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PubMed1983

Prediction of melting profiles and local helix stability for sequenced DNA.

The utility and limits of the current theory of helix-coil transition of DNA were intensively studied. Comparison of calculated and observed melting profiles affords solid criteria of a theoretical model and parameter values. Our model differs from others in that heterogeneity in stacking interactions is taken into consideration (Section II). The parameter values were estimated by fitting calculated to observed profiles for several known-sequenced DNA fragments (Section III). Calculated profiles agree quite well with observed, not only for DNAs used for the fitting but also for those not used. Such good agreement was never obtained with traditional two-term (A X T and G X C) stability assignment. It was shown that the all-or-none approximation for local melting transition (Azbel's model) provides informative but somewhat erroneous estimates of local stability. The stabilities of 10 kinds of stacking doublets estimated by the fitting accord well with known properties of DNA double helix (Subsection III-4); three-dimensional structure, calculated stacking energies, and binding specificity of some intercalative drugs are all consistent with the estimated order of stacking stabilities. Relationship between triplet stability and genetic code was discussed. The mechanisms of ionic-strength dependence of melting profiles were discussed in Section IV. Four different mechanisms were proposed and their relative contributions in various salt ranges were considered. It was suggested that at low ionic strengths melting processes deviate significantly from equilibrium, which fixes a limit to the applicability of the present theoretical mode. Locally unstable regions and frequently opening regions were located on several natural DNAs by calculating probabilities of individual base-pair doublets being in an unstacked state. With few exceptions, origins of DNA replication on various DNAs fall on frequently opening regions, indicating their functional importance. Positive correlations were also obtained between frequently opening regions and transcriptional promoters, terminators and gene boundaries (Section V).

Base Composition↗

PubMed1982

Intergovernmental relations in physician education and health planning: state adoption decisions and the impact of federal programs.

This study seeks to explain states' adoptions of programs in health planning and in physician education. It also seeks to further understanding of the impact of federal health planning and education programs on the states. Several theories and models are employed in analyzing the actions of state decision-makers. These include incremental theory, models of the diffusion of innovations, economic resources theory, and a theory of competitive partisanship. The data utilized in this research were principally derived from intensive interviews with "key" state actors and from historical, documentary materials. Only minimal federal impact appears on states' goals in physician education and health planning. Rather, there is evidence of considerable innovativeness among the states prior to Federal program initiatives. A problem-generated search for solutions seems to be a major source of this innovation. Finally, federal program implementation requirements appear to be a major source of federal--state conflict and opposition.

Diffusion of Innovation↗

PubMed2006

What can geography tell us about prostate cancer?

One of the most striking characteristics of prostate cancer is the degree of geographic variation in its patterns of occurrence and progression; this variation is apparent at local, national, and international levels. Although geographic theory, methods, and data are increasingly utilized for public health research, epidemiologic research in prostate cancer etiology and progression has not taken full advantage of the spatial sciences as partner disciplines. This article reviews the known factors influencing the biology and epidemiology of prostate cancer and some of the ways in which findings to date have benefited from geography. A model is presented for geographically integrated research in prostate cancer, with discussion of how spatially referenced data and methods could enhance approaches to answering remaining questions in prostate cancer.

Demography↗

PubMed2005

A simple classification of the volvocine algae by formal languages.

There are several explanations of why certain primitive multicellular organisms aggregate in particular forms and why their constituent cells cooperate with one another to a particular degree. Utilizing the framework of formal language theory, we have derived one possible simple classification of the volvocine algae-one of the primitive multicells-for some forms of aggregation and some degrees of cooperation among cells. The volvocine algae range from the unicellular Chlamydomonas to the multicellular Volvox globator, which has thousands of cells. The classification we use in this paper is based on the complexity of Parikh sets of families on Chomsky hierarchy in formal language theory. We show that an alga with almost no space closed to the environment, e.g., Gonium pectorale, can be characterized by PsFIN, one with a closed space and no cooperation, e.g., Eudorina elegans, by PsCF, and one with a closed space and cooperation, e.g., Volvox globator, by PslambdauSC. This classification should provide new insights into the necessity for specific forms and degrees of cooperation in the volvocine algae.

