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1.  Oral Health Knowledge, Attitude and Practices of Children and Adolescents of Orphanages in Jodhpur City Rajasthan, India 
Objectives: This study had twin objectives of assessing the oral health knowledge, attitude and practices and to assess the dental caries status and treatment needs among the orphan children of orphanages of Jodhpur city, Rajasthan, India.
Materials and Methods: This cross- sectional study was carried out on 100 children to assess the oral health knowledge, attitude and practices of children and adolescents of orphanages in Jodhpur city, Rajasthan, India. The data was collected on a pre-tested questionnaire which included 20 closed ended multiple-choice questions on perceived oral health status, knowledge of oral health and attitude, oral health practices, dietary habits and behaviour towards dental treatment. On completion of the questionnaire, each child underwent an oral examination and Dentition status and treatment needs index (WHO Oral Health Surveys- 1997) was recorded for each subject.
Results: Almost 93% of the children felt the necessity of maintaining oral hygiene. There were 69% of the children who believed that it was necessary to brush teeth after every meal, 51% children believed that regular tooth-brushing prevents all tooth problems and 93% children knew that tobacco is carcinogenic in nature. Also, it was found that 77% of the children believed that regular dental visits help in maintaining oral hygiene.
Conclusion: Many of them had acquired knowledge on oral health. More than half of the study subjects were aware of the importance of keeping good oral hygiene, regular dental visits and harmful effects of tobacco.
doi:10.7860/JCDR/2014/9026.4948
PMCID: PMC4253259  PMID: 25478441
Dental caries; Oral health; Tobacco
2.  Better health outcomes at lower costs: the benefits of primary care utilisation for chronic disease management in remote Indigenous communities in Australia’s Northern Territory 
Background
Indigenous residents living in remote communities in Australia’s Northern Territory experience higher rates of preventable chronic disease and have poorer access to appropriate health services compared to other Australians. This study compared health outcomes and costs at different levels of primary care utilisation to determine if primary care represents an efficient use of resources for Indigenous patients with common chronic diseases namely hypertension, diabetes, ischaemic heart disease, chronic obstructive pulmonary disease and renal disease.
Methods
This was an historical cohort study involving a total of 14,184 Indigenous residents, aged 15 years and over, who lived in remote communities and used a remote clinic or public hospital from 2002 to 2011. Individual level demographic and clinical data were drawn from primary care and hospital care information systems using a unique patient identifier. A propensity score was used to improve comparability between high, medium and low primary care utilisation groups. Incremental cost-effectiveness ratios and acceptability curves were used to analyse four health outcome measures: total and, avoidable hospital admissions, deaths and years of life lost.
Results
Compared to the low utilisation group, medium and high levels of primary care utilisation were associated with decreases in total and avoidable hospitalisations, deaths and years of life lost. Higher levels of primary care utilisation for renal disease reduced avoidable hospitalisations by 82-85%, deaths 72-75%, and years of life lost 78-81%. For patients with ischaemic heart disease, the reduction in avoidable hospitalisations was 63-78%, deaths 63-66% and years of life lost 69-73%. In terms of cost-effectiveness, primary care for renal disease and diabetes ranked as more cost-effective, followed by hypertension and ischaemic heart disease. Primary care for chronic obstructive pulmonary disease was the least cost-effective of the five conditions.
Conclusion
Primary care in remote Indigenous communities was shown to be associated with cost-savings to public hospitals and health benefits to individual patients. Investing $1 in primary care in remote Indigenous communities could save $3.95-$11.75 in hospital costs, in addition to health benefits for individual patients. These findings may have wider applicability in strengthening primary care in the face of high chronic disease prevalence globally.
doi:10.1186/1472-6963-14-463
PMCID: PMC4282496  PMID: 25281064
Indigenous; Northern Territory; Australia; Remote; Chronic disease; Primary care; Cost effectiveness; Hospitalisation; Mortality; YLL
3.  What core primary health care services should be available to Australians living in rural and remote communities? 
BMC Family Practice  2014;15:143.
