Destabilization and stabilization of proteins

In Part I the history of progress in the stabilization and destabilization of protein conformations by means of cosolvents is outlined in terms of distinct conceptual steps. In Part II it is shown that a straightforward application of the Kirkwood-Buff theory of solutions leads to formulas for the preferential interaction and the free energy of unfolding, which confirm and generalize the results of Part I.     

Development of a variational scheme for model inversion of multi-area model of brain. Part I: simulation evaluation

We previously developed an integrated model of the brain within a single cortical area for functional Magnetic Resonance Imaging (fMRI), electroencephalography (EEG), and magnetoencephalography (MEG) using an extended neural mass model (ENMM). We then extended ENMM from a single-area to a multi-area model to develop a neural mass model of the entire brain. To this end, we derived a nonlinear state-space representation of the multi-area model. In Parts I and II of these two companion papers (henceforth called Part I and Part II), we develop and evaluate a variational Bayesian expectation maximization (VBEM) method to estimate parameters of multi-area ENMM (MEN) using E/MEG data. In Part I, we derive a state-space representation of MEN and use VBEM method for model inversion (parameter estimation). We evaluate and validate performance of VBEM method for model inversion of MEN using simulation studies in various signal-to-noise ratios. Details of VBEM method are presented in Part II. The proposed approach provides a useful technique for analyzing effective connectivity using non-invasive EEG and MEG methods.     

设施黄瓜育成品种果实外观品质的遗传多样性分析

对我国新育成的不同生态类型的138个设施黄瓜品种的19个果实外观性状进行了调查分析,研究其遗传多样性。结果表明,参试品种质量性状的遗传多样性指数都小于数量性状,不同生态类型黄瓜品种果实外观性状的遗传多样性指数为华北型(1.33)>华南型(1.25)>欧洲温室型(1.0)。质量性状的遗传多样性指数为华南型(0.91)>华北型(0.65)>欧洲温室型(0.48);数量性状的遗传多样性指数为华北型(1.94)>华南型(1.56)>欧洲温室型(1.47)。华南型品种果实数量性状的变异系数均高于华北型和欧洲温室型品种。主坐标轴分析(PCO)将所有种质划分为3个区组,即1区为华北型种质优势区、2区为华北型华南型和欧洲温室型种质混合分布区、3区为华南型种质区。PCO结果表明,1区和2区发生了基因渗透。对交流区域中华北型品种自交分离,后代中出现的稀刺瘤和光皮种质的情况进一步验证了基因渗透的结果。参照育成品种的果实性状信息对黄瓜以后的育种工作提出了建议。     

Development of a variational scheme for model inversion of multi-area model of brain. Part II: VBEM method

In Part I and Part II of these two companion papers (henceforth called Part I and Part II), we develop and evaluate a variational Bayesian expectation maximization (VBEM) method for model inversion of our multi-area extended neural mass model (MEN). In this paper, we develop the VBEM method to estimate posterior distributions of parameters of MEN. We choose suitable prior distributions for the model parameters in order to use properties of a conjugate-exponential model in implementing VBEM. Consequently, VBEM leads to analytically tractable forms. The proposed VBEM algorithm starts with initialization and consists of repeated iterations of a variational Bayesian expectation step (VB E-step) and a variational Bayesian maximization step (VB M-step). Posterior distributions of the model parameters are updated in the VB M-step. Distribution of the hidden state is updated in the VB E-step. We develop a variational extended Kalman smoother (VEKS) to infer the distribution of the hidden state in the VB E-step and derive the forward and backward passes of VEKS, analogous to the Kalman smoother. In Part I, we evaluate and validate the VBEM method using simulation studies.     

Uncertainty in life cycle costing for long-range infrastructure. Part II: guidance and suitability of applied methods to address uncertainty

Life cycle costing (LCC) is the state-of-the-art method to economically evaluate long-term projects over their life spans. However, uncertainty in long-range planning raises concerns about LCC results. In Part I of this series, we developed a holistic framework of the different types of uncertainty in infrastructure LCCs. We also collected methods to address these uncertainties. The aim of Part II is to evaluate the suitability of methods to cope with uncertainty in LCC. Part I addressed two research gaps. It presented a systematic collection of uncertainties and methods in LCC and, furthermore, provided a holistic categorization of both. However, Part I also raised new issues. First, a combined analysis of sources and methods is still outstanding. Such an investigation would reveal the suitability of different methods to address a certain type of uncertainty. Second, what has not been assessed so far is what types of uncertainty are insufficiently addressed in LCC. This would be a feature to improve accuracy of LCC results within LCC, by suggesting options to better cope with uncertainty. To address these research gaps, we conducted a systematic literature review. Part II analyzed the suitability of methods to address uncertainties. The suitability depends on data availability, type of data (tangible, intangible, random, non-random), screened hotspots, and tested modeling specifications. We identified types of uncertainties and methods that have been insufficiently addressed. The methods include probabilistic modeling such as design of experiment or subset simulation and evolutionary algorithm and Bayesian modeling such as the Bayesian latent Markov decision process. Subsequently, we evaluated learning potential from other life cycle assessment (LCA) and life cycle sustainability assessment (LCSA). This analysis revealed 28 possible applications that have not yet been used in LCC. Lastly, we developed best practices for LCC practitioners. This systematic review complements prior research on uncertainty in LCC for infrastructure, as laid out in Part I. Part II concludes that all relevant methods to address uncertainty are currently applied in LCC. Yet, the level of application is different. Moreover, not all methods are equally suited to address different categories of uncertainty. This review offers guidance on what to do for each source and type of uncertainty. It illustrates how methods can address both based on current practice in LCC, LCA, and LCSA. The findings of Part II encourage a dialog between practitioners of LCC, LCA, and LCSA to advance research and practice in uncertainty analysis.     

