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Biomedical subjects

R Srinivasan

Publications and source records attributed to R Srinivasan.

At least 73 records · Page 4Linked to original sources
PubMed2000

The three point vernier alignment or acuity test (3Pt VA test): an analysis of variance.

A very useful clinical vernier acuity or vernier alignment test has been developed in this and associated laboratories over a span of two decades. We seek to refine further this test, to seek internal inconsistencies and to optimize parameters used in a variety of devices and environments. Vernier testing, and many aspects of this work have been considered by numerous able scientists over a long time period (not reviewed here), but none have encountered conditions faced by this group, particularly in the developing world. The three point vernier alignment (acuity) threshold test (3Pt VeA test) employed here has broad applications; it can be used as a clinical test of vision status, for triage, and as a reference standard for vision testing (in general). As one example, if sufficient luminance is employed, the test is applicable in the presence of truly dense media disorders, even advanced leucomas, mature cataracts, intraocular bleeds, as well as combinations of these disorders, with or without a window to the retina. Only retinal and centrally-based neural disorders, eccentricity from fixation, and about 50% of hypermature cataracts affect outcomes. With minor alterations, this test can be employed to assess the visual field. An analysis of variance (ANOVA) was performed on a defined set of parameters, to enable us to understand better the special properties and requirements associated with this test. Results are not significantly altered between ages 10-94 years (not assessed here). Employing settings well above threshold for test spot detection and well separated individual test spots, changes in test spot luminance, or background luminance (or adaptation level), contrast, veiling glare, test spot size, clear and variously degraded images, seem not to affect meaningfully measured outcomes. If an observer can define well a center of gravity for each test spot viewed, he can align the three points with remarkable precision.

Adult↗
PubMed1999

A physical basis for protein secondary structure.

A physical theory of protein secondary structure is proposed and tested by performing exceedingly simple Monte Carlo simulations. In essence, secondary structure propensities are predominantly a consequence of two competing local effects, one favoring hydrogen bond formation in helices and turns, the other opposing the attendant reduction in sidechain conformational entropy on helix and turn formation. These sequence specific biases are densely dispersed throughout the unfolded polypeptide chain, where they serve to preorganize the folding process and largely, but imperfectly, anticipate the native secondary structure.

Protein Conformation↗
PubMed1999

Coupling and uncoupling of tumor immunity and autoimmunity.

Self-antigens, in the form of differentiation antigens, are commonly recognized by the immune system on melanoma and other cancers. We have shown previously that active immunization of mice against the melanocyte differentiation antigen, a tyrosinase-related protein (TRP) gp75(TRP-1) (the brown locus protein) expressed by melanomas, could induce tumor immunity and autoimmunity manifested as depigmentation. In this system, tumor immunity and autoimmunity were mediated by autoantibodies. Here, we characterize immunity against another tyrosinase family glycoprotein TRP-2 (the slaty locus protein), using the same mouse model and method of immunization. As observed previously for gp75(TRP-1), immunity was induced by DNA immunization against a xenogeneic form of TRP-2, but not against the syngeneic gene, and depended on CD4(+) cells. Immunization against TRP-2 induced autoantibodies and autoreactive cytotoxic T cells. In contrast to immunization against gp75(TRP-1), both tumor immunity and autoimmunity required CD8(+) T cells, but not antibodies. Only autoimmunity required perforin, whereas tumor immunity proceeded in the absence of perforin. Thus, immunity induced against two closely related autoantigens that are highly conserved throughout vertebrate evolution involved qualitatively different mechanisms, i.e., antibody versus CD8(+) T cell. However, both pathways led to tumor immunity and identical phenotypic manifestations of autoimmunity.

Animals↗
PubMed1999

Quantitative structure-activity relationship (QSAR) analysis of surfactants influencing attachment of a Mycobacterium sp. to cellulose acetate and aromatic polyamide reverse osmosis membranes.

