Association between ambient temperature, particulate air pollution and emergency room visits for conjunctivitis.

BACKGROUND: Numerous studies have confirmed the association of ambient temperature and air pollution with a higher risk of morbidities, yet few have addressed their effect on the ocular system. The purpose of this study was to assess the association between temperature, air pollution, and emergency room visits for conjunctivitis. METHODS: In this case-crossover study, the records of all emergency room visits to Soroka University Medical Center (SUMC) from 2009 to 2014 were reviewed for patients with conjunctivitis. Daily exposure to fine and coarse particulate matter and temperature were determined by a hybrid model involving satellite sensors. Mean relative humidity was obtained from the Ministry of Environmental Protection meteorological monitoring station located in Beer-Sheva. RESULTS: Six hundred one patients were diagnosed with conjunctivitis in the SUMC emergency room. We discovered a positive association between temperature increments and incidence of conjunctivitis. The strongest effect was found during summer and autumn, with an immediate (lag0) incidence increase of 8.1% for each 1 °C increase in temperature (OR = 1.088, 95%CI: 1.046-1.132) between 24 and 28 °C in the summer and 7.2% for each 1 °C increase in temperature (OR = 1.072, 95%CI: 1.036-1.108) between 13 and 23 °C in the autumn. There was no statistically significant association between fine and coarse particulate matter and conjunctivitis incidence. CONCLUSION: Temperature increases during summer and autumn are significantly associated with an increased risk of conjunctivitis. Conjunctivitis is not associated with non-anthropogenic air pollution. These findings may help community clinics and hospital emergency rooms better predict conjunctivitis cases and will hopefully lead to improved prevention efforts that will lower the financial burden on both the individual and the public.

[New algorithm of aqueous humor dynamics assessment in glaucoma].

The purpose of the study was to develop a new algorithm of aqueous humor dynamics assessment in glaucomatous eyes, which would take into account the shape of the tonographic curve and individual elastic properties of the corneoscleral capsule. Basic ophthalmic examination supplemented with tonography and differentiated tonometry was performed on 33 patients with primary open-angle glaucoma (POAG), 8 POAG suspects, and 9 healthy controls. Obtained data were processed in accordance with the developed algorithm. A new formula for calculating the coefficient of outflow facility and several additional parameters describing the condition of aqueous pathways were proposed. In POAG patients these parameters significantly differed from those in healthy controls.

[Atomic force field FFsol for calculation of molecular interactions of in water environment].

Detailed calculations of protein interactions with explicitly considered water takes enormous computer time. The calculation becomes faster if water is considered implicitly (as a continuous media rather than as molecules); however, these calculations are much less precise, unless one uses an additional (and also volumes) computation of the solvent-accessible areas of protein atoms. The aim of our study was to obtain parameters for non-bonded atom-atom interactions for the case when water surrounding is considered implicitly and the solvent-accessible areas are not computed. Since the "in-vacuum" interactions of atoms are obtained from experimental structures of crystals and enthalpies of their sublimation, the "in-water" interactions of atoms must be corrected using solvation free energies of molecules, which can be obtained from the Henry constants. Taken 58 structures of molecular crystals and thermodynamic data on their sublimation and solubility, we obtained parameters for "in-water" attraction and repulsion of atoms typical of protein structures (H, C, N, O, S) in various covalently-bonded states, as well as parameters for electrostatic interactions. All necessary for calculations parameters of covalent interactions have been taken from the ENCAD force field, and partial charges of all atoms of separate molecules of a crystal have been obtained from quantum-mechanical calculations. The sought parameters of the "in-water" van der Waals and electrostatic interactions were optimized so as to achieve the best description of equilibrium crystal structures and their sublimation and solvation at the room temperature. With the optimized parameters, the average error in calculation of the effective cohesion energy of molecules in crystals was less than 10% both in the "in-vacuum" and "in-water" cases.

[Protein structure prediction from analogy. III. Optimization of a combination of substitution matrices and pseudo-potentials used to align protein].