Background
Australians living in rural and remote areas experience poorer access to primary health care (PHC) and poorer health outcomes compared to metropolitan populations. Current health reform in Australia aims to ensure all Australians, regardless of where they live, have access to essential PHC services. However, at a national level policy makers and health planners lack an evidence-based set of core PHC services to assist in implementing this goal.
Methods
A Delphi method was used to reach consensus on an evidence-based list of core PHC services to which all Australians should have access and their necessary support functions. Experts in rural and remote and/or Indigenous PHC, including policy-makers, academics, clinicians and consumers, were invited to consider a list of core services derived from the literature.
Results
Thirty nine experts agreed to participate. After three survey rounds there was a strong consensus (≥80% agreement) on core PHC services namely; ‘care of the sick and injured’, ‘mental health’, ‘maternal/child health’, ‘allied health’, ‘sexual/reproductive health’, ‘rehabilitation’, ‘oral/dental health’ and ‘public health/illness prevention’; and on the PHC support functions of; ‘management/governance/leadership’, ‘coordination’, ‘health infrastructure’, ‘quality systems’, ‘data systems’, ‘professional development’ and ‘community participation’. Themes emerging from qualitative data included challenges in providing equitable PHC in rural and remote areas, the importance of service coordination and diverse strategies to overcome access barriers.
Conclusion
This study identifies a basket of PHC services that consumers in rural and remote communities can expect to access. It provides rigorously derived evidence that will contribute to a more systematic approach to PHC service planning and availability and will assist policy makers in the allocation of scarce resources necessary to improve the health outcomes of residents of rural and remote areas.
doi:10.1186/1471-2296-15-143
PMCID: PMC4236500  PMID: 25143194
Primary health care; Equity; Access; Core services; Health service planning; Health policy; Rural; Remote
4.  Surfactant Protein D Inhibits HIV-1 Infection of Target Cells via Interference with gp120-CD4 Interaction and Modulates Pro-Inflammatory Cytokine Production 
PLoS ONE  2014;9(7):e102395.
Surfactant Protein SP-D, a member of the collectin family, is a pattern recognition protein, secreted by mucosal epithelial cells and has an important role in innate immunity against various pathogens. In this study, we confirm that native human SP-D and a recombinant fragment of human SP-D (rhSP-D) bind to gp120 of HIV-1 and significantly inhibit viral replication in vitro in a calcium and dose-dependent manner. We show, for the first time, that SP-D and rhSP-D act as potent inhibitors of HIV-1 entry in to target cells and block the interaction between CD4 and gp120 in a dose-dependent manner. The rhSP-D-mediated inhibition of viral replication was examined using three clinical isolates of HIV-1 and three target cells: Jurkat T cells, U937 monocytic cells and PBMCs. HIV-1 induced cytokine storm in the three target cells was significantly suppressed by rhSP-D. Phosphorylation of key kinases p38, Erk1/2 and AKT, which contribute to HIV-1 induced immune activation, was significantly reduced in vitro in the presence of rhSP-D. Notably, anti-HIV-1 activity of rhSP-D was retained in the presence of biological fluids such as cervico-vaginal lavage and seminal plasma. Our study illustrates the multi-faceted role of human SP-D against HIV-1 and potential of rhSP-D for immunotherapy to inhibit viral entry and immune activation in acute HIV infection.
doi:10.1371/journal.pone.0102395
PMCID: PMC4103819  PMID: 25036364
5.  The Welsh study of mothers and babies: protocol for a population-based cohort study to investigate the clinical significance of defined ultrasound findings of uncertain significance 
Background
Improvement in ultrasound imaging has led to the identification of subtle non-structural markers during the 18 – 20 week fetal anomaly scan, such as echogenic bowel, mild cerebral ventriculomegaly, renal pelvicalyceal dilatation, and nuchal thickening. These markers are estimated to occur in between 0.6% and 4.3% of pregnancies. Their clinical significance, for pregnancy outcomes or childhood morbidity, is largely unknown. The aim of this study is to estimate the prevalence of seven markers in the general obstetric population and establish a cohort of children for longer terms follow-up to assess the clinical significance of these markers.
