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1.  Polymorphisms in two DNA repair genes (XPD and XRCC1) – association with age related cataracts 
Molecular Vision  2011;17:127-133.
Age related cataract is the leading cause of blindness in the world today. The association between DNA damage to the lens epithelium and the development of lens opacities has been reported in many studies. Polymorphisms of DNA repair enzymes may affect repair efficiency and thereby lead to the development of age related cataract.
In this study, we aimed to determine the frequency of polymorphisms in two DNA repair enzyme genes, xeroderma pigmentosum complementation group (XPD) codon 312 and X-ray complementing group1 (XRCC1) codon 399, in a sample of 208 cataract patients (69 with cortical, 69 with nuclear and 70 with posterior sub capsular) and 151 sex and age matched healthy controls. XPD genotype was determined by Amplification Refractory Mutation System (ARMS) while XRCC1 was genotyped using the PCR-RFLP method.
There was a significant difference between frequencies for XPD-312 Asn/Asn genotype in cataract patients (21.6%) and healthy controls (13.2%; p=0.03, OR=1.97, 95% CI=1.06–3.63). Considering the types of cataract, XPD-312 Asn/Asn genotype was found to be significantly different in patients with cortical (29%) type in comparison to controls (13.2%; p=0.03, OR=2.39, 95% CI=1.11–5.12). No statistically significant difference was found for the genotypic and allelic distributions of the polymorphism in XRCC1. The MDR interaction analysis revealed weak synergism between the markers XPD-Asp312Asn and XRCC1-Arg399Gln contributing to cataract. It also showed that the AA genotype of XPD-Asp312Asn polymorphism when present in combination with the GA genotype of XRCC1-Arg399Gln had a fivefold and with AA had a fourfold risk for developing cataract.
The present study suggests that a polymorphism in XPD codon 312 may be associated with the development of maturity onset cataract. This is the first report on the association of XPD Asp312Asn polymorphism with maturity onset cataract.
PMCID: PMC3021570  PMID: 21245954
2.  Hyaluronic Acid as an Adjunct to Scaling and Root Planing in Chronic Periodontitis. A Randomized Clinical Trail 
Aim: Aim of the present study was to evaluate the adjunctive effect of local application of hyaluronon gel following scaling and root planing (SRP) in chronic periodontitis patients.
Materials and Methods: In this randomized split mouth study 33 subjects with chronic periodontitis were evaluated after full mouth SRP. In the test sites hyaluronon gel was applied immediately after SRP and one week post therapy, the control sites were treated with SRP alone. Bleeding on probing (BOP), probing pocket depth (PPD), and clinical attachment level (CAL) were recorded at baseline, 4 wk and 12 wk.
Results: Significant reduction in BOP scores was observed in both the groups at 12weeks (p<0.001). The hyaluronon group showed a greater reduction in BOP (p<0.001). In the hyaluronon group the mean PPD at baseline was 6.33±0.09 which reduced to 2.49±0.51 at 12 weeks which was statistically significant (p<0.001). In the control group the mean PPD at baseline was 6.09±1.26 which reduced to 4.36±1.29 at 12 weeks which was statistically significant (p<0.001). The CAL measurements showed a significant difference between the groups (p<0.001) at 12 wk post therapy.
Conclusion: Hyaluronic Acid (HA) has a beneficial effect on periodontal health in patients with chronic Periodontitis. HA appears to be a suitable candidate as an adjunct to SRP in chronic periodontitis patients.
PMCID: PMC4316327  PMID: 25654021
Chronic periodontitis; Clinical trial; Hyaluronic acid; Root planing
3.  Two-dimensional sum-frequency generation (2D SFG) reveals structure and dynamics of a surface-bound peptide 
Surface-bound polypeptides and proteins are increasingly used to functionalize inorganic interfaces such as electrodes, but their structural characterization is exceedingly difficult with standard technologies. In this paper, we report the first two-dimensional sum-frequency generation (2D SFG) spectra of a peptide monolayer, which is collected by adding a mid-IR pulse shaper to a standard femtosecond SFG spectrometer. On a gold surface, standard FTIR spectroscopy is inconclusive about the peptide structure because of solvation-induced frequency shifts, but the 2D lineshapes, anharmonic shifts, and lifetimes obtained from 2D SFG reveal that the peptide is largely α-helical and upright. Random coil residues are also observed, which do not themselves appear in SFG spectra due to their isotropic structural distribution, but which still absorb infrared light and so can be detected by cross-peaks in 2D SFG spectra. We discuss these results in the context of peptide design. Because of the similar way in which the spectra are collected, these 2D SFG spectra can be directly compared to 2D IR spectra, thereby enabling structural interpretations of surface-bound peptides and biomolecules based on the well-studied structure/2D IR spectra relationships established from soluble proteins.
