STON: A novel method for protein three-dimensional structure comparison

Protein structure comparison is an important problem in bioinformatics and has many applications in the study of structural and functional genomics. During the last decades, various heuristic methods have been developed to solve the protein structure comparison problem. Most of the protein structure comparison methods give the alignment based on the minimum RMSD (root mean square deviation) and ignore many significant local alignments that may be important for evolutional or functional studies. We have developed a new algorithm to find aligned residues in two proteins with desired RMSD value. The parameterized distance and rotation in this program enable us to search for strongly or weakly similar aligned fragments in two proteins.     

A modified method of endothelium impregnation suitable for pathology studies]

Prolonged fixation worsens the quality of the endothelium boundaries silver impregnation. A modified method is suggested: the vessel segment is fixed in 2.5% glutaraldehyde for 5 min with subsequent conservation in the saline till the impregnation. Incubation in the saline for 24 hours preserves the susceptibility of endothelium to silver impregnation.     

A method for the differential staining of muscle and connective tissues from organs and their complexes]

The method of differential staining of muscles and connective tissue in the genitourinary organs (urinary bladder, ureters, renal pelvis) and gastrointestinal tract is suggested. The method consists of the intermittent use of known tissue van Gieson dyes (picric acid and fuchsin). When applied at pH = 7.2-8.0 (phosphate or citrate buffer) they stain the connective tissue in red and muscles in gold-yellow colour. A saturated solution of picric acid was mixed at equal proportions with water-free glycerol. Fuchsin was taken as 0.3% buffered solution or as 1% solution applied on the organ intermittently with picric acid. The organs, before staining, are fixed in 0.3 alcoholic solution of carbonic acid.     

New method of studying the release of fibrinolysis activators in tissue cultures

Tissue culture in the presence of a standard fibrin clot containing plasminogen can be used to detect and estimate quantitatively the release of fibrinolysis activators into the media (by measuring the quantity of fibrin-fibrinogen degradation products). By the method described it is possible to study regulation of the release of fibrinolysis activators by tissues in vitro.Laboratory for the Study of Blood Clotting, General Hospital, Malmö, Sweden. (Presented by Academician of the Academy of Medical Sciences of the USSR S. E. Severin.) Translated from Byulleten' Éksperimental'noi Biologii i Meditsiny, Vol. 84, No. 8, pp. 250–253, August, 1977.     

A method for studying shape change in children

A method is given measuring shape change with age, utilizing two dimensional body outlines. Problems of standardization for overall size are discussed and it is shown how the method can be used to draw D'Arcy Thompson-type transformation grids. The method is applied to serial measurements on a girl from 31/2 to 19 years of age.     

A new three-dimensional dose distribution reduction scheme for tubular organs

In tubular structures, spatial aspects of the dose distribution may be important in determining the normal tissue response. Conventional dose-volume-histograms (DVHs) and dose-surface-histograms (DSHs) lack spatial information and may not be adequate to represent the three-dimensional (3D) dose data. A new 3D dose distribution data reduction scheme which preserves its longitudinal and circumferential character is presented. Dose distributions were generated at each axial level for esophagus or rectum in 123 patients with lung cancer or prostate cancer. Dose distribution histograms at each axial level were independently analyzed along the esophageal or rectal circumference to generate dose-circumference-histogram (DCH) sheets. Two types of plots were then generated from the DCH sheet. The first considered the percentage of the circumference at each axial level receiving various doses. The second considered the minimum dose delivered to any percentage of the circumference at each axial level. The DCH as a treatment planning tool can be easily implemented in a 3D planing system and is potentially useful for the study of the relationship between the complication risk and the longitudinal and circumferential dose distributions.     

Immunofluorescent method of studying autopsy material in acute pneumonia]

The immunofluorescent procedure in examinations of the autopsy material from 304 fatal cases hospitalized for acute pneumonia permitted to diagnose influenza A2 in 29.0%, influenza B in 18.1%, parainfluenza in 3.5%, adenovirus infection in 9.2% and respiratory syncytial virus infection in 3.5% of the cases. In the period of a high incidence of acute respiratory infection, influenza A2 was detected by this method in 40.9% and influenza B in 50% of the cases. Simultaneous examinations of the material in the influenza epidemic period by virological and immunofluorescent methods (63 cases) in 13 cases positive results were obtained with both methods, in 6 cases where influenza viruses were detected the immunofluorescent test was negative, and in 28 cases the positive diagnosis by the immunofluorescent test could not be confirmed virologically. Among the cases examined, 33 were found by the immunofluorescence test to have a mixed respiratory infection, including influenza A2 with other forms of respiratory infection in 18, and influenza B with other respiratory infections in 19 cases. Serological examinations by the complement fixation and hemagglutination inhibition tests on the blood from fatal cases irrespective of the time of examination, as a rule, revealed antibody in low titres which did not confirm the diagnosis.     