Methods/Design
All women receiving antenatal care within six of seven Welsh Health Boards who had an 18 to 20 week ultrasound scan in Welsh NHS Trusts between July 2008 and March 2011 were eligible for inclusion. Data were collected on seven markers (echogenic bowel, cerebral ventriculomegaly, renal pelvicalyceal dilatation, nuchal thickening, cardiac echogenic foci, choroid plexus cysts, and short femur) at the time of 18 – 20 week fetal anomaly scan. Ultrasound records were linked to routinely collected data on pregnancy outcomes (work completed during 2012 and 2013). Images were stored and reviewed by an expert panel.
The prevalence of each marker (reported and validated) will be estimated. A projected sample size of 23,000 will allow the prevalence of each marker to be estimated with the following precision: a marker with 0.50% prevalence to within 0.10%; a marker with 1.00% prevalence to within 0.13%; and a marker with 4.50% prevalence to within 0.27%. The relative risk of major congenital abnormalities, stillbirths, pre-term birth and small for gestational age, given the presence of a validated marker, will be reported.
Discussion
This is a large, prospective study designed to estimate the prevalence of markers in a population-based cohort of pregnant women and to investigate associations with adverse pregnancy outcomes. The study will also establish a cohort of children that can be followed-up to explore associations between specific markers and longer-term health and social outcomes.
doi:10.1186/1471-2393-14-164
PMCID: PMC4029820  PMID: 24884594
Ultrasound; Anomaly; Markers; Echogenic bowel; Cerebral ventriculomegaly; Renal pelvicalyceal dilatation; Nuchal thickening; Cardiac echogenic foci; Choroid plexus cysts; Short femur; Congenital abnormality; Stillbirths; Pre-term birth; Small for gestational age
6.  “The Clock Is Ticking”: The Timely Management of a Painful Skin Rash in a Seventy-Year-Old Woman 
Case Reports in Medicine  2014;2014:641058.
Necrotizing fasciitis is an uncommon but a potentially fatal condition and can affect any part of the body. Most patients have pre-existing conditions that render them susceptible to infection, although etiology is unclear. Diagnosis is primarily clinical and is often delayed because of the unfamiliarity of the condition among clinicians. Management consists of immediate resuscitation, early surgical debridement, and administration of broad spectrum intravenous antibiotics. We report a case of a 70 year old woman who presented with a painful erythematous rash, was admitted as a case of cellulitis, later developed worsening of symptoms and septic shock, and was diagnosed as necrotizing fasciitis.
doi:10.1155/2014/641058
PMCID: PMC3970449  PMID: 24715917
7.  CAMP: Collection of sequences and structures of antimicrobial peptides 
Nucleic Acids Research  2013;42(Database issue):D1154-D1158.
Antimicrobial peptides (AMPs) are gaining importance as anti-infective agents. Here we describe the updated Collection of Antimicrobial Peptide (CAMP) database, available online at http://www.camp.bicnirrh.res.in/. The 3D structures of peptides are known to influence antimicrobial activity. Although there exists databases of AMPs, information on structures of AMPs is limited in these databases. CAMP is manually curated and currently holds 6756 sequences and 682 3D structures of AMPs. Sequence and structure analysis tools have been incorporated to enhance the usefulness of the database.
doi:10.1093/nar/gkt1157
PMCID: PMC3964954  PMID: 24265220
8.  Classification of the Gait Patterns of Boys With Duchenne Muscular Dystrophy and Their Relationship to Function 
Journal of child neurology  2010;25(9):1103-1109.
Corticosteroids have recently been shown to reduce expected loss of muscle strength in patients with Duchenne muscular dystrophy and extend the time they can walk. We evaluated 43 boys with the condition to determine whether taking corticosteroids is associated with differences in gait pattern, gross motor skills, energy efficiency, and timed motor performance. We used the gait deviation index to quantify the degree of gait pathology and a single measure of gait quality. There were minimal differences in gait pattern, gross motor skills, energy efficiency, or timed motor performance in boys who took corticosteroids compared with those who did not. Clustering by gait deviation index, however, revealed subtle differences between groups in gait patterns, gross motor skills, and energy efficiency. We conclude that, in boys with Duchenne muscular dystrophy, gait pattern deviations are related to function, which can provide further insight into the understanding of disease progression and treatment options to enhance function and maintain ambulation.