PMCID: PMC3956615  PMID: 24372101
4.  Evaluation of antibacterial and antifungal activity of new calcium-based cement (Biodentine) compared to MTA and glass ionomer cement 
To evaluate the antibacterial and antifungal properties of calcium-based cement, Biodentine (Ca3SiO2), compared to commercial glass ionomer cements (GICs) and mineral trioxide aggregate (MTA).
Materials and Methods:
Pellets of GICs, ProRoot MTA, and Biodentine were prepared to test the influence of these cements on the growth of four oral microbial strains: Streptococcus mutans, Enterococcus faecalis, Escherichia coli, and Candida albicans; using agar diffusion method. Wells were formed by removing the agar and the manipulated materials were immediately placed in the wells. The pellets were lodged in seeded plates and the growth inhibition diameter around the material was measured after 24-72 h incubation at 37°C. The data were analyzed using analysis of variance (ANOVA) test to compare the differences among the three cements at different concentrations.
Test indicates that the antimicrobial activity of Biodentine, on all the microorganisms tested, was very strong, showing a mean inhibition zone of 3.2 mm, which extends over time towards all the strains. For Biodentine, GIC, and MTA, the diameters of the inhibition zones for S. mutans were significantly larger than for E. faecalis, Candida, and E. coli (P < 0.05).
All materials showed antimicrobial activity against the tested strains except for GIC on Candida. Largest inhibition zone was observed for Streptococcus group. Biodentine created larger inhibition zones than MTA and GIC.
PMCID: PMC4313478  PMID: 25657526
Antibacterial activity; giodentine; inhibition zone; MTA
5.  Adapting to the health impacts of climate change in a sustainable manner 
Globalization and Health  2014;10(1):82.
The climate is changing and this poses significant threats to human health. Climate change is one of the greatest challenges facing Pacific Island countries and territories due to their unique geophysical features, and their social, economic and cultural characteristics. The Pacific region also faces challenges with widely dispersed populations, limited resources and fragmented health systems. Over the past few years, there has been a substantial increase in international aid for health activities aimed at adapting to the threats of climate change. This funding needs to be used strategically to ensure an effective approach to reducing the health risk from climate change. Respecting the principles of development effectiveness will result in more effective and sustainable adaptation, in particular, 1) processes should be owned and driven by local communities, 2) investments should be aligned with existing national priorities and policies, and 3) existing systems must not be ignored, but rather expanded upon and reinforced.
PMCID: PMC4271334  PMID: 25498769
Climate; Change; Adaptation; Health; Resilience; Development effectiveness; Harmonisation; Alignment
6.  Surface Bond Strength in Nickel Based Alloys 
Bonding of ceramic to the alloy is essential for the longevity of porcelain fused to metal restorations. Imported alloys used now a days in processing them are not economical. So this study was conducted to evaluate and compare the bond strength of ceramic material to nickel based cost effective Nonferrous Materials Technology Development Center (NFTDC), Hyderabad and Heraenium S, Heraeus Kulzer alloy. An Instron testing machine, which has three-point loading system for the application of load onto the specimen was utilized for analyzing bond strength of both alloys. Student t test was conducted and t value obtained was 0.644, and the mean value of flexural bond strength of indigenous alloy is 81.75 with standard deviation of 12.25 and of imported alloy is 84.42 with standard deviation of 10.35, indicating that there was no significant difference between the two alloys. Due to ever increasing cost of imported non-precious alloy the need for a cost-effective replacement was fulfilled by indigenous NFTDC alloy.
PMCID: PMC3792308  PMID: 24431791
Nickel based alloy; Surface bond strength; Flexural strength
7.  Recent Developments in β-Cell Differentiation of Pluripotent Stem Cells Induced by Small and Large Molecules 
Human pluripotent stem cells, including human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs), hold promise as novel therapeutic tools for diabetes treatment because of their self-renewal capacity and ability to differentiate into beta (β)-cells. Small and large molecules play important roles in each stage of β-cell differentiation from both hESCs and hiPSCs. The small and large molecules that are described in this review have significantly advanced efforts to cure diabetic disease. Lately, effective protocols have been implemented to induce hESCs and human mesenchymal stem cells (hMSCs) to differentiate into functional β-cells. Several small molecules, proteins, and growth factors promote pancreatic differentiation from hESCs and hMSCs. These small molecules (e.g., cyclopamine, wortmannin, retinoic acid, and sodium butyrate) and large molecules (e.g. activin A, betacellulin, bone morphogentic protein (BMP4), epidermal growth factor (EGF), fibroblast growth factor (FGF), keratinocyte growth factor (KGF), hepatocyte growth factor (HGF), noggin, transforming growth factor (TGF-α), and WNT3A) are thought to contribute from the initial stages of definitive endoderm formation to the final stages of maturation of functional endocrine cells. We discuss the importance of such small and large molecules in uniquely optimized protocols of β-cell differentiation from stem cells. A global understanding of various small and large molecules and their functions will help to establish an efficient protocol for β-cell differentiation.