We describe a general and fast method of maximization of a "recognition ability" of a linear combination of an arbitrary number of various methods used to recognize protein structures and produce the sequence-to-structure alignments. It is shown that, at a low level of sequence similarity, the optimal combined method has a significantly higher "recognition ability" than each of participating separate method, the leading role in this combination being played by (1) pseudo-potentials of long-range interactions; (2) matrices of secondary structure similarity; and, finally, (3) amino acid substitution matrices. As to a high level of sequence similarity, here the leading and virtually the sole role in the optimal combination is played by substitution matrices, although admixture of pseudo-potentials of long-range interactions and matrices of secondary structure similarity somewhat increases the "recognition ability" of the combined method.

[Protein structure prediction from analogy. I. New database of spatially similar and dissimilar structures of protein domains for testing and optimization of prediction methods].

The paper describes creation and analysis of a database 3Dfold_test. This database consists of a large set of pairs of spatially-similar structures of protein domains and of an accompanying, much larger control set of "decoys", i.e., spatially-dissimilar protein structures, having approximately the same size and compactness as each member of a pair of spatially-similar proteins. The database 3Dfold_test can be found at the site http://phys.protres.ru/resources/prediction analogy/3Dfold/.

[On the role of some conserved and nonconserved amino acid residues in transition state and in intermediate of apomyoglobin folding].

The effect of some amino acid residues in A, B, G, and H helices on the folding nucleus and folding intermediate state formation was estimated. For four apomyoglobin mutant forms with point replacements of hydrophobic amino acid residues by Ala, the influence of the substitutions on the stability of native (N) protein and its folding intermediate state (I) was studied, as well as on the protein folding/unfolding rates. Equilibrium and kinetic studies on mutant proteins over a wide range of urea concentrations have shown that the protein native state was strongly destabilized in comparison with that of the wild type protein. At the same time, stability of the intermediate state changed insignificantly. It was shown that amino acid residues of A, G, and H helices make a small contribution to apomyoglobin folding nucleus stabilization in the rate-limiting I reversible N transition, which occurred after the intermediate state was formed. But the amino acid residue of B-helix was very important for the folding nucleus stabilization in the transition state upon the I reversible N transition.

[On prediction of folding nuclei in globular proteins].

The approach described in this paper on the prediction of folding nuclei in globular proteins with known three dimensional structures is based on a search of the lowest saddle points through the barrier separating the unfolded state from the native structure on the free-energy landscape of protein chain. This search is performed by a dynamic programming method. Comparison of theoretical results with experimental data on the folding nuclei of two dozen of proteins shows that our model provides good phi value predictions for proteins whose structures have been determined by X-ray analysis, with a less limited success for proteins whose structures have been determined by NMR techniques only. Consideration of a full ensemble of transition states results in more successful prediction than consideration of only the transition states with the minimal free energy. In conclusion we have predicted the localization of folding nuclei for three dimensional protein structures for which kinetics of folding is studied now but the localization of folding nuclei is still unknown.

[A quantitative study of regional and stage specific reaction of African clawed frog embryonic tissues on mechanical stress]. / Kolichestvennoe issledovanie regional'nykh i stadiespetsifichnykh reaktsii émbrional'nykh tkanei shportsevoi liagushki na mekhanicheskuiu razgruzku.

Residual deformation of fragments of the embryonic tissues preserved after relaxation of the stretching force serve as a criterion of active redistribution of their cells caused by this stretching. We measured residual deformations of the Xenopus laevis ventral and dorsal ectoderm at the early gastrula and lateral ectoderm at the late gastrula-early neurula after stretching of varying time and force. While the samples responded to moderate (up to 40%) short-term stretching as elastic bodies (residual deformations were absent), residual deformation appeared in the early gastrula tissues after 30-60-min stretching, which were more pronounced in the ventral tissues than in the dorsal ones. On the contrary, a contractile reaction developed in the late gastrula-early neurula tissues in response to 60-min stretching, which almost relaxed residual deformation within 20 min after unloading. A conclusion was drawn that gastrulation and neurulation proceed under the conditions of relaxing and nonrelaxing mechanical tensions, respectively. Mechanical bases and morphogenetic role of the described reactions is discussed.

