PubMed Health⌕ Search

Biomedical subjects

S Selvaraj

Publications and source records attributed to S Selvaraj.

At least 19 recordsLinked to original sources
PubMed2006

FOLD-RATE: prediction of protein folding rates from amino acid sequence.

We have developed a web server, FOLD-RATE, for predicting the folding rates of proteins from their amino acid sequences. The relationship between amino acid properties and protein folding rates has been systematically analyzed and a statistical method based on linear regression technique has been proposed for predicting the folding rate of proteins. We found that the classification of proteins into different structural classes shows an excellent correlation between amino acid properties and folding rates of two and three-state proteins. Consequently, different regression equations have been developed for proteins belonging to all-alpha, all-beta and mixed class. We observed an excellent agreement between predicted and experimentally observed folding rates of proteins; the correlation coefficients are, 0.99, 0.97 and 0.90, respectively, for all-alpha, all-beta and mixed class proteins. The prediction server is freely available at http://psfs.cbrc.jp/fold-rate/.

Internet↗
PubMed2006

Suicide in farmers in Scotland.

INTRODUCTION: Farmers and farm workers have higher than expected rates of suicide and undetermined deaths in UK studies, and some rural areas of Scotland have higher than average male suicide rates. Firearm access seems to be an influencing factor in England and Wales. Type of farming, and farming social networks may also be important. This article describes suicide and undetermined deaths in male farmers and farm workers in Scotland from 1981-1999 using anonymised, routine data. METHOD: Deaths of men aged 15-74 years from suicide or undetermined cause were identified from anonymised Scottish death records. Farmers and farm workers were identified using occupation codes. Methods of suicide used by farmers were compared with those of the general male population of the same age. A multiple linear regression was used to examine the influence of farm type, and the proportion of farmers in the working population of an area. RESULTS: 307 male farmers or farm workers died by suicide or undetermined cause in the time period. The overall rate was 31.4/100,000 per year (95% CI 28.1-35.1). Deaths using firearms were over-represented (29% of farming deaths compared with 3.6% in the general male population). There was no significant association between the male suicide rate in an area, and the farming suicide rate. Areas with lower proportions of farmers tended to have higher rates of farming suicide and undetermined deaths. This one factor described 85% of the variance among areas. CONCLUSION: Deaths were substantially more likely to involve firearms than suicide and undetermined deaths in the general male population. Less use of other methods did not completely compensate for this, indicating that method availability is likely to contribute to farming suicide rates. Farmers in areas where farming is less common were more likely to die by suicide, and this described most of the differences among areas. Networks and social supports may be important protective factors for farmers.

Accidental Falls↗
PubMed2005

Deprivation, smoking, and quality of life in asthma.

AIMS: To explore associations of deprivation and smoking, with prevalence of asthma, wheeze, and quality of life. METHODS: Survey, using International Study of Asthma and Allergies in Childhood (ISAAC) methodology, of children aged 13-14 years attending Scottish schools previously surveyed in 1995. RESULTS: 4665/5247 (89%) pupils completed questionnaires. 3656/4665 (78.4%) had missed school for any reason in the last 12 months, 587 (12.6%) because of asthma or wheeze. Compared to children with 1-3 wheeze attacks per year, those with >12 attacks in the last year were more likely to have missed school, twice as likely to have missed physical education in the last month, to report interference with home activities, or to have visited accident and emergency departments, and three times more likely to have been hospitalised. Deprivation was not independently associated with self-reported asthma or wheeze, but was associated with school absence, either for any reason or specifically for asthma or wheeze, but not with use of services such as accident and emergency visits, doctor visits, or hospital admissions. Active smoking was associated with wheezy symptoms, and active and passive smoking with use of medical services. These associations were independent of wheeze severity, treatment taken, and other associated atopic conditions. Smoking also had an impact on school absence and home and school activities. CONCLUSIONS: Deprivation does not affect the prevalence of asthma or wheeze. Exposure to cigarette smoke was associated with the increased use of services. Deprivation and smoking have independent adverse effects on the quality of life in subjects with asthma or wheeze.

Absenteeism↗
PubMed2004

Randomized double-blind clinical trial comparing topical and sub-Tenon's anaesthesia in routine cataract surgery.

