Dynamical principles in biological processes: A model of charge migration in proteins and DNA

The generalized master equations (GMEs) that contain multiple time scales have been derived quantum mechanically. The GME method has then been applied to a model of charge migration in proteins that invokes the hole hopping between local amino acid sites driven by the torsional motions of the floppy backbones. This model is then applied to analyze the experimental results for sequence-dependent long-range hole transport in DNA reported by Meggers et al. [Meggers, E., Michel-Beyerle, M. E., & Giese, B. (1998) J. Am. Chem. Soc. 120, 12950–12955]. The model has also been applied to analyze the experimental results of femtosecond dynamics of DNA-mediated electron transfer reported by Zewail and co-workers [Wan, C., Fiebig, T., Kelley, S. O., Treadway, C. R., Barton, J. K. & Zewail, A. H. (1999) Proc. Natl. Acad. Sci. USA 96, 6014–6019]. The initial events in the dynamics of protein folding have begun to attract attention. The GME obtained in this paper will be applicable to this problem.

Midbrain injection of recombinant adeno-associated virus encoding rat glial cell line-derived neurotrophic factor protects nigral neurons in a progressive 6-hydroxydopamine-induced degeneration model of Parkinson’s disease in rats

A recombinant adeno-associated virus (rAAV) vector capable of infecting cells and expressing rat glial cell line-derived neurotrophic factor (rGDNF), a putative central nervous system dopaminergic survival factor, under the control of a potent cytomegalovirus (CMV) immediate/early promoter (AAV-MD-rGDNF) was constructed. Two experiments were performed to evaluate the time course of expression of rAAV-mediated GDNF protein expression and to test the vector in an animal model of Parkinson’s disease. To evaluate the ability of rAAV-rGDNF to protect nigral dopaminergic neurons in the progressive Sauer and Oertel 6-hydroxydopamine (6-OHDA) lesion model, rats received perinigral injections of either rAAV-rGDNF virus or rAAV-lacZ control virus 3 weeks prior to a striatal 6-OHDA lesion and were sacrificed 4 weeks after 6-OHDA. Cell counts of back-labeled fluorogold-positive neurons in the substantia nigra revealed that rAAV-MD-rGDNF protected a significant number of cells when compared with cell counts of rAAV-CMV-lacZ-injected rats (94% vs. 51%, respectively). In close agreement, 85% of tyrosine hydroxylase-positive cells remained in the nigral rAAV-MD-rGDNF group vs. only 49% in the lacZ group. A separate group of rats were given identical perinigral virus injections and were sacrificed at 3 and 10 weeks after surgery. Nigral GDNF protein expression remained relatively stable over the 10 weeks investigated. These data indicate that the use of rAAV, a noncytopathic viral vector, can promote delivery of functional levels of GDNF in a degenerative model of Parkinson’s disease.

Structural model of cytochrome b559 in photosystem II based on a mutant with genetically fused subunits

Photosystem II is a reaction center protein complex located in photosynthetic membranes of plants, algae, and cyanobacteria. Using light energy, photosystem II catalyzes the oxidation of water and the reduction of plastoquinone, resulting in the release of molecular oxygen. A key component of photosystem II is cytochrome b559, a membrane-embedded heme protein with an unknown function. The cytochrome is unusual in that a heme links two separate polypeptide subunits, α and β, either as a heterodimer (αβ) or as two homodimers (α2 and β2). To determine the structural organization of cytochrome b559 in the membrane, we used site-directed mutagenesis to fuse the coding regions of the two respective genes in the cyanobacterium Synechocystis sp. PCC 6803. In this construction, the C terminus of the α subunit (9 kDa) is attached to the N terminus of the β subunit (5 kDa) to form a 14-kDa αβ fusion protein that is predicted to have two membrane-spanning α-helices with antiparallel orientations. Cells containing the αβ fusion protein grow photoautotrophically and assemble functional photosystem II complexes. Optical spectroscopy shows that the αβ fusion protein binds heme and is incorporated into photosystem II. These data support a structural model of cytochrome b559 in which one heme is coordinated to an α2 homodimer and a second heme is coordinated to a β2 homodimer. In this model, each photosystem II complex contains two cytochrome b559 hemes, with the α2 heme located near the stromal side of the membrane and the β2 heme located near the lumenal side.

A modified gambler's ruin model of polyethylene chains in the amorphous region.

Polyethylene chains in the amorphous region between two crystalline lamellae M unit apart are modeled as random walks with one-step memory on a cubic lattice between two absorbing boundaries. These walks avoid the two preceding steps, though they are not true self-avoiding walks. Systems of difference equations are introduced to calculate the statistics of the restricted random walks. They yield that the fraction of loops is (2M - 2)/(2M + 1), the fraction of ties 3/(2M + 1), the average length of loops 2M - 0.5, the average length of ties 2/3M2 + 2/3M - 4/3, the average length of walks equals 3M - 3, the variance of the loop length 16/15M3 + O(M2), the variance of the tie length 28/45M4 + O(M3), and the variance of the walk length 2M3 + O(M2).

An n-allele model for progressive amplification in the FMR1 locus.

