Calculation of molecular integrals over Slater-type orbitals using recurrence relations for overlap integrals and basic one-center Coulomb integrals

The recurrence relations are established for the basic one-center Coulomb integrals over Slater-type orbitals (STOs). These formulae and the recurrence relations for basic overlap integrals are utilized for the calculation of multicenter electron-repulsion integrals. The calculations of multicenter electron-repulsion integrals are performed by the use of translation formulae for STOs obtained from the Lambda and Coulomb Sturmian exponential-type functions (ETFs). It is shown that these integrals show a faster convergence rate in the case of Coulomb Sturmian ETFs. The accuracy of the results is quite high for the quantum numbers of STOs and for the arbitrary values of internuclear distances and screening constants of atomic orbitals.     

Addition theorems for Slater-type orbitals in momentum space and their application to three-center overlap integrals

Using addition theorems for complete orthonormal sets of exponential type orbitals in the momentum representation introduced by the author, the addition theorems are established for Slater type orbitals in momentum space. With the help of these addition theorems, the general series expansion formulae in terms of the product of two-center overlap integrals are established for the three-center overlap integrals that arise in the solution of atomic and molecular problems occurring when explicitly correlated methods are employed. The formulae obtained for addition theorems and three-center overlap integrals are valid for arbitrary location and parameters of orbitals.     

Calculation of multicenter electric field gradient integrals over Slater-type orbitals using unsymmetrical one-range addition theorems

The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range addition theorems introduced by one of the authors, the sets of series expansion relations for multicenter electric field gradient integrals over Slater-type orbitals in terms of multicenter charge density expansion coefficients and two-center basic integrals are presented. The convergence of the series is tested by calculating concrete cases for different values of quantum numbers, parameters and locations of orbitals.     

Addition theorems for Slater-type orbitals and their application to multicenter multielectron integrals of central and noncentral interaction potentials

By the use of complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, m1, m2,...) introduced by the author, new addition theorems are derived for STOs and arbitrary central and noncentral interaction potentials (CIPs and NCIPs). The expansion coefficients in these addition theorems are expressed through the Gaunt and Gegenbauer coefficients. Using the addition theorems obtained for STOs and potentials, general formulae in terms of three-center overlap integrals are established for the multicenter t-electron integrals of CIPs and NCIPs that arise in the solution of the N-electron atomic and molecular problem (2hthN) when a Hylleraas approximation in Hartree-Fock-Roothaan theory is employed. With the help of expansion formulae for translation of STOs, the three-center overlap integrals are expressed through the two-center overlap integrals. The formulae obtained are valid for arbitrary quantum numbers, screening constants and location of orbitals.     

Isolated small intestinal segments support auxiliary livers with maintenance of hepatic functions

We determine here the functional integrity of auxiliary livers in containers fashioned from the small intestine. Liver microfragments from dipeptidyl peptidase 4 (DPP4)-deficient rats were transplanted into syngeneic normal animals with isolated intestinal segments characterized by mucosal denudation but intact vascular supply. Transplanted liver fragments were restored to confluent tissue with normal hepatic architecture and development of DPP4-positive vessels, indicating angiogenesis and revascularization. Auxiliary liver units expressed multiple hepatotrophic and angiogenic genes, and transplanted tissues remained intact for up to the 6-week duration of the studies with neither ischemic injury nor significant hepatocellular proliferation. Hepatic metabolic, transport and synthetic functions were preserved in auxiliary livers, including uptake and biliary excretion of (99m)Tc-mebrofenin in syngeneic recipients of liver from F344 rats, as well as secretion of albumin in allografted Nagase analbuminemic rats. This ability to produce functionally competent auxiliary livers in vascularized intestinal segments offers therapeutic potential for liver disease and genetic deficiency.     

Evaluation of ligand-binding affinity using polynomial empirical scoring functions

Assessing protein-ligand interaction is of great importance for virtual screening initiatives in order to discover new drugs. The present work describes a set of empirical scoring functions to assess the binding affinity, involving terms for intermolecular hydrogen bonds and contact surface. The results show that our methodology works better to predict protein-ligand affinity when compared with XSCORE, a popular empirical scoring function.     