BACKGROUND: Several local anaesthetic techniques are available for cataract surgery. Recently, topical anaesthesia has gained in popularity. A randomized trial was designed to compare patient discomfort and intraoperative complications following routine cataract surgery under topical or sub-Tenon's anaesthesia. METHODS: A randomized double-blinded placebo-controlled clinical trial of 210 patients assigned to either a sub-Tenon's group (sub-Tenon's anaesthesia with placebo topical balanced salt solution, n=140) or a topical anaesthesia group (topical anaesthesia with placebo sub-Tenon's injection of balanced salt solution, n=70) was carried out. All patients underwent phacoemulsification with intraocular lens implantation. Patients in the sub-Tenon's group received a single injection (3 ml) of a combination of lidocaine 2% (2 ml) and bupivacaine 0.75% (1 ml), and four doses of topical placebo (balanced salt solution). Patients in the topical anaesthesia group received four doses of topical proxymethocaine 0.5% and a placebo sub-Tenon's injection (3 ml) of balanced salt solution. No intracameral injection of local anaesthetic was given. A 10-point visual analogue pain scale was used preoperatively and for postoperative pain assessment immediately after the operation and 30 min postoperatively. The intraoperative complications in the two groups were recorded. RESULTS: The mean pain score immediately after surgery was 2.42 (sd 2.2) in the sub-Tenon's group and 3.44 (2.3) in the topical anaesthesia group (P=0.0043). The mean pain score 30 min after surgery was 1.24 (1.7) in the sub-Tenon's group and 2.25 (2.2) in the topical anaesthesia group (P=0.0009). CONCLUSIONS: Patients undergoing cataract surgery under topical anaesthesia experience more postoperative discomfort than patients receiving sub-Tenon's anaesthesia. Surgery-related complications were similar in both groups.

Adult↗
PubMed2004

Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins.

Understanding the folding pathways of proteins is a challenging task. The Phi value approach provides a detailed understanding of transition-state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two-state proteins and compared the Phi values of each mutant residue. We found that most of the residues with high Phi value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as alpha-helical, SH3 domains of all-beta proteins, beta-sandwich, and alpha/beta proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Phi values with long-range contacts, which will be helpful to understand the transition-state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long-range contacts during the transition state.

Acid Anhydride Hydrolases↗
PubMed2004

A(1,3)-strain mediated epimerization of 2e,3e,5e,6e-tetraarylpiperidin-4-one oximes.

A series of tri- and tetraarylpiperidin-4-one oximes were synthesized from 2e,3e,6e-tri- and 2e,3e,5e,6e-tetraarylpiperidin-4-ones, respectively. In the case of the latter compounds, oximation is accompanied by epimerization at C-5 to avoid the A(1,3)-strain between the oxime OH group and the 5e-aryl ring of the initially formed oxime resulting in 2e,3e,5a,6e-tetraarylpiperidin-4-one oximes. 1H, 13C and 2D NMR spectroscopic data were employed to characterize and investigate the stereochemistry of these compounds.

Anti-Infective Agents↗
PubMed2004

Inter-residue interactions in protein folding and stability.

During the process of protein folding, the amino acid residues along the polypeptide chain interact with each other in a cooperative manner to form the stable native structure. The knowledge about inter-residue interactions in protein structures is very helpful to understand the mechanism of protein folding and stability. In this review, we introduce the classification of inter-residue interactions into short, medium and long range based on a simple geometric approach. The features of these interactions in different structural classes of globular and membrane proteins, and in various folds have been delineated. The development of contact potentials and the application of inter-residue contacts for predicting the structural class and secondary structures of globular proteins, solvent accessibility, fold recognition and ab initio tertiary structure prediction have been evaluated. Further, the relationship between inter-residue contacts and protein-folding rates has been highlighted. Moreover, the importance of inter-residue interactions in protein-folding kinetics and for understanding the stability of proteins has been discussed. In essence, the information gained from the studies on inter-residue interactions provides valuable insights for understanding protein folding and de novo protein design.

Animals↗
PubMed2004

Folding mechanism of all-beta globular proteins.