An “Ethnic” Arboretum

Part I of this three-part series deals generally with sound and its pollution. Part II will move on to measurement, effects, and indoor learning activities. Outdoor activities and references will make up Part III.     

MEDICAL PROGRESS: ISOTOPES IN CLINICAL AND EXPERIMENTAL MEDICINE (Part I)

This is Part I of an article in two parts. Part II, Important Applications of Isotopes in Experimental Medicine, will appear in the August issue.     

MEDICAL PROGRESS: ISOTOPES IN CLINICAL AND EXPERIMENTAL MEDICINE

This is Part II of an article in two parts. Part I appeared in the July issue of California Medicine, and with it were the list of references for the entire article and the Table 1 referred to in the following text.     

A glossary of plant hair terminology

This is a compilation of English terms having to do with hairs and hairy surfaces of plants. The glossary is divided into two sections. Part I includes terms for types and attributes of individual hair kinds and hair clusters. Part II deals with kinds and characteristics of induments.     

Cannabidiol: an overview of some chemical and pharmacological aspects. Part I: chemical aspects

Over the last few years considerable attention has focused on cannabidiol (CBD), a major non-psychotropic constituent of Cannabis. In Part I of this review we present a condensed survey of the chemistry of CBD; in Part II, to be published later, we shall discuss the anti-convulsive, anti-anxiety, anti-psychotic, anti-nausea and anti-rheumatoid arthritic properties of CBD. CBD does not bind to the known cannabinoid receptors and its mechanism of action is yet unknown. In Part II we shall also present evidence that it is conceivable that, in part at least, its effects are due to its recently discovered inhibition of anandamide uptake and hydrolysis and to its anti-oxidative effect.     

The Structure of Ellipsoidal Distributions I. Canonical Analysis

This study is concerned with the structure of variables having ellipsoidal distributions. In Part I it is shown that many normal-theory results in canonical analysis are exact for all ellipsoidal distributions under a specified model for sampling. In Part II similar conclusions are drawn regarding the use of principal components. These findings suggest using normal-theory procedures in canonical and principal components analyses as approximate large-sample procedures for distributions attracted to ellipsoidal stable laws.     

The theory and practice of psychological medicine in the Ayurvedic tradition

In this paper I attempt to elucidate and render intelligible to a non-Western reader the internal logic and the consistency in both theory and practice of Ayurvedic psychological medicine. In Part 1, I deal with the classical metaphysical base (Sämkya philosophy) on which the Ayurvedic concept of mind rests. I also deal with the theory of psychological medicine as stated in ancient Sanskrit texts. In Part II, I deal with the manner in which the classic theory is implemented in contemporary practice in Sri Lanka, while Part III deals with case studies of two patients taking Ayurvedic therapy.     

Analysis of genetic data on Jewish populations. I. Historical background, demographic features, and genetic markers.

Part I describes the data sets on which the analysis of Part II is based. This covers the nature of the populations sampled, the extent to which the samples are representative, and a brief review of historical and demographic facts on the populations involved.     

Homologous comparisons of photosynthetic system I genes among cyanobacteria and chloroplasts

It has now believed that chloroplasts arose from cyanobacteria, however, during endosymbiosis, the photosynthetic genes in chloroplasts have been reduced. How these changes occurred during plant evolution was the focus of the present study. Beginning with photosystem I (PSI) genes, a homologous comparison of amino acid sequences of 18 subunits of PSI from 10 species of cyanobacteria, chloroplasts in 12 species of eucaryotic algae, and 28 species of plants (including bryophytes, pteridophytes, gymnospermae, dicotyledon and monocotyledon) was undertaken. The data showed that 18 genes of PSI can be divided into two groups: Part I including seven genes ( psaA , psaB , psaC , psaI , psaJ , ycf3 and ycf4 ) shared both by cyanobacteria and plant chloroplasts; Part II containing another 11 genes ( psaD , psaE , psaF , psaK , psaL , psaM , btpA , ycf3 7, psaG , psaH and psaN ) appeared to have diversified in different plant groups. Among Part I genes, psaC , psaA and psaB had higher homology in all species of cyanobacteria and chloroplasts. Among Part II genes, only psaG , psaH and psaN emerged in seed plants.     