PMCID: PMC4284775  PMID: 25526563
beta (β) cells; diabetes; differentiation; stem cells; pancreas
8.  Secretory prostate apoptosis response (Par)-4 sensitizes multicellular spheroids (MCS) of glioblastoma multiforme cells to tamoxifen-induced cell death 
FEBS Open Bio  2014;5:8-19.
•Multicellular spheroids (MCS) express low levels of Par-4 and are resistant to TAM-induced cytotoxicity.•Par-4 is secreted in TAM-treated monolayers but not MCS and is crucial for cell death.•Secretory Par-4 (from TAM-treated cells) renders MCS sensitive to cell death.•Inhibitors to AKT/PKCζ sensitized MCS to TAM-induced cytotoxicity.•A combination of TAM with PI3K inhibitor resulted in secretory Par-4.
Glioblastoma multiforme (GBM) is the most malignant form of brain tumor and is associated with resistance to conventional therapy and poor patient survival. Prostate apoptosis response (Par)-4, a tumor suppressor, is expressed as both an intracellular and secretory/extracellular protein. Though secretory Par-4 induces apoptosis in cancer cells, its potential in drug-resistant tumors remains to be fully explored. Multicellular spheroids (MCS) of cancer cells often acquire multi-drug resistance and serve as ideal experimental models. We investigated the role of Par-4 in Tamoxifen (TAM)-induced cell death in MCS of human cell lines and primary cultures of GBM tumors. TCGA and REMBRANT data analysis revealed that low levels of Par-4 correlated with low survival period (21.85 ± 19.30 days) in GBM but not in astrocytomas (59.13 ± 47.26 days) and oligodendrogliomas (58.04 ± 59.80 days) suggesting low PAWR expression as a predictive risk factor in GBM. Consistently, MCS of human cell lines and primary cultures displayed low Par-4 expression, high level of chemo-resistance genes and were resistant to TAM-induced cytotoxicity. In monolayer cells, TAM-induced cytotoxicity was associated with enhanced expression of Par-4 and was alleviated by silencing of Par-4 using specific siRNA. TAM effectively induced secretory Par-4 in conditioned medium (CM) of cells cultured as monolayer but not in MCS. Moreover, MCS were rendered sensitive to TAM-induced cell death by exposure to conditioned medium (CM)-containing Par-4 (derived from TAM-treated monolayer cells). Also TAM reduced the expression of Akt and PKCζ in GBM cells cultured as monolayer but not in MCS. Importantly, combination of TAM with inhibitors to PI3K inhibitor (LY294002) or PKCζ resulted in secretion of Par-4 and cell death in MCS. Since membrane GRP78 is overexpressed in most cancer cells but not normal cells, and secretory Par-4 induces apoptosis by binding to membrane GRP78, secretory Par-4 is an attractive candidate for potentially overcoming therapy-resistance not only in malignant glioma but in broad spectrum of cancers.
PMCID: PMC4309838
CM, conditioned medium; GBM, glioblastoma multiforme; LGG, low grade gliomas; MCS, multicellular spheroids; TAM, tamoxifen; TCGA, The Cancer Genome Atlas; Glioblastoma; Par-4; Drug resistance; Multicellular spheroids (MCS); Tamoxifen; Cytotoxicity
9.  Sclerotium rolfsii Lectin Induces Stronger Inhibition of Proliferation in Human Breast Cancer Cells than Normal Human Mammary Epithelial Cells by Induction of Cell Apoptosis 
PLoS ONE  2014;9(11):e110107.
Sclerotium rolfsii lectin (SRL) isolated from the phytopathogenic fungus Sclerotium rolfsii has exquisite binding specificity towards O-linked, Thomsen-Freidenreich (Galβ1-3GalNAcα1-Ser/Thr, TF) associated glycans. This study investigated the influence of SRL on proliferation of human breast cancer cells (MCF-7 and ZR-75), non-tumorigenic breast epithelial cells (MCF-10A) and normal mammary epithelial cells (HMECs). SRL caused marked, dose-dependent, inhibition of proliferation of MCF-7 and ZR-75 cells but only weak inhibition of proliferation of non-tumorigenic MCF-10A and HMEC cells. The inhibitory effect of SRL on cancer cell proliferation was shown to be a consequence of SRL cell surface binding and subsequent induction of cellular apoptosis, an effect that was largely prevented by the presence of inhibitors against caspases -3, -8, or -9. Lectin histochemistry using biotin-labelled SRL showed little binding of SRL to normal human breast tissue but intense binding to cancerous tissues. In conclusion, SRL inhibits the growth of human breast cancer cells via induction of cell apoptosis but has substantially less effect on normal epithelial cells. As a lectin that binds specifically to a cancer-associated glycan, has potential to be developed as an anti-cancer agent.