A series of 23 neutral, anionic, and zwitterionic surfactants were tested at a concentration of 0.1% wt/vol for their influence on attachment of a Mycobacterium sp. to cellulose acetate (CA) and polyamide (PA) reverse osmosis (RO) membranes. Four cell attachment bioassays were used: (1) semiconcurrent addition of surfactant and bacteria to RO coupons (standard assay); (2) surfactant pretreatment of RO membranes (membrane pretreatment assay); (3) surfactant treatment of adsorbed cells (detachment assay); and (4) surfactant pretreatment of mycobacteria (cell pretreatment assay). Seventeen surfactants inhibited attachment to PA membranes, whereas 15 inhibited attachment to CA in standard assays and, in 13 cases, the same surfactant inhibited attachment to both PA and CA. Despite greater cell attachment to PA than CA, surfactants were typically more effective in the former membrane system. More surfactants were effective in impairing cell attachment than in promoting detachment and a number enhanced attachment in membrane pretreatment assays, suggesting surface modification of RO membranes. Cell pretreatment inhibited attachment to CA membranes, suggesting the bacterial surface was also a target for detergent activity. Multivariate regression and cluster analyses indicated that critical micellar concentration (CMC) was positively correlated with Mycobacterium attachment in CA and PA standard assays. Surfactant dipole moment and octanol/water partitioning (LogP) also contributed to detergent activity in the PA system, whereas dipole moment, molecular topology (i.e., connectivity indices), and charge properties influenced activity in the CA system. Influential variables in membrane pretreatment assays included the LogP, topology indices, and charge properties, whereas CMC played a diminished role. Surfactant dipole moment was most influential in CA membrane detachment assays. Increasing system ionic strength by LiBr addition strengthened inhibition of cell attachment to CA membranes by dodecylbenzene sulfonic acid (DBSA) and promoted DBSA adsorption to CA surfaces as indicated by attenuated total reflection Fourier-transform infrared spectrometry. Results indicate that inhibition of bacterial attachment to RO membranes may be maximized by manipulating surfactant molecular structure to optimize surface adsorption behavior.

Bacterial Adhesion↗
PubMed1999

A complete conformational map for RNA.

A simple stereochemical framework for understanding RNA structure has remained elusive to date. We present a comprehensive conformational map for two nucleoside-5',3'-diphosphates and for a truncated dinucleotide derived from a grid search of all potential conformers using hard sphere steric exclusion criteria to define allowed conformers. The eight-dimensional conformational space is presented as a series of two-dimensional projections. These projections reveal several well-defined allowed and disallowed regions which correlate well with data obtained from X-ray crystallography of both large and small RNA molecules. Furthermore, the two-dimensional projections show that consecutive and ribose ring-proximal torsion angles are interdependent, while more distant torsion angles are not. Remarkably, using steric criteria alone, it is possible to generate a predictive conformational map for RNA.

Nucleic Acid Conformation↗
PubMed1999

Increased synchronization of neuromagnetic responses during conscious perception.

In binocular rivalry, the observer views two incongruent images, one through each eye, but is conscious of only one image at a time. The image that is perceptually dominant alternates every few seconds. We used this phenomenon to investigate neural correlates of conscious perception. We presented a red vertical grating to one eye and a blue horizontal grating to the other eye, with each grating continuously flickering at a distinct frequency (the frequency tag for that stimulus). Steady-state magnetic fields were recorded with a 148 sensor whole-head magnetometer while the subjects reported which grating was perceived. The power of the steady-state magnetic field at the frequency associated with a grating typically increased at multiple sensors when the grating was perceived. Changes in power related to perceptual dominance, presumably reflecting local neural synchronization, reached statistical significance at several sensors, including some positioned over occipital, temporal, and frontal cortices. To identify changes in synchronization between distinct brain areas that were related to perceptual dominance, we analyzed coherence between pairs of widely separated sensors. The results showed that when the stimulus was perceived there was a marked increase in both interhemispheric and intrahemispheric coherence at the stimulus frequency. This study demonstrates a direct correlation between the conscious perception of a visual stimulus and the synchronous activity of large populations of neocortical neurons as reflected by stimulus-evoked steady-state neuromagnetic fields.