doi:10.1177/0883073810371002
PMCID: PMC3794706  PMID: 20587736
Duchenne muscular dystrophy; gait; function; energy
9.  Impaired humoral immunity and tolerance in K14-VEGFR-3-Ig mice that lack dermal lymphatic drainage 
Lymphatic vessels transport interstitial fluid, soluble antigen, and immune cells from peripheral tissues to lymph nodes (LNs), yet the contribution of peripheral lymphatic drainage to adaptive immunity remains poorly understood. We examined immune responses to dermal vaccination and contact hypersensitivity (CHS) challenge in K14-VEGFR-3-Ig mice, which lack dermal lymphatic capillaries and experience markedly depressed transport of solutes and dendritic cells from the skin to draining LNs. In response to dermal immunization, K14-VEGFR-3-Ig mice produced lower antibody titers. In contrast, although delayed, T cell responses were robust after 21 days, including high levels of antigen-specific CD8+ T cells and production of IFN-γ, IL-4 and IL-10 upon restimulation. T cell-mediated CHS responses were strong in K14-VEGFR-3-Ig mice, but importantly, their ability to induce CHS tolerance in the skin was impaired. Additionally, one-year-old mice displayed multiple signs of autoimmunity. These data suggest that lymphatic drainage plays more important roles in regulating humoral immunity and peripheral tolerance than in effector T cell immunity.
doi:10.4049/jimmunol.1103545
PMCID: PMC3424306  PMID: 22844119
lymphedema; VEGF-C; lymph node; adaptive immunity; contact hypersensitivity
10.  Relationship Between Clinical Outcome Measures and Parent Proxy Reports of Health-related Quality of Life in Ambulatory Children with Duchenne Muscular Dystrophy 
Journal of child neurology  2010;25(9):1130-1144.
In Duchenne muscular dystrophy, data directly linking changes in clinical outcome measures to patient-perceived well-being are lacking. Our study evaluated the relationship between clinical outcome measures used in clinical trials of ambulatory Duchenne muscular dystrophy (Vignos functional grade, quantitative knee extension strength, timed functional performance measures, and gait velocity) and 2 health-related quality of life measures — the PODCI and PedsQL™ — in 52 ambulatory Duchenne muscular dystrophy subjects and 36 controls. Those with the disease showed significant decrements in parent proxy-reported health-related quality of life measures versus controls across all domains. The PODCI transfers/basic mobility, PODCI sports/physical function, and PedsQL™ physical functioning domains had significant associations with age (and hence disease progression), and traditional clinical outcome measures employed in clinical trials of ambulatory boys with Duchenne muscular dystrophy. Selected domains of the PODCI and generic PedsQL™ are potential patient-reported outcome measures for clinical trials in ambulatory individuals with the disease.
doi:10.1177/0883073810371509
PMCID: PMC3695468  PMID: 20558672
Duchenne muscular dystrophy; clinical outcome measures; health related quality of life; clinical trials; PODCI; PedsQL
11.  The role of DNA mismatch repair in generating genetic diversity and drug resistance in malaria parasites 
Although the mechanisms by which malaria parasites develop resistance to drugs are unclear, current knowledge suggests a main mechanism of resistance is the alteration of target enzymes by point mutation. In other organisms, defects in DNA mismatch repair have been linked to increased mutation rates and drug resistance. We have identified an unusual complement of mismatch repair genes in the Plasmodium genome. An initial functional test of two of these genes (PfMSH2-1 and PfMSH2-2) using a dominant mutator assay showed an elevation in mutation frequency with the PfMSH2-2 homolog, indirectly demonstrating a role for this gene in mismatch repair. We successfully disrupted PbMSH2-2 in the P. berghei laboratory isolate NK65, and showed that this gene is not essential for parasite growth in either the asexual (rodent) or sexual (mosquito) stages of the lifecycle. Although we observed some differences in levels of drug resistance between wild type and mutant parasites, no uniform trend emerged and preliminary evidence does not support a strong link between PbMSH2-2 disruption and dramatically increased drug resistance. We found microsatellite polymorphism in the PbMSH2-2 disrupted parasites in less than 40 life cycles post-transfection, but not in PbMap2K disrupted controls or mosquito passaged wild type parasites, which suggests a possible role for PbMSH2-2 in preventing microsatellite slippage, similar to MSH2 in other organisms. Our studies suggest that Plasmodium species may have evolved a unique variation on the highly conserved system of DNA repair compared to the mismatch repair systems in other eukaryotes.