PMCID: PMC4217719  PMID: 25364905
10.  Fish oil rich in eicosapentaenoic acid protects against oxidative stress-related renal dysfunction induced by TCDD in Wistar rats 
Cell Stress & Chaperones  2013;19(3):409-419.
Humans are systemically exposed to persistent organic pollutants, of which 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has become a major environmental concern. Exposure to TCDD results in a wide variety of adverse health effects which is mediated by oxidative stress through CYP1A1 activation and arachidonic acid metabolites. Eicosapentaenoic acid (EPA) exhibits antioxidant property and competes with arachidonic acid in membrane phospholipids and produces anti-inflammatory EPA derivatives. Since both EPA and its derivatives have been reported to enhance the antioxidant mechanism, the present study aimed at studying whether EPA could offer protection against TCDD-induced oxidative stress and nephrotoxicity in Wistar rats. Estimation of kidney markers (serum urea and creatinine) and histopathological studies revealed that EPA treatment significantly reduced TCDD-induced renal damage. TCDD-induced oxidative damage was reflected in a significant increase in CYP1A1 activity and lipid peroxide levels with a concomitant decline in non-enzymic antioxidant (GSH) and various enzymic antioxidants such catalase (CAT), superoxide dismutase (SOD), glutathione-S-transferase (GST), and glutathione peroxidase (GPx). In addition, TCDD-induced oxidative stress also resulted in decline in Na+-K+ and Mg2+ATPases activities with increase in Ca2+ ATPases activity. Oral treatment with EPA showed a significant cytoprotection against TCDD-induced renal oxidative stress by decreased CYP1A1 activity and enhanced antioxidant status. TCDD-induced alterations in ATPase enzyme activities were also prevented by EPA treatment. Our results show clear evidence that EPA ameliorates TCDD-induced oxidative stress and kidney damage; thus suggest the potential of EPA as an effective therapeutic agent against toxic effects mediated through redox imbalance.
PMCID: PMC3982028  PMID: 24114387
CYP1A1; EPA; Fish oil; Oxidative stress; TCDD
11.  NS1 Antigen Capture ELISA an Effective Method for Diagnosis of Early Dengue Infection - Report of an Outbreak at Angul District, Odisha, India 
Background: An outbreak of dengue infection occurred in Angul district of Odisha in the month of August & September, 2011. The study was undertaken to detect NS1 antigen positivity among the study population, to compare IgM capture ELISA with NS1 antigen detection for diagnosis of dengue and to identify the predominant genotype of Dengue virus responsible for the outbreak.
Materials and Methods: Total 1020 serum samples were collected from clinically suspected cases of dengue from the outbreak. All were subjected for NS1 antigen detection, 92 were selected based on their clinical severity of illness (fever, rash, bleeding manifestation, arthralgia) for further study of IgM ELISA and platelet count and 148 NS1 positive samples were selected from different Blocks of Anugul district for RT-PCR at NIV, Pune, India.
Results: Five hundred and thirteen (50.2%) samples were positive for NS1 antigen (highly significant p-value <0.0001, C.I - 95%) with 88% positivity during 1-5 days. The NS1 Ag positivity was peaked to 86.9% on days 3 to 5 (Sensitivity & NPV - 100% each) & declined to 6.2% during 6-10 days with a low sensitivity of 7.14% but 100% specificity & PPV. However, the IgM antibody positivity was 81.2% on days 6 to 10 and 87.5% after 10 days (Sensitivity- 100%, Specificity-13.33%,PPV-7.14% & NPV - 100%). RT-PCR resulted 32.4% positivity (6- DEN1, 39 - DEN 2 & 3- DEN 3) among which 20% were in IgM +ve & 68% in IgM -ve cases.
Conclusion: Therefore, early diagnosis of dengue could be mainly by NS1 antigen detection whereas Ig M ELISA is a better tool during the later stage of infection &RT-PCR is more effective in IgM -ve cases.The predominant genotype responsible for the outbreak was found to be DEN-2.
PMCID: PMC4190715  PMID: 25302194
Antigen detection; Dengue outbreak; IgM ELISA
12.  Comparison of Stresses Around Dental Implants Placed in Normal and Fibula Reconstructed Mandibular Models using Finite Element Analysis 
Purpose: This study was formulated to evaluate and compare stresses around endosseous implants in various normal and fibula reconstructed mandibular models using finite element analysis method.