Adult↗
PubMed1999

Gene identification in bacterial and organellar genomes using GeneScan.

The performance of the GeneScan algorithm for gene identification has been improved by incorporation of a directed iterative scanning procedure. Application is made here to the cases of bacterial and organnellar genomes. The sensitivity of gene identification was 100% in Plasmodium falciparum plastid-like genome (35 kb) and in 98% in the Mycoplasma genitalium genome (approximately 580 kb) and the Haemophilus influenzae Rd genome (approximately 1.8 Mb). Sensitivity was found to improve in both the Open Reading Frames (ORFs) which have been identified as genes (by homology or by other methods) and those that are classified as hypothetical. False positive assignments (at the nucleotide level) were 0.25% in H. influenzae genome and 0.3% in M. genitalium. There were no false positive assignments in the plastid-like genome. The agreement between the GeneScan predictions and GeneMark predictions of putative ORFs was 97% in M. genitalium genome and 86% in H. influenzae genome. In terms of an exact match between predicted genes/ORFs and the annotation in the databank, GeneScan performance was evaluated to be between 72% and 90% in different genomes. We predict five putative ORFs that were not annotated earlier in the GenBank files for both M. genitalium and H. influenzae genomes. Our preliminary analysis of the newly sequenced G + C rich genome of Mycobacterium tuberculosis H37Rv also shows comparable sensitivity (99%).

Algorithms↗
PubMed1999

EEG coherency II: experimental comparisons of multiple measures.

OBJECTIVE: A concentric spheres model was used in an earlier paper to estimate the effects of volume conduction, reference electrode and spatial filtering on different EEG coherence measures. EEG data are used here to verify theoretical predictions. METHODS: Three EEG data sets were: (1) 64 channel, recorded during 7 alternating periods of resting and mental calculation. (2) 128 channel, for comparison of eyes open versus eyes closed coherence. (3) 128 channel, recorded during deep sleep (stages 3 and 4) and REM. RESULTS: The directions of large scale (lobeal) coherency changes between brain states are relatively independent of coherence measure. However, coherence between specific electrode pairs is sensitive to method and frequency. Average reference and digitally linked mastoids provide reasonable semi-quantitative estimates of large-scale neocortical source coherence. Close bipolar, Laplacian, and dura image methods remove most reference electrode and volume conduction distortion, but may underestimate coherence by spatial filtering. CONCLUSION: Each EEG coherence method has its own potential sources of error and provides coherence estimates for different neural population sizes located in different locations. Thus, studies of coherence and brain state should include several different kinds of estimates to take full advantage of information in recorded signals.

Adolescent↗
PubMed1999

Spatial structure of the human alpha rhythm: global correlation in adults and local correlation in children.

OBJECTIVE: The maturation of the neocortex during childhood and adolescence involves dramatic increases in white-matter volume. EEG recordings from children and adults were examined to determine whether there are associated changes in spatial properties of dynamic processes in the neocortex. METHODS: Spontaneous eyes-closed and eyes-open EEG were recorded at 128 electrodes in 20 children aged 6-11 years and 23 adults aged 18-23 years. The surface Laplacian algorithm was applied to improve the spatial resolution of each electrode. Power and coherence were used to characterize the spatial structure of the alpha rhythm. A stochastic field model was used to eliminate coherences that are inflated due to volume conduction. RESULTS: In adults, the alpha rhythm is characterized by very high coherence between distant electrodes. The children demonstrated reduced anterior power and coherence between anterior and posterior electrodes at the peak alpha frequency in comparison to the adults. The Laplacian alpha rhythm demonstrated much higher power in the children at both anterior and posterior electrodes, but was weakly correlated between electrodes. CONCLUSIONS: The maturation of neocortex in late childhood involves increased global correlation by long-range corticocortical connections. The local correlation that contributes power to each electrode, independent of other electrodes, is reduced as the global correlation increases.