[Kinetics of folding nuclei formation in proteins]. / Nukleatsiia i skorost' svorachivaniia v belkakh.

When a protein folds or unfolds, it passes through many half-folded microstates. Only a few of them can accumulate and be seen experimentally, and this happens only when the folding (or unfolding) occurs far from the point of thermodynamic equilibrium between the native and denatured states. The universal features of folding, though, are observed in the vicinity of the equilibrium point. Here the "two-state" transition proceeds without any accumulation of metastable intermediates, and only the transition state ("folding nucleus") is outlined by its key influence on the folding/unfolding kinetics. This review covers recent experimental and theoretical studies of folding nuclei.

[When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. / Kak i kogda otdalennye gomologi mogut prevozmoch' pogreshnosti énergeticheskikh otsenok i sdelat' vozmozhnym predskazaniie prostranstvennykh struktur belkov.

One still cannot predict the 3D fold of a protein from its amino acid sequence, mainly because of errors in the energy estimates underlying the prediction. However, a recently developed theory [1] shows that having a set of homologs (i.e., the chains with equal, in despite of numerous mutations, 3D folds) one can average the potential of each interaction over the homologs and thus predict the common 3D fold of protein family even when a correct fold prediction for an individual sequence is impossible because the energies are known only approximately. This theoretical conclusion has been verified by simulation of the energy spectra of simplified models of protein chains [2], and the further investigation of these simplified models shows that their true "native" fold can be found by folding of the chain where each interaction potential is averaged over the homologs. In conclusion, the applicability of the "homolog-averaging" approach is tested by recognition of real protein 3D structures. Both the gapless threading of sequences onto the known protein folds [3] and the more practically important gapped threading (which allows to consider not only the known 3D structures, but the more or less similar to them folds as well) shows a significant increase in selectivity of the native chain fold recognition.

[Estimation of quality of approximation of atom-atom contacts of amino acid residues in proteins by the contacts of the residue force centers]. / Orsenka kachestva priblizheniia atom-atomnykh kontaktov aminokislotnykhostatkov v belkakh kontaktami silobykh tsentrov etikh ostatkov.

How precisely the atom-atom contacts of amino acid residues in proteins can be approximated by the contacts of amino acid residue "force centers"? To answer this question, we examined the force centers positioned in the C alpha-atom, the C beta-atom, in the optimal point of the C alpha-C beta axis, and in the geometrical center of residues. The maximal coefficient of correlation between the residue force center contacts and the presence of atom-atom contacts of the residues (85%) was obtained for the force centers positioned in geometrical centers of the residues. The correlation is 80% for the optimal position of the centers on the C alpha-C beta axes; a somewhat smaller value (78%) is obtained for the force centers positioned in C beta-atoms, and 71% only for the centers positioned in C alpha-atoms. The obtained results allow one to estimate the limit of precision of calculations which replace the atom-atom interactions by interactions of amino acid residues taken as a whole.

[The morphogenetic reactions of the ectoderm in the early gastrula of the clawed toad to mechanical stretching]. / Morfogeneticheskie reaktsii éktodermy rannei gastruly shportsevoi liagushki na mekhanicheskoe rastiazhenie.

The ventral ectoderm explants of the Xenopus laevis early gastrula were stretched on an elastic substrate 1.5- to twofold for 30 min, then fixed in the stretched state and incubated for up to 6 h. The stretching of explants generated their two-phase active reaction, which was estimated using the criterion of eccentricity of cells and whole explants developed in this study. At the first phase, during the external force application, the explant cells were elongated towards its stretching to a markedly greater extent than the whole explant: eccentricity of the whole cells exceeded that of the whole explants. Cell processes elongated in the same direction appeared, cell contacts and apical cytoskeleton structures developed, and mechanical tensions increased. At the second phase, within 5 h after the stretching, the shape of individual cells, rather than the whole explant, returned to the initial one (approximately isotropic), mechanical tensions decreased, and visible morphogenesis of the explant proceeded: it acquired a complex shape with longitudinal groove and polar thickenings. We conclude that intercalary movements of the cells are present at the second phase of the active explant reaction and morphogenesis is realized at the phase of relaxation of mechanical tensions.