Materials and Methods: CT scan data of a completely edentulous patient and a fibula reconstructed patient was made and the Dicom images were used to design 3-D mandibular models using software. Based on the information from the scan data, various types of reconstructed FEA models were made. Implants (fixtures) and superstructures were then embedded in each model and Von Mises stress around the neck of each implant under a vertical loading of 200 N and Horizontal load of 50 N was calculated using finite element structural analysis software. The results were compared between the reconstructed mandible and their respective normal mandible.
Results: Higher stress values were obtained for all the reconstructed types under horizontal loading and in reconstructed models involving larger area of reconstruction the stress were more. In the models involving smaller area of reconstruction like symphysis alone or body alone there is no significant change in the stress values on vertical loading.
Conclusion: Stresses were comparatively smaller in mandibles involving a smaller area of reconstruction. Hence, fixed prosthesis could be advised and a bar retained over denture for reconstruction for larger area of reconstruction.
PMCID: PMC4190793  PMID: 25302267
Fibula graft; Finite element analysis; Mandible reconstruction; Mandible rehabilitation; Von mises stress
13.  Congenital lymphatic hypoplasia in unilateral lower limb with abnormal technetium-99m sulphur colloid uptake in both breasts 
We present a patient with Meige like lymphedema (left lower limb hypoplasia) with asymptomatic minimal accumulation of Technetium-99m sulfur colloid in bilateral breasts. We attribute the possible pathology to accumulation of interstitial fluid in hypoplastic left lower limb leading to dilatation of the remaining outflow tracts and valvular incompetence. This may be causing reversal of flow from subcutaneous tissues into the dermal plexus involving the breast. Other possibilities include formation of spontaneous lymphovenous shunt or lymphatic intercommunication at lower trunk level as a result of increased pressure leading to minimal lymph accumulation in breasts. Later a mammogram was performed which was found to be normal. MR also confirmed no cisterna chyli abnormalities or aberrant lymphatic channels in lower thorax region that may be the explanation for the abnormal sulphur colloid uptake in both breasts.
PMCID: PMC4228596  PMID: 25400372
Congenital lymphedema; lymphoscintigraphy; lymphatic lower limb hypoplasia; sulfur colloid uptake in breasts; technetium-99m sulfur colloid
14.  ACE-II genotype and I allele predicts ischemic stroke among males in south India 
Meta Gene  2014;2:661-669.
Two hundred ischemic stroke patients and 193 age and sex matched healthy controls were studied for the presence of Angiotensin Converting Enzyme Insertion/Deletion (ACE I/D) gene polymorphism. The PCR studies revealed that ACE ‘II’ (OR = 2.055; p = 0.004) genotype and ‘I’ (OR = 1.411; p = 0.018) alleles were significantly associated with IS patients. Gender specific analysis revealed a strong association of ‘II’ (OR = 2.044; p = 0.014) genotype and ‘I’ (OR = 1.531; p = 0.011) allele with male sex. Classification of patients based on TOAST criteria, revealed a significant association for ‘II’ genotype (OR = 1.713; p = 0.043) and ‘I’ (OR = 1.382; p = 0.039) allele in LVD patients only. When the data was stratified based on age and sex, a statistically significant association was observed for ACE ‘II’ genotype (OR = 2.288; p = 0.006) and ‘I’ allele (OR = 1.395; p = 0.054) in IS male patients of > 50 years of age. The ACE ‘D’ allele was found to be increased in controls (OR = 0.709; p = 0.018) than IS patients. Multivariate logistic regression analysis showed that smoking and diabetes were the most powerful independent risk factor in LVD type of stroke. Thus, we presented here an evidence for a strong association of ACE ‘II’ genotype and ‘I’ allele compounded by factors such as smoking and diabetes among south Indian IS patients.
•ACE II and I allele were significantly associated with south Indian IS patients.•Gender specific association (ACE II and I) were observed only in IS male patients.•Smoking was the most powerful independent predictor for LVD subtypes of stroke.
PMCID: PMC4287818  PMID: 25606450
Ischemic stroke; Large vessel disease; ACE (I/D); Genotype; Polymorphism; Hypertension
15.  High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon 
G3: Genes|Genomes|Genetics  2014;4(11):2219-2230.
We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.