Adolescent↗
PubMed1999

Recombinant expression and characterization of dentin matrix protein 1.

Dentin matrix protein 1 (DMP1) is an extracellular matrix noncollagenous protein (NCP) initially isolated from dentin and now found to be present in calcified tissues like calvaria and long bone. The characteristic feature of DMP1 is that it contains a large number of acidic domains and has properties which implicate it as a key participant in regulating matrix mineralization. The level of DMP1 in the tissue is sparse and it is not easily isolated from dentin because it copurifies with other dentin NCPs. The exact function of DMP1 is not known and this is due to the inherent difficulty of obtaining enough protein from the mineralized tissues. In order to understand the physiologic role for DMP1 during the formation of mineralized tissues we have produced milligram quantities of recombinant DMP1 in E. coli. The objective of this work was: (1) to prepare unmodified apoprotein so that it could be used for studying the function of DMP1; and (2) to prepare polyclonal antibody against the recombinant DMP1 antigen. The DMP1 polyclonal antibody did not cross-react with other NCPs present in dentin or with bone acidic glycoprotein-75 (BAG-75) present in the bone matrix, confirming the specificity of this antibody and thus making it a valuable tool to determine the in vivo function of DMP1.

Amino Acid Sequence↗
PubMed1999

Sessile polypoid gastric heterotopia of rectum: a report of 2 cases and review of the literature.

OBJECTIVE: The term heterotopia, a term derived from Greek, implies "other place." It refers to the finding of normal tissues at foreign sites. Heterotopic gastric tissue rarely involves the large bowel. We report 2 cases of this rare entity. DATA SOURCES: Case reports of 2 patients with sessile polypoid lesion in the rectum, with a review of the available literature, using both MEDLINE and relevant bibliographies of published articles. RESULTS: Biopsies of the rectal lesions in our 2 cases revealed the presence of gastric tissue. Only 27 other such cases have been reported in the English literature. CONCLUSIONS: Patients with rectal gastric heterotopia usually present with bleeding, but other presentations and complications are possible. Endoscopic or surgical excision is the treatment of choice, although the lesions also respond to histamine 2 receptor blockers.

Adult↗
PubMed1999

Expression of the c-erbB-3/HER-3 and c-erbB-4/HER-4 growth factor receptors and their ligands, neuregulin-1 alpha, neuregulin-1 beta, and betacellulin, in normal endometrium and endometrial cancer.

The objective of this study was to determine the immunohistochemical expression of the c-erbB-3 and c-erbB-4 growth factor receptors and their principal ligands, the neuregulins and betacellulin, in normal endometrium and determine whether there was evidence of under- or overexpression in endometrial adenocarcinoma. Immunohistochemistry was performed using well-characterized antibodies against each of the five proteins analyzed on formalin-fixed, paraffin-embedded archival material. Forty-three normal endometrial samples (16 proliferative, 19 secretory, and 8 hyperplastic) and 41 endometrial adenocarcinoma cases were analyzed. There was variable expression of the growth factor receptors and the ligands in the two principal phases of the menstrual cycle as well as in endometrial adenocarcinoma. In normal endometrium, the c-erbB-3 receptor was weakly expressed in both phases. The c-erbB-4 receptor and all of the ligands examined, neuregulin alpha, neuregulin beta, and betacellulin, were expressed at significantly higher levels in the secretory as compared with the proliferative phase of the menstrual cycle, suggesting a role for these proteins in endometrial maturation. In endometrial adenocarcinoma, overexpression of c-erbB-3, c-erbB-4, and betacellulin with underexpression of neuregulin a as compared with normal controls was observed. Neuregulin beta expression was not found to be significantly different in the two groups. These results suggest that signaling through the c-erbB-3 and c-erbB-4 receptors and the ligands neuregulin alpha, neuregulin beta, and betacellulin are important in endometrial carcinogenesis.