Animals↗

PubMed2006

Expanding to fill the gap: a possible role for inert biopolymers in regulating the extent of the 'macromolecular crowding' effect.

We discuss the potential for inert biopolymers existing in cells to play a role in regulating the macromolecular crowding effect via their ability to undergo shape changing structural transitions. We have explored this possibility by the use of theory and experiment. The theoretical component utilized Monte-Carlo based simulations to examine the folding of a hypothetical protein in a concentrated environment of hard spheres which are themselves capable of reversible expansion and contraction. The experimental component of the study involved examination of the effect of different sized crowding agents on the thermally induced denaturation of cytochrome c [in phosphate buffered saline solution containing 1.0M guanidinium hydrochloride at pH 7.0]. On the basis of our findings we suggest that in a crowded solution environment the presence of a non-reactive polymer capable of reversible expansion/contraction via folding and unfolding may alter the excluded volume component of the solution. This ability would confer on the non-reactive polymer a novel role in influencing other processes in solution affected by macromolecular crowding.

Animals↗

PubMed1971

Fiber interaction in a nerve trunk.

This paper is concerned with the nature of the transmembrane potential induced in an inactive nerve fiber lying in an impressed potential field within a nerve trunk. The impressed potential field is assumed to be produced by the synchronous activity of other fibers within the trunk; an expression for the induced transmembrane potential is obtained utilizing the principles of electromagnetic field theory. The results strongly indicate that membrane capacitance is the main determinant of the induced transmembrane potential wave form.

Action Potentials↗

PubMedDate not supplied

Cognitive behavior therapy for functional somatic complaints. The example of chronic fatigue syndrome.

Somatic complaints such as pain and fatigue that are unexplained by conventional disease are common in medical practice and are referred to as functional, somatoform, or somatization symptoms. Despite frequent chronicity, disability, and high associated medical costs, patients with these complaints are rarely offered either constructive explanations or effective treatment. In this perspective, a cognitive-behavioral approach to the problem is described, using chronic fatigue syndrome as an example. It is concluded that the utility of the cognitive-behavioral theory and the proven effectiveness cognitive behavior therapy provide the basis for a new evidence-based approach to psychosomatics.

Cognitive Behavioral Therapy↗

PubMed2002

State-event relations among indicators of susceptibility to mental distress in Wythenshawe in the UK.

This paper explores the utility of concepts drawn from psychosocial theory as predictors of the proneness to mental distress among the residential population of a large suburban council estate (Wythenshawe, South Manchester). In this respect, items are selected and tested to form composite variables measuring individual ratings with regard to notions of structural risk, personal vulnerability, goal-setting behaviour, quality of life, and the frequency of life events and restricted opportunities. Mental distress is enumerated on the standard GHQ12-point scale. The design makes the distinction between composite variables that record persistent states and those which count events and aspirations immediate to the individual's present experience. To examine the consequences of this difference between indicators of prevalence and incidence, our analysis adopts a two-stage multiple regression format. The first examines these state-event interactions among the composite variables, while the second tests the separate significance of these types as predictors of GHQ12. The findings reveal significant proportions of the variation in GHQ12 are be explained either by associations with the ageing process or by those linked to subjective indicators of the quality of life. In contrast, structural deprivation correlates less significantly with the reporting of psychiatric distress in this socially homogeneous population. The discussion considers the methodological implications of these relationships for understanding common mental health problems together with their connotations for health policy.

Adolescent↗

PubMed2003

Spectroscopic and computational studies of a Ni(+)-CO model complex: implications for the acetyl-CoA synthase catalytic mechanism.