PMCID: PMC4232547  PMID: 25227227
high-density genetic map; genotyping by sequencing; genome-wide recombination rate; linkage disequilibrium; selective sweep; watermelon
16.  The Effects of Two Different Ankle-Foot Orthoses on Gait of Patients with Acute Hemiparetic Cerebrovascular Accident 
Objective. To compare the effects of two types of ankle-foot orthoses on gait of patients with cerebrovascular accident (CVA) and to evaluate their preference in using each AFO type. Design. Thirty individuals with acute hemiparetic CVA were tested without an AFO, with an off-the-shelf carbon AFO (C-AFO), and with a custom plastic AFO (P-AFO) in random order at the time of initial orthotic fitting. Gait velocity, cadence, stride length, and step length were collected using an electronic walkway and the subjects were surveyed about their perceptions of each device. Results. Subjects walked significantly faster, with a higher cadence, longer stride, and step lengths, when using either the P-AFO or the C-AFO as compared to no AFO (P < 0.05). No significant difference was observed between gait parameters of the two AFOs. However, the subjects demonstrated a statistically significant preference of using P-AFO in relation to their balance, confidence, and sense of safety during ambulation (P < 0.05). Moreover, if they had a choice, 50.87 ± 14.7% of the participants preferred the P-AFO and 23.56 ± 9.70% preferred the C-AFO. Conclusions. AFO use significantly improved gait in patients with acute CVA. The majority of users preferred the P-AFO over the Cf-AFO especially when asked about balance and sense of safety.
PMCID: PMC4174983  PMID: 25276433
17.  Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon 
BMC Genomics  2014;15(1):767.
A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. The marker density required for conducting successful association mapping depends on the extent of linkage disequilibrium (LD) within a population. Use of genotyping by sequencing reveals large numbers of SNPs that in turn generate opportunities in genome-wide association mapping and marker-assisted selection, even in crops such as watermelon for which few genomic resources are available. In this paper, we used genome-wide genetic diversity to study LD, selective sweeps, and pairwise FST distributions among worldwide cultivated watermelons to track signals of domestication.
We examined 183 Citrullus lanatus var. lanatus accessions representing domesticated watermelon and generated a set of 11,485 SNP markers using genotyping by sequencing. With a diverse panel of worldwide cultivated watermelons, we identified a set of 5,254 SNPs with a minor allele frequency of ≥ 0.05, distributed across the genome. All ancestries were traced to Africa and an admixture of various ancestries constituted secondary gene pools across various continents. A sliding window analysis using pairwise FST values was used to resolve selective sweeps. We identified strong selection on chromosomes 3 and 9 that might have contributed to the domestication process. Pairwise analysis of adjacent SNPs within a chromosome as well as within a haplotype allowed us to estimate genome-wide LD decay. LD was also detected within individual genes on various chromosomes. Principal component and ancestry analyses were used to account for population structure in a genome-wide association study. We further mapped important genes for soluble solid content using a mixed linear model.
Information concerning the SNP resources, population structure, and LD developed in this study will help in identifying agronomically important candidate genes from the genomic regions underlying selection and for mapping quantitative trait loci using a genome-wide association study in sweet watermelon.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-767) contains supplementary material, which is available to authorized users.
PMCID: PMC4246513  PMID: 25196513
Linkage disequilibrium; GWAS; Selective sweep; Population structure; Genotyping by sequencing; Watermelon; Citrullus lanatus var. lanatus
18.  High Prevalence of Exfoliative Toxins Among Carrier Isolates of Staphylococcus aureus from Healthy Individuals from Various Communities in Chennai, South India 
Indian Journal of Microbiology  2013;53(3):288-290.
Staphylococcusaureus causes infections both in community and hospital settings, nasal carriage is the important source of these infections. A total of 103 carrier isolates of S. aureus from 352 asymptomatic individuals were screened for methicillin-resistant S. aureus (MRSA) and exfoliative toxins (A, B and D) by two sets of multiplex PCRs. The overall nasal carriage of MRSA was found to be 13/352 (3.7 %), of which 4 were found to be positive for Panton valentine leucocidin (PVL). Twelve (11.65 %) strains were found to carry exfoliative toxins and belonged to one of the following spa types t159, t209 and t1515. High prevalence of exfoliative toxins, pvl and MRSA pose a major threat to public health, since the isolates were from the healthy in various community settings.
PMCID: PMC3689394  PMID: 24426124
CA-MRSA; pvl; Exfoliative toxins; t159; t209; SCCmec
19.  Truncation of the peptide sequence in bifunctional ligands with mu and delta opioid receptor agonist and neurokinin 1 receptor antagonist activities 
Bioorganic & medicinal chemistry letters  2013;23(17):10.1016/j.bmcl.2013.06.065.
The optimization and truncation of our lead peptide-derived ligand TY005 possessing eight amino-acid residues was performed. Among the synthesized derivatives, NP30 (Tyr1-DAla2-Gly3-Phe4-Gly5-Trp6-O-[3′,5′-Bzl(CF3)2]) showed balanced and potent opioid agonist as well as substance P antagonist activities in isolated tissue-based assays, together with significant antinociceptive and antiallodynic activities in vivo.