Evaluation of basic mitochondrial functions using rat tissue homogenates

The primary attempt in diagnostic and experimental studies of numerous pathological states associated with mitochondrial dysfunction is a precise evaluation of changes in function, content and structure of mitochondrial OXPHOS system. The analysis of rat heart, liver, brain and kidney by oxygraphy, enzyme activities, membrane potential, and BN/SDS-PAGE western blotting demonstrated that tissue homogenates can substitute for isolated mitochondria, providing comparable qualitative mitochondrial parameters. The use of homogenate avoids the loss of the majority of mitochondria during their isolation. Only 50–100 mg of the tissue is required for the complex OXPHOS analysis, i.e. five times less as compared with isolated mitochondria.     

Independent functions for the N- and C-termini in the overlap region of tropomyosin

Tropomyosin (TM) is a coiled-coil that binds head-to-tail along the helical actin filament. The ends of 284-residue tropomyosins are believed to overlap by about nine amino acids. The present study investigates the function of the N- and C-terminal overlap regions. Recombinant tropomyosins were produced in Escherichia coli in which nine amino acids were truncated from the N-terminal, C-terminal, or both ends of striated muscle alpha-tropomyosin (TM9a) and TM2 (TM9d), a nonmuscle alpha-tropomyosin expressed in many cells. The two isoforms are identical except for the C-terminal 27 amino acids encoded by exon 9a (striated) or exon 9d (TM2). Removal of either end greatly reduces the actin affinity of both tropomyosins in all conditions and the cooperativity with which myosin promotes tropomyosin binding to actin in the open state. N-Terminal truncations generally are more deleterious than C-terminal truncations. With TM9d, truncation of the N-terminus is as deleterious as both for myosin S1-induced binding. None of the TM9d variants binds well to actin with troponin (+/-Ca(2+)). TM9a with the truncated N-terminus binds more weakly to actin with troponin (-Ca(2+)) than when the C-terminus is removed but more strongly than when both ends are removed; the actin binding of all three forms is cooperative. The results show that the ends of TM9a, though important, are not required for cooperative function and suggest they have independent functions beyond formation of an overlap complex. The nonadditivity of the TM9d truncations suggests that the ends may primarily function as a complex in this isoform. A surprising result is that all variants bound with the same affinity, and noncooperatively, to actin saturated with myosin S1. Evidently, end-to-end interactions are not required for high-affinity binding to acto-myosin S1.     

Mixing s orbitals into p and d orbitals. An attempt at bridging the angular overlap model and the valence shell electron pair repulsion model. Critique of the cellular ligand-field model

The stereochemistries of main group molecules have been discussed by using the angular overlap model in its molecular orbital oriented form (MO-AOM). Either ligand-field stabilisation of the ground state s²p^q−2 configuration, or s-p mixing, or both, provide a consistent bonding model for the stereochemistries. The transformation of the non-bonding orbitals into equivalent orbitals leads invariably to agreement with the lone-pair locations of the valence shell electron pair repulsion (VSEPR) model. The concepts of Hamiltonian-generated hybrids and pseudohemispherical molecular systems are found useful in this context. The MO-AOM formalism is also used for discussing s-d mixing in transition metal systems, and the energetic consequences within the ligand-field AOM (LF-AOM) are included. This is a second-order effect, which depends on squares and cross-products of radial parameters. It may still be quite large for tetragonal systems and for systems that deviate strongly from orthoaxiality. The usual ligand-additive property of the AOM is lost when the symmetry is lower than tetragonal and so is the energy separability into angular and radial factors. The cellular ligand-field model is found to be identical with the LF-AOM, except that its users consider it important not to acknowledge the formal hierarchy, MO-AOMLF-AOM, as relevant. The unintelligible concept of an active coordination void is found to be unnecessary and insufficient.     

Evaluation of species-area functions using Sonoran Desert plant data: not all species-area curves are power functions

Ecologists have been studying the relationship between species richness and area for about a century. As area increases, more species are typically observed. Many mathematical functions have been proposed to describe the pattern of increase. Numerous researchers have assumed that the relationship is a power function despite the fact that there are many possible alternatives. There has been limited work in evaluating which species-area functions are most appropriate for field data. This study examines which of a variety of functions best describe how Sonoran Desert plant species richness of remnant habitat patches in the Phoenix metropolitan area vary with sampled area and the area of entire patches. No single species-area function was adequate for describing all empirical datasets. Sample curves of woody species were most frequently best described by the sigmoid logistic, Hill, and Lomolino functions, whereas herbaceous datasets were best fit by the sigmoid logistic or convex rational functions. A curve depicting the relationship between patch-level woody species richness and patch area was best fit by the convex exponential function. The power function provided the best fit for only one case. This study demonstrates the utility of testing alternative functions for statistical fit rather than assuming that any particular equation adequately describes the species-area relationship.     