The four-coordinate Ni(+) complex [PhTt(t)(Bu)]Ni(I)CO, where PhTt(t)()(Bu) = phenyltris((tert-buthylthio)methyl)borate (a tridentate thioether donor ligand), serves as a possible model for key Ni-CO reaction intermediates in the acetyl-CoA synthase (ACS) catalytic cycle. Resonance Raman, electronic absorption, magnetic circular dichroism (MCD), variable-temperature variable-field MCD, and electron paramagnetic resonance spectroscopies were utilized in conjunction with density functional theory and semiemperical INDO/S-CI calculations to investigate the ground and excited states of [PhTt(t)()(Bu)]Ni(I)CO. These studies reveal extensive Ni(+) --> CO pi-back-bonding interactions, as evidenced by a low C-O stretching frequency (1995 cm(-)(1)), a calculated C-O stretching force constant of 15.5 mdyn/A (as compared to k(CO)(free CO) = 18.7 mdyn/A), and strong Ni(+) --> CO charge-transfer absorption intensities. Calculations reveal that this high degree of pi-back-bonding is due to the fact that the Ni(+) 3d orbitals are in close energetic proximity to the CO pi acceptor orbitals. In the ACS "paramagnetic catalytic cycle", the high degree of pi-back-bonding in the putative Ni(+)-CO intermediate (the NiFeC species) is not expected to preclude methyl transfer from CH(3)-CoFeSP.

Acetate-CoA Ligase↗

PubMed2003

Meta-conjugation and excited-state coupling in phenylacetylene dendrimers.

Traditional pictures of optical properties in phenylacetylene dendrimers view the molecule as a collection of independent chromophores, linked by meta-substitution at the central phenyl ring. While this picture is reasonable for explaining the observed absorption trends, it breaks down in describing the emission behavior. We utilize a combination of ab initio theory and experiment to demonstrate that differences in the absorbing and emitting states can be described using an exciton model with very weak chromophore coupling for the absorption geometry and strong coupling for the emission geometry. This result may have significant implications for the design of energy-funneling dendrimeric molecules.

Journal Article↗

PubMed2005

Synthesis, structure determination, and spectroscopic/computational characterization of a series of Fe(II)-thiolate model complexes: implications for Fe-S bonding in superoxide reductases.

A combined synthetic/spectroscopic/computational approach has been employed to prepare and characterize a series of Fe(II)-thiolate complexes that model the square-pyramidal [Fe(II)(N(His))(4)(S(Cys))] structure of the reduced active site of superoxide reductases (SORs), a class of enzymes that detoxify superoxide in air-sensitive organisms. The high-spin (S = 2) Fe(II) complexes [(Me(4)cyclam)Fe(SC(6)H(4)-p-OMe)]OTf (2) and [FeL]PF(6) (3) (where Me(4)cyclam = 1,4,8,11-tetramethylcyclam and L is the pentadentate monoanion of 1-thioethyl-4,8,11-trimethylcyclam) were synthesized and subjected to structural, magnetic, and electrochemical characterization. X-ray crystallographic studies confirm that 2 and 3 possess an N(4)S donor set similar to that found for the SOR active site and reveal molecular geometries intermediate between square pyramidal and trigonal bipyramidal for both complexes. Electronic absorption, magnetic circular dichroism (MCD), and variable-temperature variable-field MCD (VTVH-MCD) spectroscopies were utilized, in conjunction with density functional theory (DFT) and semiemperical INDO/S-CI calculations, to probe the ground and excited states of complexes 2 and 3, as well as the previously reported Fe(II) SOR model [(L(8)py(2))Fe(SC(6)H(4)-p-Me)]BF(4) (1) (where L(8)py(2) is a tetradentate pyridyl-appended diazacyclooctane macrocycle). These studies allow for a detailed interpretation of the S-->Fe(II) charge transfer transitions observed in the absorption and MCD spectra of complexes 1-3 and provide significant insights into the nature of Fe(II)-S bonding in complexes with axial thiolate ligation. Of the three models investigated, complex 3 exhibits an absorption spectrum that is particularly similar to the one reported for the reduced SOR enzyme (SOR(red)), suggesting that this model accurately mimics key elements of the electronic structure of the enzyme active site; namely, highly covalent Fe-S pi- and sigma-interactions. These spectral similarities are shown to arise from the fact that 3 contains an alkyl thiolate tethered to the equatorial cyclam ring, resulting in a thiolate orientation that is very similar to the one adopted by the Cys residue in the SOR(red) active site. Possible implications of our results with respect to the electronic structure and reactivity of SOR(red) are discussed.

Binding Sites↗

PubMed2005

Equilibrium adsorption in cylindrical mesopores: a modified Broekhoff and de Boer theory versus density functional theory.