PMCID: PMC3810412  PMID: 23899615
bifunctional compounds; opioid receptor agonists; neutokinin-1 receptor antagonists; Truncation of peptide sequence; NMR structure
20.  Comparative Evaluation of Tensile Bond Strength between Silicon Soft Liners and Processed Denture Base Resin Conditioned by Three Modes of Surface Treatment: An Invitro Study 
Soft denture liners act as a cushion for the denture bearing mucosa through even distribution of functional load, avoiding local stress concentrations and improving retention of dentures there by providing comfort to the patient. The objective of the present study was to compare and evaluate the tensile bond strengths of silicone-based soft lining materials (Ufi Gel P and GC Reline soft) with different surface pre treatments of heat cure PMMA denture base acrylic resin. Stainless steel dies measuring 40 mm in length; 10 mm in width and 10 mm in height (40 × 10 × 10) were machined to prepare standardized for the polymethyl methacrylate resin blocks. Stainless steel dies (spacer for resilient liner) measuring 3 mm thick; 10 mm long and 10 mm wide were prepared as spacers to ensure uniformity of the soft liner being tested. Two types of Addition silicone-based soft lining materials (room temperature polymerised soft lining materials (RTPSLM): Ufi Gel P and GC Reline soft) were selected. Ufi Gel P (VOCO, Germany), GC Reline soft (GC America) are resilient, chairside vinyl polysiloxane denture reliners of two different manufacturers. A total of 80 test samples were prepared of which 40 specimens were prepared for Group A (Ufi Gel P) and 40 specimens for Group B (GC Reline soft). In these groups, based on Pre-treatment of acrylic resin specimens each group was subdivided into four sub groups of 10 samples each. Sub-group I—without any surface treatment. Sub-group II—sand blasted Sub-group III—treated with Methyl Methacrylate monomer Sub-group IV-treated with chemical etchant Acetone. The results were statistically analysed by Kruscal Wallis test, Mann–Whitney U test, and Independent t test. The specimens treated with MMA monomer wetting showed superior and significant bond strength than those obtained by other surface treatments. The samples belonging to subgroups of GC Reline soft exhibit superior tensile bond strength than subgroups of Ufi Gel P. The modes of failure of all specimens were mostly adhesive in nature. Surface pre treatments by chemical means improved the bond strength between the silicone liners and denture base.
PMCID: PMC3732717  PMID: 24431747
Silicone soft denture liner; Denture base resin; Tensile bond strength
21.  Mineral bone disease in maintenance hemodialysis patients: Association with morbidity and mortality 
Indian Journal of Nephrology  2014;24(5):302-307.
There is a paucity of data on mineral bone disease in maintenance hemodialysis (MHD) patients from India. This retrospective analysis was undertaken on 858 (males: 599; females: 259) patients from two medical centers on MHD from 1998 to 2010. Age, gender, months on dialysis, hours per session of dialysis, hemoglobin, serum calcium, inorganic phosphorus, intact parathyroid hormone (iPTH), urine output, erythropoietin dosage per week, blood sugar, blood pressure, urea reduction rate, gain in fluid and fluid removed per session, serum albumin, alkaline phosphatase, vitamin D level, supplemental vitamin D and use of phosphate binder for therapy were documented. Overall, 191 patients died (22%) during the observation period. There was an 86% patient survival rate at 1 year on dialysis and an overall predicted 3-year survival rate of 78%. A relatively higher iPTH (P = 0.012), a need for vitamin D supplementation (P = 0.003), less hours on dialysis per session (P = 0.046) and a non-vegetarian diet (P = 0.022) were significantly associated with mortality.
PMCID: PMC4165055  PMID: 25249720
Asia; mineral bone disease; hemodialysis
22.  Risk Factors and Etiologies of Ischemic Strokes in Young Patients: A Tertiary Hospital Study in North India 
Journal of Stroke  2014;16(3):173-177.
Background and Purpose
Stroke in young adults has a special significance in developing countries, as it affects the most economically productive group of the society. We identified the risk factors and etiologies of young patients who suffered ischemic strokes and were admitted to a tertiary referral hospital in North India.
A retrospective review of case records from patients with ischemic stroke in the age range of 18-45 years was conducted from 2005 to 2010. Data regarding patients' clinical profiles, medical histories, diagnostic test results, and modified Rankin Scale scores at hospital discharge were examined. Stroke subtyping was conducted in accordance with the Trial of Org 10172 in Acute Stroke Treatment (TOAST) criteria.