Amino Acid Sequence↗
PubMed1999

Injection of DNA encoding granulocyte-macrophage colony-stimulating factor recruits dendritic cells for immune adjuvant effects.

An important issue for effective vaccines is the development of potent adjuvants that can facilitate induction or augmentation of immunity. Granulocyte-macrophage colony-stimulating factor (GM-CSF) is a growth factor for myeloid progenitors of monocytes and dendritic cells (DC), which upon maturation are antigen-presenting cells (APC). The adjuvant effects of inoculation of DNA encoding GM-CSF into skin were studied. Initial experiments examined whether the GM-CSF gene injected into the skin of mice could affect the density of epidermal DC (Langerhans cells). DNA encoding GM-CSF delivered by particle bombardment into skin resulted in a significant increase of epidermal DC at the inoculation site. Kinetic analysis of epidermal recruitment after GM-CSF inoculation showed an increase in DC that peaked at seven days. This increase was accompanied by recruitment of DC into draining lymph nodes. The adjuvant effects of DNA encoding GM-CSF inoculated into skin were measured by the ability to augment antibody and T-cell responses against poorly immunogenic tumor antigens. Peptide immunization at skin sites containing epidermal DC newly recruited by GM-CSF DNA elicited T-cell responses against mutant p53, whereas peptide immunization of control skin sites did not elicit any detectable T-cell responses. Likewise, generation of antibodies following immunization with DNA encoding human gp75TRP1, a tyrosinase family member expressed by melanomas, was accelerated and protection from tumor challenge augmented by GM-CSF DNA.

Adjuvants, Immunologic↗
PubMed1999

Bacterial contamination of anterior chamber during IOL surgery.

PURPOSE: To study the nature and frequency of bacterial contamination during cataract surgery. METHODS: The preoperative smears from the conjunctiva and anterior chamber (AC) fluid aspirates during extra-capsular cataract surgery (ECCE) with posterior chamber intraocular lens (PCIOL) implantation in 40 eyes were analysed for aerobic and anaerobic bacteria. Any change in the bacterial strains isolated before and after cataract surgery was also studied. RESULTS: AC fluid aspirates were positive for bacteria in 15 eyes (37.5%). Coagulase-negative Staphylococcus was the most common aerobe (39.4%) and Propionibacterium acnes the most common anaerobe. Of the 15 cases with positive AC fluid cultures, 6 showed an organism in the AC aspirate different from the conjunctival smear. CONCLUSION: Clinically there was no endophthalmitis in any of the eyes. Factors such as preoperative antibiotic use, the antibacterial properties of aqueous, or low inoculum size could explain this. The preoperative conjunctival smear may not be useful in predicting the AC fluid contamination or outcome of cataract surgery.

Adult↗
PubMed1999

Susceptibility of Phlebotomus argentipes and P. papatasi (Diptera: Psychodidae) to insecticides.

Field collected fully fed adults of Phlebotomus argentipes and P. papatasi were screened in the laboratory for susceptibility to DDT, BHC, malathion, deltamethrin, permethrin, lambdacyhalothrin and bendiocarb. Pondichery strain of P. papatasi and P. argentipes showed variations in their susceptibility to insecticides. Both the species were resistant to permethrin but tolerant to DDT and malathion with LD99.99 values of 13.88, 1.92, 1.08 and 34.63, 4.69, 16.32 times more than the deterministic doses respectively. However, they were susceptible to bendiocarb with LD99.99 7.6 and 1.6 times lower than the deterministic doses. While P. papatasi was susceptible to BHC, P. argentipes showed tolerance (1.6 times). The former showed tolerance to deltamethrin and the latter exhibited resistance (34 times). It was reverse in case of lamdacyhalothrin. High susceptibility of the vector sandflies to bendiocarb suggests that this insecticide could be used effectively against OP and pyrethroid resistant populations for Kalaazar control.

Animals↗