This paper presents a thermodynamic analysis of capillary condensation phenomena in cylindrical pores. Here, we modified the Broekhoff and de Boer (BdB) model for cylindrical pores accounting for the effect of the pore radius on the potential exerted by the pore walls. The new approach incorporates the recently published standard nitrogen and argon adsorption isotherm on nonporous silica LiChrospher Si-1000. The developed model is tested against the nonlocal density functional theory (NLDFT), and the criterion for this comparison is the condensation/evaporation pressure versus the pore diameter. The quantitative agreement between the NLDFT and the refined version of the BdB theory is ascertained for pores larger than 2 nm. The modified BdB theory was applied to the experimental adsorption branch of adsorption isotherms of a number of MCM-41 samples to determine their pore size distributions (PSDs). It was found that the PSDs determined with the new BdB approach coincide with those determined with the NLDFT (also using the experimental adsorption branch). As opposed to the NLDFT, the modified BdB theory is very simple in its utilization and therefore can be used as a convenient tool to obtain PSDs of all mesoporous solids from the analysis of the adsorption branch of adsorption isotherms of any subcritical fluids.

Journal Article↗

PubMed2006

Alkylation of phenol: a mechanistic view.

The current work utilizes the ab initio density functional theory (DFT) to develop a molecular level of the mechanistic understanding on the phenol alkylation in the presence of a cation-exchange resin catalyst, Amberlyst-15. The catalyst is modeled with the benzene sulfonic acid, and the effect of this acid on olefins such as isopropene (i-Pr) and tributene (t-Bu) in a phenol solution mimics the experimental condition. A neutral-pathway mechanism is established to account for early-stage high concentration of the phenolic ether observed in experiments. The mechanism involves an exothermic reaction between olefin and the benzene sulfonic acid to form ester followed by three reaction pathways leading to direct O-alkylation, o-C-alkylation, and p-C-alkylation. Our calculations conclude that O-alkylation to form the phenolic ether is the most energetically favorable in the neutral condition. An ionic rearrangement mechanism describes intramolecular migrations of the alkyl group from the phenolic ether to form C-alkylphenols, while the positively charged protonation significantly lowers transition barriers for these migrations. The ionic rearrangement mechanism accounts for high yields of o-C-alkylphenol and p-C-alkylphenol. Competition between the H atom and the alkyl R group at the substitutive site of the protonated ortho configuration is found to be the determining factor to the ortho/para ratio of C-alkylation products.

Algorithms↗

PubMed2006

Bond length alternation and energy band gap of polyyne.

The bond length alternation (BLA) and energy band gap of polyyne are investigated by various first-principles theories, including Hartree-Fock, MP2, hybrid, and nonhybrid density functional theories. Both solid-state calculations utilizing periodic boundary conditions on polymers and molecular quantum mechanical calculations on extra-long oligomers were performed with consistent results. By validation on similar linear conjugated polymers, polyacetylene and polydiacetylene, the combination of hybrid-DFT schemes, B3LYP//BHandHLYP or B3LYP//KMLYP, is shown to give the best predictions for both geometry and band gap of polyyne based on available experimental data. We conclude that the best estimate of the BLA of polyyne is about 0.13 A and that of the band gap is about 2.2 eV.

Journal Article↗

PubMed2006

Spectroscopic and computational studies on the coordination-driven self-assembly complexes (ZnL)2 and (NiL)2 [L= bis(2,4-dimethyldipyrrin-3-yl)methane].

FT-IR, FT-Raman and electronic absorption spectroscopies were utilized in conjunction with density functional theory (DFT) calculations to investigate the ground and excited states of self-assembled dinuclear dimeric helicates (ZnL)2 and (NiL)2 [L = bis(2,4-dimethyldipyrrin-3-yl)methane]. These studies afford a detailed description of the ground-state geometric and electronic structures of (ZnL)2 and (NiL)2 and provide a comparison with similar geometrical metal-porphyrins. The results demonstrate that enlarging the basis set used in the DFT calculations results in an obvious alteration of the calculated bond lengths but negligible alteration of the calculated bond angles. The predicted spectra are in good agreement with the experimental ones with the deviations generally less than 30 cm(-1). In comparison with vibrational spectra of metal-porphyrins, the breathing vibration of the pyrrole ring is shifted by over 100 cm(-1) toward higher wavenumber due to local conjugation of molecular geometry. Time-dependent density functional theory (TD-DFT) provides a good description of the excitation energy. Because of the break in symmetry, the absorption band (corresponding to the Q-band of porphyrin) of (ZnL)2 and (NiL)2 is no longer weak. Local conjugation makes the absorption wavelength of (NiL)2 and (ZnL)2 shift to the blue compared with those of NiP and ZnP.