Elucidating the mechanism for the fast folding of proteins is a challenging task. In our earlier work, we introduced the concept of "long-range order" and related it successfully to protein folding rates. In this article, we propose a new hypothesis for the folding of two-state all-beta proteins. The mechanism is based on the formation of a hydrophobic core, propagation of beta-strands, and the establishment of hydrogen bonds. Our hypothesis has been strengthened by the observation of a folding nucleus in beta-strands and the hydrogen-bonding network between residues in beta-strands. Our insights on protein folding show an excellent agreement with experimental observations.

Algorithms↗
PubMed2004

Childhood asthma in the Highlands of Scotland--morbidity and school absence.

BACKGROUND: The prevalence of childhood asthma in Scotland is one of the highest in the world. The morbidity secondary to allergic diseases is significant in terms of costs to the nation and effects on the family including the child. AIMS: The aims of this study were to describe the prevalence of asthma, eczema and hay fever in the Highlands of Scotland and in the Shetland Isles and to examine factors in relation to quality of life and social deprivation. METHOD: A total population survey of 12 year old children using a parent completed questionnaire. RESULTS: 86.3% (2658/3080) returned questionnaires. Of the 2549 questionnaires analysed, 476 (18.7%) reported asthma ever, 362 (14.2%) wheeze in last 12 months, 508 (19.9%) reported hay fever ever and 555 (21.8%) reported eczema ever. Of the children reporting asthma or wheeze, 35.4% (229/647) had missed school because of asthma or wheeze, 38.0% (246/647) had missed physical education. 62.5% (354/566) of subjects with wheeze ever reported sleep disturbance. Deprivation measured by DEPCAT scores was associated with maternal smoking and bronchitis in the child but not with allergic diseases. CONCLUSION: Compared with previous studies, the prevalence of asthma was unchanged but eczema has increased in Highland adolescents. Allergic disease has a significant impact on school attendance and physical activity. Deprivation was associated with maternal smoking and bronchitis in the child but not with allergic diseases. The impact of allergic diseases in rural areas may be different from urban areas.

Absenteeism↗
PubMed2003

Role of hydrophobic clusters and long-range contact networks in the folding of (alpha/beta)8 barrel proteins.

Analysis on the three dimensional structures of (alpha/beta)(8) barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered (alpha/beta)(8) barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent beta-strands of the (alpha/beta)(8) barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (alpha/beta)(8) barrel proteins are proposed.

Algorithms↗
PubMed2003

Characteristics associated with reported CAM use in patients attending six GP practices in the Tayside and Grampian regions of Scotland: a survey.

OBJECTIVES: To study the nature of CAM use in primary care attenders, the involvement of their NHS healthcare professionals in their CAM care and differences in characteristics between CAM users and non-users. DESIGN: Postal questionnaire for primary care attenders and analysis of practice leaflets. SETTING: Six Scottish GP practices with a range of practice size, CAM provision within practice, deprivation and rurality. RESULTS: Five hundred and fourteen primary care attenders described 1194 incidences of CAM use and gave details about their main therapy. 37% had contact with a practitioner, the rest mainly self-prescribed. The perceived effectiveness of CAM was high. Patients used CAM for a variety of health problems, mainly as an adjuvant to orthodox medicine rather than an alternative. The involvement of the NHS in CAM delivery was small but there is a significant role to ensure patient safety, especially regarding herb-drug interactions. Disclosure rate of CAM use was low. CAM offered options in areas where the provision in the NHS is difficult, including musculo-skeletal and mental health problems. Provision of CAM by the GP is associated with higher CAM use in primary care attenders. CONCLUSIONS: It is recommended that healthcare professionals include patients' use of CAM in history taking and clinical decision making.

Adolescent↗
PubMed2002

Influence of medium- and long-range interactions in different folding types of globular proteins.