Evaluation of normal swallowing functions by using dynamic high-density surface electromyography maps

Background

Swallowing is a continuous process with substantive interdependencies among different muscles, and it plays a significant role in our daily life. The aim of this study was to propose a novel technique based on high-density surface electromyography (HD sEMG) for the evaluation of normal swallowing functions.

Methods

A total of 96 electrodes were placed on the front neck to acquire myoelectric signals from 12 healthy subjects while they were performing different swallowing tasks. HD sEMG energy maps were constructed based on the root mean square values to visualize muscular activities during swallowing. The effects of different volumes, viscosities, and head postures on the normal swallowing process were systemically investigated by using the energy maps.

Results

The results showed that the HD sEMG energy maps could provide detailed spatial and temporal properties of the muscle electrical activity, and visualize the muscle contractions that closely related to the swallowing function. The energy maps also showed that the swallowing time and effort was also explicitly affected by the volume and viscosity of the bolus. The concentration of the muscular activities shifted to the opposite side when the subjects turned their head to either side.

Conclusions

The proposed method could provide an alternative method to physiologically evaluate the dynamic characteristics of normal swallowing and had the advantage of providing a full picture of how different muscle activities cooperate in time and location. The findings from this study suggested that the HD sEMG technique might be a useful tool for fast screening and objective assessment of swallowing disorders or dysphagia.

     

Expression, assembly and auxiliary functions of photosystem II oxygen-evolving proteins in higher plants

The oxygen-evolving complex (OEC) of higher plant photosystem II (PSII) consists of an inorganic Mn₄Ca cluster and three nuclear-encoded proteins, PsbO, PsbP and PsbQ. In this review, we focus on the assembly of these OEC proteins, and especially on the role of the small intrinsic PSII proteins and recently found “novel” PSII proteins in the assembly process. The numerous auxiliary functions suggested during the past few years for the OEC proteins will likewise be discussed. For example, besides being a manganese-stabilizing protein, PsbO has been found to bind calcium and GTP and possess a carbonic anhydrase activity. In addition, specific roles have been suggested for the two isoforms of the PsbO protein in Arabidopsis thaliana. PsbP and PsbQ seem to play an additional role in the formation of PSII supercomplexes and in grana stacking, besides their originally recognized role in providing a proper calcium and chloride ion concentration for water splitting.     

Novel functions of acyl-CoA thioesterases and acyltransferases as auxiliary enzymes in peroxisomal lipid metabolism

Peroxisomes are single membrane bound organelles present in almost all eukaryotic cells, and to date have been shown to contain approximately 60 identified enzymes involved in various metabolic pathways, including the oxidation of a variety of lipids. These lipids include very long-chain fatty acids, methyl branched fatty acids, prostaglandins, bile-acid precursors and xenobiotics that are either β-oxidized or α-oxidized in peroxisomes. The recent identification of several acyl-CoA thioesterases and acyltransferases in peroxisomes has revealed their various functions in acting as auxiliary enzymes in α- and β-oxidation in this organelle. To date, 9 functional acyl-CoA thioesterases and acyltransferases have been identified in mouse and 4 functional acyl-CoA thioesterases and acyltransferases in human, thus these enzymes make up a substantial portion of peroxisomal proteins. This review will therefore focus on new and emerging roles for these enzymes in assisting with the oxidation of various lipids, amidation of lipids for excretion from peroxisomes, and in controlling coenzyme A levels in peroxisomes.     

Controlling size and uniformity of molecularly imprinted nanoparticles using auxiliary template

Molecularly imprinted nanomaterials are gaining substantial importance. As a simple and efficient synthetic method, precipitation polymerization has been used to prepare uniform molecularly imprinted microspheres for numerous template compounds. Despite of its general applicability, the difficulty of obtaining uniform particles for some difficult templates by precipitation polymerization has been reported. In this work, we attempted to produce uniform atrazine-imprinted nanoparticles using propranolol as an auxiliary template under standard precipitation polymerization condition. When propranolol was added in the prepolymerization mixture for atrazine imprinting, it displayed a significant effect on particle size and size distribution of atrazine-imprinted polymers. The molecular binding characteristics of the molecularly imprinted polymer (MIP) nanoparticles were found to be dependent on the relative ratios of the two templates. Under an optimal template propranolol-atrazine ratio of 1:3 mol/mol, very uniform imprinted nanoparticles (d(H) =?106?nm) with a polydispersity index of 0.07 were obtained. The loading of the auxiliary template (propranolol) could be reduced to as low as 5% without sacrificing the uniformity of the MIP nanoparticles. The uniform MIP nanoparticles could be easily encapsulated into polyethylene terephthalate nanofibers using a simple electrospinning technique. The composite nanofibers containing the MIP nanoparticles maintained specific molecular binding capability for both atrazine and propranolol.     