An n-allele model is developed for the FMR1 locus, which causes the fragile X syndrome, where n is the number of triplet repeats in the first exon. Frequencies in the general population and in index families are used to generate an n to n + delta transition matrix that predicts specific risks in satisfactory agreement with observation. However, until sequencing distinguishes between stable and unstable alleles with the same value of n, it is premature to infer whether allelic frequencies at the FMR1 locus are at equilibrium or, as some have suggested, are evolving toward higher frequencies of the pathogenic allele.

A model intercomparison of changes in the Atlantic thermohaline circulation in response to increasing atmospheric CO2 concentration

As part of the Coupled Model Intercomparison Project, integrations with a common design have been undertaken with eleven different climate models to compare the response of the Atlantic thermohaline circulation ( THC) to time-dependent climate change caused by increasing atmospheric CO2 concentration. Over 140 years, during which the CO2 concentration quadruples, the circulation strength declines gradually in all models, by between 10 and 50%. No model shows a rapid or complete collapse, despite the fairly rapid increase and high final concentration of CO2. The models having the strongest overturning in the control climate tend to show the largest THC reductions. In all models, the THC weakening is caused more by changes in surface heat flux than by changes in surface water flux. No model shows a cooling anywhere, because the greenhouse warming is dominant.

EmotiBlog: a fine-grained model for emotion detection in non-traditional textual genres

This paper presents the first version of EmotiBlog, an annotation scheme for emotions in non-traditional textual genres such as blogs or forums. We collected a corpus composed by blog posts in three languages: English, Spanish and Italian and about three topics of interest. Subsequently, we annotated our collection and carried out the inter-annotator agreement and a ten-fold cross-validation evaluation, obtaining promising results. The main aim of this research is to provide a finer-grained annotation scheme and annotated data that are essential to perform evaluation focused on checking the quality of the created resources.

A Model to Visualize Information in a Complex Streets’ Network

his paper discusses a process to graphically view and analyze information obtained from a network of urban streets, using an algorithm that establishes a ranking of importance of the nodes of the network itself. The basis of this process is to quantify the network information obtained by assigning numerical values to each node, representing numerically the information. These values are used to construct a data matrix that allows us to apply a classification algorithm of nodes in a network in order of importance. From this numerical ranking of the nodes, the process finish with the graphical visualization of the network. An example is shown to illustrate the whole process.

Organizational design, quality management and competitive advantage in hotels

Purpose – The aim of this study is to examine the relationship between practices of quality management (QM) and the characteristics of organizational design, and QM and competitive advantage. Design/methodology/approach – The study uses a partial least squares approach to test these relationships in 350 hotels in Spain. Findings – The findings show that QM influences specialization, formalization and interdepartmental interactions, and that QM practices influence both cost and differentiation competitive advantage. The results also indicate the importance of QM strategic and operational systems as practices that have a key impact on the characteristics of organizational design. Similarly, the QM operational system is key in the relationship between QM and cost competitive advantage. Finally, the QM operational, information and strategic systems positively influence differentiation competitive advantage. Practical implications – When hotels adopt QM practices, there will be significant changes in a number of organizational variables, including specialization, formalization and interdepartmental interactions. This paper provides empirical evidence that QM practices improve both cost and differentiation competitive advantage in the hotel industry. Originality/value – There has been little research on the effects of QM on organizational design in the hotel industry. The contribution of this paper is that analyze the effects of QM on organizational design and competitive advantage, extending knowledge about these issues in a specific sector.

MODEL COUNTRIES IN POLITICAL ANALYSIS. Is Turkey a Model for State-Building in the Arab World? Jean Monnet Occasional Paper No. 10/2014

This study analyzes the Turkish case as a model country for the state-building processes in the Arab world in the aftermath of the Arab revolts that took place in Tunisia, Egypt and Libya. To this end, it deals with the Turkish case in three phases: the founding of the Turkish Republic, political developments until 2002, and the post-2002 Justice and Development Party period. The study focuses on state-society relations manifested in the form of a secular-religious cleavage intertwined with problematic civil-military relations. Each phase of Turkey’s history is compared to cleavages and civil-military relations in Egypt, Tunisia and Libya. After analyzing the constitution-making processes in the latter three countries following the Arab revolts, the study concludes by discussing the viability of the Turkish model in the light of Turkey’s search for a new constitution.

The strengh model of self-control in sport and exercise psychology

The strength model of self-control assumes that all acts of self-control (e.g., emotion regulation, persistence) are empowered by a single global metaphorical strength that has limited capacity. This strength can become temporarily depleted after a primary self-control act, which, in turn, can impair performance in subsequent acts of self-control. Recently, the assumptions of the strength model of self-control also have been adopted and tested in the field of sport and exercise psychology. The present review paper aims to give an overview of recent developments in self-control research based on the strength model of self-control. Furthermore, recent research on interventions on how to improve and revitalize self-control strength will be presented. Finally, the strength model of self-control has been criticized lately, as well as expanded in scope, so the present paper will also discuss alternative explanations of why previous acts of self-control can lead to impaired performance in sport and exercise.

Model of partial switching in polycrystalline ferromagnetics /

Thesis (M.S.)--University of Illinois at Urbana-Champaign, 1966.