Recognition of protein fold from amino acid sequence is a challenging task. The structure and stability of proteins from different fold are mainly dictated by inter-residue interactions. In our earlier work, we have successfully used the medium- and long-range contacts for predicting the protein folding rates, discriminating globular and membrane proteins and for distinguishing protein structural classes. In this work, we analyze the role of inter-residue interactions in commonly occurring folds of globular proteins in order to understand their folding mechanisms. In the medium-range contacts, the globin fold and four-helical bundle proteins have more contacts than that of DNA-RNA fold although they all belong to all-alpha class. In long-range contacts, only the ribonuclease fold prefers 4-10 range and the other folding types prefer the range 21-30 in alpha/beta class proteins. Further, the preferred residues and residue pairs influenced by these different folds are discussed. The information about the preference of medium- and long-range contacts exhibited by the 20 amino acid residues can be effectively used to predict the folding type of each protein.

Amino Acids↗
PubMed2002

Important amino acid properties for determining the transition state structures of two-state protein mutants.

Understanding the mechanism in the folding pathways of proteins is an important problem in molecular biology. The Phi-value analysis provides insight into the transition state structures during protein folding. In this work, we have analyzed the relationship between the observed Phi values upon mutations in two-state proteins (FK506 binding protein, chymotrypsin inhibitor and src SH3 domain) and the changes in 48 various physico-chemical, energetic and conformational properties. We found that the classification of mutations based on solvent accessibility improved the correlation significantly. The relationship between conformational properties and Phi values determines the presence/absence of secondary structures in the transition state. In buried mutations, the physical properties volume, shape and flexibility, and the thermodynamic properties enthalpy, entropy and free-energy change have significant correlation with Phi. The short and medium-range non-bonded energy in partially buried mutations and average long-range contacts in exposed mutations showed a strong correlation with Phi values. Multiple regression analysis incorporating combinations of three properties from among all possible combinations of the 48 properties increased the correlation coefficient up to 0.99, by an average rise of 20% for all the data sets. Information about local sequence and structure is more important in surface mutations than those in buried mutations for explaining the transition state structures of two-state proteins. Further, the implications of our results for understanding the process of protein folding have been discussed.

Amino Acid Sequence↗
PubMed2002

The Sivaganga eye survey: I. Blindness and cataract surgery.

PURPOSE: To assess the prevalence of visual acuity impairment, blindness, and cataract surgery among older adults in rural southern India. METHODS: Random selection of village- and urban-based clusters was used to identify a cross-sectional sample of persons 50 years of age or older from the Sivaganga district of Tamil Nadu. Subjects in 25 selected clusters were enumerated through a door-to-door survey and invited to examination sites for measurement of uncorrected, presenting, and best-corrected visual acuity and ocular examination in 1999. The principal cause was identified for eyes with presenting visual acuity worse than 6/18. Quality assurance monitoring of visual acuity measurements took place in five of the study clusters. RESULTS: A total of 5081 persons in 3517 households were enumerated, and 4642 (91.4%) were examined. Thirty-six percent presented with visual acuity worse than 6/18 in the better eye. The prevalence of blindness, based on visual acuity worse than 6/60 in both eyes, was 6.0% (95% confidence interval [CI]: 5.1% to 6.9%) with presenting vision, and 2.5% (95% CI: 1.8% to 3.1%) with best correction. Blindness with presenting visual acuity was associated with older age and illiteracy. Cataract was the principal cause of blindness in one or both eyes in 69.4% of those presenting blind, and uncorrected aphakia and other refractive error affected 35.6% in at least one eye. The prevalence of cataract surgery was 14.7% (95% CI: 13.0% to 16.4%); low surgical coverage among the cataract blind was associated with illiteracy. CONCLUSIONS: It appears that much has been done in the prevention of blindness in Sivaganga. Nevertheless, blindness remains an important public health problem, mainly because of cataract and refractive error. Prevention of blindness programs in the area should target these two causes, with special emphasis on the elderly and the illiterate.

Age Distribution↗
PubMed2002

The Sivaganga eye survey: II. Outcomes of cataract surgery.