A method for studying antibiotic concentrations in inflammatory exudate

A new technique is described for studying antibiotic concentrations in an experimental inflammatory exudate in vivo. In most exudates concentrations of four antistaphylococcal drugs which were of potential therapeutic significance could be assayed, and fucidin appeared to diffuse best. Higher concentrations of all antibiotics gained access to the lesion in the first two hours of inflammation, suggesting that their mobility did not depend on binding to cells during the inflammatory response. The technique may ultimately help to elucidate the relationship between antibiotics and host defences at the primary sites of infection.     

A thermoelectric method for studying the cerebral circulation in unanesthetized dogs

Summary The use of a thermoelectric method for the study of blood supply to the brain in unanesthetized dogs is described. Modified flat Noyons' thermoelectrodes were placed on the intact dura mater in the partetal region or in the area of the superior sagittal sinus. 4 dogs with such thermoelectrodes were under continuous observation from 7 to 19 days following the operation. It was established by these experiments that in these conditions the thermoelectrodes are quite sensitive to the changes of the blood flow of the brain. These changes in the superior sagittal sinus and in the parietal region are similar when the same influence is exerted.Presented by Active Member of the Acad. Med. Sci. USSR V. V. Parin     

A simulation method for studying scintillation camera collimators

This paper presents a computer simulation of photon interaction with collimator septa, which allows the point spread function of scintillation camera collimators to be calculated. The method simulates photon attenuation along their propagation direction in a determinist way. Using this simulation, the spatial resolution, geometric efficiency and penetration index of collimators may be easily assessed. Results obtained with this method are presented and compared with those obtained from standard formulae. We show the usefulness of the simulation which precisely accounts for effects of septum penetration. Measurements performed on two collimators with 131I and 99Tcm point sources provide results consistent with those obtained from the simulation method. In conclusion we show that this method is an accurate tool to assist conception of collimators for nuclear medicine.     

The fine structure of human Golgi tendon organs as studied by three-dimensional reconstruction

Summary Human Golgi tendon organs (GTOs) found at the musculo-tendinous junctions of lumbrical muscles were studied using serial sections for light and electron microscopy as the basis for a three-dimensional reconstruction.These GTOs had a thick capsule and were filled with longitudinally arranged collagen bundles. The GTOs were divided into three small compartments by septal cells: the neuronal compartment containing myelinated nerve fibres, the terminal compartment having axon terminals, and the fibrous compartment containing only collagen fibrils. The three-dimensional reconstruction demonstrated that myelinated fibres rotated spirally before losing their myelin sheaths, and ended as unmyelinated axon terminals in the terminal compartment. Axons abruptly changed course at the beginning of the terminals. Axon terminals extended many thin processes between the collagen fibrils, partially encircling them. Part of the axolemma of such indentations lacked Schwann cell coverings. The intimate contact of collagen fibrils with the axon teminals, especially in the indentations of the axons, are the presumptive site that could transmit shearing stresses to the axolemma, especially in areas devoid of Schwann cell cytoplasm.     

A search for a model tissue for studying effects of thiazide diuretics

A search was made for a model tissue of NaCl absorption which would be sensitive to inhibition by diuretics of the thiazide type. A lack of such a model through the years has hampered the analysis of the cellular mechanism of action of this important class of drugs. Using the short-circuit current technique, the urinary bladders of the toads Bufo spinosus and Bufo marinus, and the frog Rana temporaria were investigated regarding the effects of various thiazides. These bladders have NaCl absorptive properties similar to those of the distal renal tubules, and are claimed to be sensitive to the inhibitory effect of thiazides on sodium transport. The short-circuit current (SCC), which is representative of the sodium transport across the epithelium, was reduced by cyclopenthiazide and polythiazide, but only at high concentrations (above 0.1 mM). To rule out the possibility that this was an unspecific effect, attempts were made to block the effect by the 'thiazide blocker' Ex 4877, but without success. This finding, together with the fact that dose-response curves were difficult to obtain, would indicate that these epithelia are not suitable for the stated purpose. Preliminary studies were also conducted on the urinary bladder of the plaice, Pleuronectes platessa, which has a different system of NaCl absorption that is claimed to be rapidly and reversibly inhibited by thiazides. Polythiazide, added to both sides of the bladder, had no effect on SCC.     

A simple method for studying operant wheel running in rats

The present report describes an operant running device for rats. The apparatus makes use of an activity wheel driven by a small electric motor. The motor is started by a bar press; one activated, the wheel turns for 3–30 sec. depending on the setting of a timing device. The system is well suited to long term studies of activity patterns.