Journal Article↗

PubMed2003

Prevention of type 2 diabetes in young people: a theoretical perspective.

Type 2 diabetes in youth is an increasing public health concern, especially in certain minority populations. The current paper consists of four sections. First, we establish the significance of the problem by presenting an overview of epidemiological and physiological evidence. Second, we discuss behavioral issues relevant to the prevention of type 2 diabetes in youth. Third, a qualitative review of existing prevention interventions specific to type 2 diabetes in youth is presented. Results suggest that modest improvements in social cognitive, dietary, and exercise outcomes are possible with diabetes intervention studies, although beneficial changes are difficult to sustain over the long term. Although theoretical frameworks are not always explicit, most studies have utilized elements of the social cognitive theory. Less attention has been paid to sociocultural and community organization variables. Finally, the paper discusses issues of risk definition and intervention sustainability, and presents a comprehensive, theoretically diverse model for the prevention of type 2 diabetes in youth. In summary, we suggest that theories of the natural history and pathophysiology of type 2 diabetes are important to identify modifiable risk factors, while theories of behavioral change are essential to modify the risk factors identified. The combination of sound physiological and behavioral theories should form the basis of prevention intervention design. In addition, an ecologic approach that takes into consideration the dynamic interactions of personal, social, and environmental factors would best promote the long-term adoption of healthful behaviors in a supportive, meaningful, and personally enjoyable context.

Adolescent↗

PubMed1998

Are shame and guilt related to distinct self-discrepancies? A test of Higgins's (1987) hypotheses.

A study of 229 undergraduates examined whether specific self-discrepancies are differentially related to shame proneness and guilt proneness. Contrary to E. T. Higgins (1987), but in line with the present authors' expectations, the tendency to experience shame, but not guilt, was positively related to all types of self-discrepancies. An attempt was also made to replicate E. T. Higgins, Klein, and Strauman's (1985) findings that specific self-discrepancies are associated with distinct emotion syndromes. No support was found for the central hypotheses of self-discrepancy theory. Finally, the authors evaluated the utility of two methods for assessing self-discrepancies. Higgins's qualitative method and quantitative adjective ratings. The two methods yielded essentially identical relationships to other variables. The very high correlations among different types of self-discrepancies within each method, however, raise discriminant validity concerns.

Adolescent↗

PubMed2002

The role of Raman spectroscopy in the analytical chemistry of potable water.

Advances in instrumentation are making Raman spectroscopy the tool of choice for an increasing number of chemical applications. For example, many recalcitrant industrial process monitoring problems have been solved in recent years with in-line Raman spectrometers. Raman is attractive for these applications for many reasons, including remote non-invasive sampling, minimal sample preparation and tolerance of water. To a lesser extent, Raman spectroscopy is beginning to play a significant role in environmental analysis for the same reasons. At present, the environmental applications typically apply only to the most contaminated situations due to the still relatively high limits of detection. However, some emerging sampling technologies hold out the promise that Raman may soon be more widely applicable to the analytical chemistry of potable water. Herein we discuss these recent advances, summarize some examples of environmental applications to aqueous systems and suggest avenues of future developments that we expect to be most useful for potable water analysis. Also, a simplified, but detailed, theory of normal Raman scattering is presented. While resonance-enhanced Raman spectroscopy, surface-enhanced Raman spectroscopy and non-linear Raman techniques are briefly discussed, their theories and instrumental configurations are not addressed. Also, this article deals primarily with the modern dispersive Raman experiment (as opposed to the Fourier transform Raman experiment), because it seems most suited for potable water analysis. The goal of this article is to give the environmental scientist with no specialized knowledge of the topic just enough theory and background to evaluate the utility of this rapidly developing analytical tool.

Chemistry Techniques, Analytical↗