PURPOSE: To assess the clinical outcomes of cataract surgery in rural southern India. METHODS: Cluster sampling was used in randomly selecting a cross-sectional sample of persons 50 years of age or older for visual acuity measurement, refraction, and ocular examination in 1999. Subjects were queried as to the date and place of surgery for each cataract-operated eye. Surgical complications were noted and the principal cause of reduced vision was identified for eyes with presenting visual acuity worse than 6/18. RESULTS: Within the cataract-operated sample of 682 persons, 13.8% had presenting visual acuity worse than 6/60 in both eyes, 25.2% better than or equal to 6/18 in both eyes, and 37.8% were bilaterally operated on. For aphakic eyes, 50.5% presented with visual acuity better than or equal to 6/18; 82.6% with best-correction. For pseudophakic eyes, the corresponding percentages were 78.0% and 94.5%. Over one-third of all eyes were pseudophakic, and nearly three-fourths had been operated on in non-governmental facilities. Uncorrected aphakia and other refractive error were the main causes of vision impairment. In multiple logistic regression modeling, poor presenting visual acuity in aphakic eyes was associated with illiteracy, rural residence, and surgery in government facilities; gender and time period of surgery were not predictors of vision outcomes. None of these variables were associated with best-corrected outcomes in aphakic eyes, nor with presenting and best-corrected outcomes in pseudophakic eyes. CONCLUSIONS: Visual acuity outcomes in pseudophakic eyes were good. More attention must be given to needless vision impairment among the cataract-operated because of inadequate aphakic correction, especially among those operated on in government facilities, the illiterate, and those living in rural villages.

Aged↗
PubMed2002

Snow sports injuries in Scotland: a case-control study.

OBJECTIVES: To examine the incidence and patterns of snow sports injuries at the three largest commercial ski areas in Scotland and to identify factors associated with injury risk. METHODS: A prospective case-control study of all injured people at Cairngorm, Glenshee, and Nevis Range ski areas during the 1999-2000 winter season. Personal details, snow sports related variables, diagnosis, and treatment were recorded. Control data were collected at random from uninjured people at all three areas. Random counts were performed to analyse the composition of the on slope population. RESULTS: A total of 732 injuries were recorded in 674 people. Control data were collected from 336 people. The injury rate for the study was 3.7 injuries per 1000 skier days. Alpine skiers comprised 67% of the on slope population, snowboarders 26%, skiboarders 4%, and telemark skiers 2%. Lower limb injuries and sprains were the commonest injuries in alpine skiers and skiboarders. Snowboarders sustained more injuries to the upper limb and axial areas. Skiboarders and snowboarders had a higher incidence of fractures. After adjustment for other variables, three factors were all independently associated with injury: snowboarding (odds ratio (OR) 4.07, 95% confidence interval (CI) 1.65 to 10.08), alpine skiing (OR 3.82, CI 1.6 to 9.13), and age <16 years (OR 1.9, CI 1.14 to 3.17). More than five days of experience in the current season and at least one week of experience in total had a protective effect against injury. CONCLUSIONS: Despite a change in the composition of the alpine population at Scottish ski areas, the overall rate and pattern of injury are similar to those reported previously in comparable studies. Several factors are associated with an increased risk of injury and should be targeted in future injury prevention campaigns.

Adolescent↗
PubMed2001

Role of medium--and long-range interactions in discriminating globular and membrane proteins.

The analysis of inter-residue interactions in protein structures provides considerable insight to understand their folding and stability. We have previously analyzed the role of medium- and long-range interactions in the folding of globular proteins. In this work, we study the distinct role of such interactions in the three-dimensional structures of membrane proteins. We observed a higher number of long-range contacts in the termini of transmembrane helical (TMH) segments, implying their role in the stabilization of helix-helix interactions. The transmembrane strand (TMS) proteins are having appreciably higher long-range contacts than that in all-beta class of globular proteins, indicating closer packing of the strands in TMS proteins. The residues in membrane spanning segments of TMH proteins have 1.3 times higher medium-range contacts than long-range contacts whereas that of TMS proteins have 14 times higher long-range contacts than medium-range contacts. Residue-wise analysis indicates that in TMH proteins, the residues Cys, Glu, Gly, Pro, Gln, Ser and Tyr have higher long-range contacts than medium-range contacts in contrast with all-alpha class of globular proteins. The charged residue pairs have higher medium-range contacts in all-alpha proteins, whereas hydrophobic residue pairs are dominant in TMH proteins. The information on the preference of residue pairs to form medium-range contacts has been successfully used to discriminate the TMH proteins from all-alpha proteins. The statistical significance of the results obtained from the present study has been verified using randomized structures of TMH and TMS protein templates.

Amino Acids↗