶晶化 超硬效应}     

Entropic stochastic resonance: the constructive role of the unevenness

We demonstrate the existence of stochastic resonance (SR) in confined systems arising from entropy variations associated to the presence of irregular boundaries. When the motion of a Brownian particle is constrained to a region with uneven boundaries, the presence of a periodic input may give rise to a peak in the spectral amplification factor and therefore to the appearance of the SR phenomenon. We have proved that the amplification factor depends on the shape of the region through which the particle moves and that by adjusting its characteristic geometric parameters one may optimize the response of the system. The situation in which the appearance of such entropic stochastic resonance (ESR) occurs is common for small-scale systems in which confinement and noise play an prominent role. The novel mechanism found could thus constitute an important tool for the characterization of these systems and can put to use for controlling their basic properties.     

Investigations of the electron paramagnetic resonance parameters and the tetragonal local structure for (VCl6)4- coordination complex in MCl:V2+ (M=Na, K, Rb) systems

By simulating the electron paramagnetic resonance (EPR) and optical spectra on the basis of the 120×120 complete energy matrix, this paper determines the local lattice structure parameters R1 and R2 for MCl:V2+ (M=Na, K, Rb) systems at 77 K, 195 K and RT (room temperature 295 K or 302 K), respectively. The theoretical results indicate that there exists a compressed distortion in MCl:V2+ systems. Meanwhile, it finds that the structure parameters R1, R2 and |△R| (= R1-R2) increase with the rising temperature. Subsequently, from the analysis it concludes that the relation of EPR parameter D vs.△R is approximately linear. Finally, the effects of orbital reduction factor k on the g factors for the three systems have been discussed.     

插层化合物LixTiS2中Li离子-空位二维有序结构稳定性的第一性原理研究

根据局域密度近似下的密度泛函理论，用第一性原理方法对TiS₂，LiTiS₂和Li_xTiS₂(x=1/4, 1/3, 1/2, 2/3, 3/4)有序系统进行了几何优化和总能量计算.将计算结果与已有的实验和理论结果进行了对比，得到的归一化结构参量增量Δa₀和Δc₀随离子浓度单调地增加，与实验结果符合较好.Li_{关键词： x}TiS₂')" href="#">Li_xTiS₂ 有序结构 第一性原理计算 密度泛函理论     

<ξ1 Representation of the Inverse of Two-Particle Relative Posit ion and Its Application

We derive the <ξ| representation of the inverse of two particles' relative position which turns out to be an integration operation on the representation and is related to two particles' masses. The representation is useful in conveniently solving energy level formula for some dynamic systems.