Of the 2,634 patients admitted for ischemic stroke, 440 (16.7%) were in the 18-45 year age range and the majority (83.4%) were male. The most common risk factors were hypertension (34.4%) and dyslipidemia (26.5%). The most common subtype of stroke was undetermined (57%), followed by other determined causes (17.3%). Among the category of undetermined etiology, incomplete evaluation was the most common. Most of the patients demonstrated good functional outcomes.
Young adults account for 16.7% of all stroke patients in North India. Risk factors are relatively prevalent, and a high proportion of the patients are categorized under undetermined and other determined causes. The results highlight the needs for aggressive management of traditional risk factors and extensive patient work-ups to identify stroke etiology in India.
PMCID: PMC4200587  PMID: 25328875
Young adult; Ischemic stroke; India; TOAST classification
23.  Dental Fluorosis and Dental Caries Prevalence among 12 and 15-Year-Old School Children in Nalgonda District, Andhra Pradesh, India 
Fluoride is a double edged sword. The assessment of dental caries and fluorosis in endemic fluoride areas will facilitate in assessing the relation between fluoride concentrations in water with dental caries, dental fluorosis simultaneously.
The objective of the following study is to assess the dental caries and dental fluorosis prevalence among 12 and 15-year-old school children in Nalgonda district, Andhra Pradesh, India.
Subjects and Methods:
This was a cross-sectional study. Two stage cluster sampling technique was employed to select 20 schools from Nalgonda district. The oral examination of available 12 and 15-year-old children fulfilling the inclusion and exclusion criteria was carried out to assess dental caries and fluorosis. The examination was conducted by a single trained and calibrated examiner using the mouth mirror and community periodontal index probe under natural daylight. These areas were divided into four categories, low, medium, high and very high fluoride areas based on the fluoride concentration at the time of statistical analysis. The data was analyzed using Statistical Package for the Social Sciences version 16 (IBM, Chicago, USA).
The caries prevalence was less among 12-year-old children (39.9% [369/924]) compared with 15-years-old children (46.7% [444/951]). The prevalence was more among females (50.4% [492/977]) than males (35.8% [321/898]). The prevalence was more in low fluoride area (60.5% [300/496]) followed by very high fluoride area (54.8% [201/367]), high fluoride area (32.4% [293/904]) and medium fluoride area (17.6% [19/108]) in the descending order. The fluorosis prevalence increased with increasing fluoride concentration with no difference in gender and age distribution.
Low fluoride areas require fluoridation or alternate sources of fluoride, whereas high fluoride areas require defluoridation. Defluoridation of water is an immediate requirement in areas with fluoride concentration of 4 parts per million and above as dental fluorosis is a public health problem in these areas with 100% prevalence.
PMCID: PMC4212385  PMID: 25364597
Defluoridation; Dental caries; Dental fluorosis; Endemic fluoride area; Prevalence
24.  99mTc DTPA renogram indentifies Bochdalek hernia with an intra thoracic kidney as its content 
World Journal of Nuclear Medicine  2014;13(3):193-196.
Congenital diaphragmatic hernia (CDH) is a rare anomaly with reported incidence of 1 in 16,000 and is associated with herniation of stomach, intestinal loops, spleen, and kidney through a chest wall defect. We report a case of 1-year-old male child with history of recurrent fever and non-visualization of left kidney on ultrasonogram. Patient was referred to us to look for ectopic left kidney.99mTc-diethylenetriaminepentaacetic acid renogram was performed. An ectopically placed intrathoracic left kidney was identified. Subsequently a chest X-ray was done that showed bowel loops and diagnosis of CDH was confirmed. The patient underwent thoracoscopic repair of CDH and hernial contents were found to be left kidney, intestinal loops and spleen.
PMCID: PMC4262879  PMID: 25538492
Bowel in thorax; diaphragmatic hernia; diethylenetriamine pentaacetic acid renogram; intrathoracic kidney
25.  H2S as an Indicator of Water Supply Vulnerability and Health Risk in Low-Resource Settings: A Prospective Cohort Study 
In this large-scale longitudinal study conducted in rural Southern India, we compared a presence/absence hydrogen sulfide (H2S) test with quantitative assays for total coliforms and Escherichia coli as measures of water quality, health risk, and water supply vulnerability to microbial contamination. None of the three indicators showed a significant association with child diarrhea. The presence of H2S in a water sample was associated with higher levels of total coliform species that may have included E. coli but that were not restricted to E. coli. In addition, we observed a strong relationship between the percent positive H2S test results and total coliform levels among water source samples (R2 = 0.87). The consistent relationships between H2S and total coliform levels indicate that presence/absence of H2S tests provide a cost-effective option for assessing both the vulnerability of water supplies to microbial contamination and the results of water quality management and risk mitigation efforts.
PMCID: PMC3741245  PMID: 23716404

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