Evaluation of soil aggregate stability in Algerian northwestern soils using pedotransfer functions and artificial neural networks

Since, aggregate stability is the main physical property regulating erodibility; its observations can act as a useful indicator for monitoring and managing soil degradation. In this context, this study carried out in the alluvial plain of Cheliff, a semi-arid area aimed to predict aggregate stability through Mean Weight Diameter (MWD), using pedotransfer functions (PTFs) with different stratifications (textural, salinity and organic-textural) and artificial neural networks (ANNs). Results showed that the best MWD predictions were those related to organic-textural PTFs, in this stratification the silty-clay moderately rich OM class showed the highest significant determination coefficient R² (0.65) and the lowest mean square error (0.03), whereas, the textural and salinity PTFs were a very weak predictors with a very low R². It was also found that the performances of ANNs in predicting MWD were better than those of PTFs, regarding ANNs input variables the best predictions were those obtained with a large number of input variables, furthermore, by using a large number of hidden neurons, the performances of Radial Basis Function (RBF) were better than those of Multilayer Perceptron (MLP). It was also noted that the best RBF results were always related to the Gaussian hidden activation, whereas, MLP was not related to a specific hidden activation.     

Histochemical demonstration of creatine kinase activity using polyvinyl alcohol and auxiliary enzymes

Creatine kinase activity (EC 2.7.3.2.) has been demonstrated in myocardium and skeletal muscle from rats by a method based on the incubation of cryostat sections with a polyvinyl alcohol-containing medium and the use of auxiliary enzymes. Hexokinase and glucose-6-phosphate dehydrogenase were spread on object glasses before mounting the sections to be incubated. In this way, the auxiliary enzymes were interposed between glass slide and section thus preventing loss of formazan generated within the sections. Creatine kinase activity was found to be localized in finely dispersed form along the myofibrils and as large granules in the sarcoplasm of myocardium and skeletal muscle. The formazan produced specifically by creatine kinase (test minus control), as measured cytophotometrically at 585 nm, was completely inhibited by 2 mM 2,4-dinitrofluorobenzene, a specific inhibitor of creatine kinase activity. The control reaction was unaffected by the inhibitor. The results obtained with the present method are similar to results obtained with the far more complicated semipermeable membrane technique. The introduction of auxiliary enzymes in the polyvinyl alcohol method enables the development of histochemical methods for many enzymes by linking the reactions to a dehydrogenase reaction.     

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.

This paper presents a new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies. It is based on a dynamic programming algorithm from applied mathematics, and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature. Its power is demonstrated in the folding of a 459 nucleotide immunoglobulin gamma 1 heavy chain messenger RNA fragment. We go beyond the basic method to show how to incorporate additional information into the algorithm. This includes data on chemical reactivity and enzyme susceptibility. We illustrate this with the folding of two large fragments from the 16S ribosomal RNA of Escherichia coli.     

Evaluation of some immune functions in a patient affected by common variable immunodeficiency using luminescent techniques

Common variable immunodeficiency is a primary immunodeficiency characterized by a failure of antibody synthesis, whose fundamental immunologic abnormality is still unknown. In our study, we evaluated some immune functions using chemiluminescence in a 32-year-old woman affected by common variable immunodeficiency. In particular, we showed an impairment of her lymphomonocyte proliferative response which was evaluated using a method based on the bioluminescent measurement of ATP. Besides, we found a reducton of her lymphomonocyte IL2 and IL4 production: the IL4 production was evaluated through an ELISA method, whereas the IL2 activity was determined by its ability to support the IL2-dependent murine T-cell line (CTLL) proliferation which was established through a method based on the bioluminescent measurement of ATP. Finally, we evaluated both yeast-induced and fMLP-induced polymorphonuclear and monocyte oxidative metabolism through a luminol-amplified chemiluminescence; these functions were within normal values. Therefore, in our patient affected by common variable immunodeficiency, we demonstrated an impairment of cellular immunity, which might contribute to the pathogenesis of the disease. © 1997 John Wiley & Sons, Ltd.