A review of the enforcement regime for vessel‐source oil pollution control

Abstract

The purpose of this article is to identify the currently applicable international law intended to regulate vessel‐source pollution. Part I delineates the elements relevant for this study. Part II discusses the development of a sequence of incremental conventions. Part III examines the significance and weaknesses of the 1973 MARPOL Convention with its 1978 Protocol and of the 1982 UN. Convention on the Law of the Sea. Part IV explores alternative and/or supplementary legal approaches for handling the vessel‐source oil pollution threat.     

Inductive Capacities for the Dorsal Mesoderm of the Dorsal Marginal Zone and Pharyngeal Endoderm in the Very Early Gastrula of the Newt,and Presumptive Pharyngeal Endoderm as an Initiator of the Organization Center*

The organization center of Cynops pyrrhogaster was divided into Parts 1, 2 and 3 of equal size (0.3×0.4 mm²) with presumptive fates as pharyngeal, pharyngeal+prechordal+trunk notochord, and trunk-tail notochord, respectively. Movements and changes in size and shape of each part were followed through gastrulation. Differentiation tendencies of each part were examined under three conditions: I, isolated; II, sandwiched with presumptive ectoderm; 111, sandwiched with presumptive ectoderm after preculture in isolation for various times. In I, Parts 2 and 3 differentiated into dorsal mesoderm. In II, each part induced dorsal mesoderm and neural tissues, the frequency being highest in Part 2 and lowest in Part 3. In III, Parts 1 and 2 realized their presumptive fates, through changes in inductive capacities from trunk-tail to head. This change progressed rapidly in Part 1, and slowly in Part 2. Part 3 required induction by neighbouring Part 2 to realize its presumptive fate. Changes of inductive capacity of Parts 1 and 2 respectively, were chronologically similar in normal development and in preculture experiments. Lastly, the primary presumptive pharyngeal zone at blastula was proposed to act as an initiator of the organization center, its programmed information being transmitted to Part 2, and then to Part 3.     

Human behavioral ecology: II

Human behavioral ecology is an interdisciplinary field of study applying theory from evolutionary ecology to a variety of anthropological questions. In Part I of this essay,¹ which appeared in an earlier issue, I surveyed key theoretical and methodological elements of the field, and summarized representative studies and issues in the topical area of subsistence strategies. In Part II, I turn to studies of reproductive strategies, and those analyzing patterns of cooperation and competition in an ecological and adaptive framework. I conclude with a brief look at possible future developments in the field.     

Gating mechanisms of mechanosensitive channels of large conductance, II: systematic study of conformational transitions

Part II of this study is based on the continuum mechanics-based molecular dynamics-decorated finite element method (MDeFEM) framework established in Part I. In Part II, the gating pathways of Escherichia coli-MscL channels under various basic deformation modes are simulated. Upon equibiaxial tension (which is verified to be the most effective mode for gating), the MDeFEM results agree well with both experiments and all-atom simulations in literature, as well as the analytical continuum models and elastic network models developed in Part I. Different levels of model sophistication and effects of structural motifs are explored in detail, where the importance of mechanical roles of transmembrane helices, cytoplasmic helices, and loops are discussed. The conformation transitions under complex membrane deformations are predicted, including bending, torsion, cooperativity, patch clamp, and indentation. Compared to atom-based molecular dynamics simulations and elastic network models, the MDeFEM framework is unusually well-suited for simulating complex deformations at large length scales. The versatile hierarchical framework can be further applied to simulate the gating transition of other mechanosensitive channels and other biological processes where mechanical perturbation is important.     

From analysis to synthesis: new ligand binding sites on the lactate dehydrogenase framework. Part I

In Part I of this article, the naturally evolved protein framework of lactate dehydrogenase is investigated by genetically introduced modifications which reveal the structural basis of its catalytic and substrate-binding properties. In Part II (to be published in the April issue of TIBS), this analytical information is exploited in the design of two modified forms of the enzyme; one which is specific for a new substrate and one which lacks allosteric regulation.     

Altruism and mental disorders

Data suggest that the theories of kin selection and reciprocal altruism are viable working models to explain altruistic behavior. It remains to be demonstrated if these models can explain the behavior of persons with mentaL disorders for whom altruistic behavior is reported to be reduced. This paper addresses this issue. Part I reviews proximate factors that are thought to influence both altruistic decision making and interindividual variation in altruistic behavior. The focus is on trait signaling by potential beneficiaries and the evaluation of signals and altruistic decision making by potential altruists. In Part II, points developed in Part I are combined with clinical and empirical findings to analyze data on personality disorders and dysthymic disorder. The analysis leads to three causal hypotheses: Reduced altruistic behavior may be an evolved strategy, a consequence of dysfunctional recognition systems or algorithms, and/or a secondary response to an increase in symptoms. Different disorders and features of disorders are explained by each hypothesis.