doi:10.1016/j.molbiopara.2007.05.003
PMCID: PMC3683857  PMID: 17583362
DNA mismatch repair; Plasmodium falciparum; Plasmodium berghei; malaria; MSH2; drug resistance
12.  In Silico Study on Binding Specificity of Gonadotropins and Their Receptors: Design of a Novel and Selective Peptidomimetic for Human Follicle Stimulating Hormone Receptor 
PLoS ONE  2013;8(5):e64475.
Gonadotropins bind to specific receptors in spite of sharing a high level of sequence and structural similarity. This specific binding is crucial for maintaining the reproductive health of an organism. In this study, residues that dictate the receptor binding specificity of the gonadotropins (FSH and LH) have been identified using combination of in silico methods. Docking studies (ZDOCK), based on the systematic replacement of these residues, confirmed its importance in receptor binding. An interesting observation is that the relative positioning of the residues conferring binding specificity varied for the gonadotropin-receptor complexes. This spatial difference of the key residues could be exploited for design of specific modulators. Based on the identified residues, we have rationally designed a peptidomimetic (FSHP) that displays good binding affinity and specificity for hFSHR. FSHP was developed by screening 3.9 million compounds using pharmacophore-shape similarity followed by fragment-based approach. It was observed that FSHP and hFSHâ can share the same receptor binding site thereby mimicking the native hFSHR-FSH interactions. FSHP also displayed higher binding affinity to hFSHR as compared to two reported hFSHR antagonists. MD simulation studies on hFSHR-FSHP complex revealed that FSHP is conformationally rigid and the intermolecular interactions are maintained during the course of simulation.
doi:10.1371/journal.pone.0064475
PMCID: PMC3659097  PMID: 23700481
13.  A Chemical Proteomics Approach to Profiling the ATP-binding Proteome of Mycobacterium tuberculosis *  
Tuberculosis, caused by Mycobacterium tuberculosis, remains one of the leading causes of death worldwide despite extensive research, directly observed therapy using multidrug regimens, and the widespread use of a vaccine. The majority of patients harbor the bacterium in a state of metabolic dormancy. New drugs with novel modes of action are needed to target essential metabolic pathways in M. tuberculosis; ATP-competitive enzyme inhibitors are one such class. Previous screening efforts for ATP-competitive enzyme inhibitors identified several classes of lead compounds that demonstrated potent anti-mycobacterial efficacy as well as tolerable levels of toxicity in cell culture. In this report, a probe-based chemoproteomic approach was used to selectively profile the M. tuberculosis ATP-binding proteome in normally growing and hypoxic M. tuberculosis. From these studies, 122 ATP-binding proteins were identified in either metabolic state, and roughly 60% of these are reported to be essential for survival in vitro. These data are available through ProteomeXchange with identifier PXD000141. Protein families vital to the survival of the tubercle bacillus during hypoxia emerged from our studies. Specifically, along with members of the DosR regulon, several proteins involved in energy metabolism (Icl/Rv0468 and Mdh/Rv1240) and lipid biosynthesis (UmaA/Rv0469, DesA1/Rv0824c, and DesA2/Rv1094) were found to be differentially abundant in hypoxic versus normal growing cultures. These pathways represent a subset of proteins that may be relevant therapeutic targets for development of novel ATP-competitive antibiotics.
doi:10.1074/mcp.M112.025635
PMCID: PMC3675820  PMID: 23462205
14.  Acetabular retroversion in post slipped capital femoral epiphysis deformity 
Purpose
While the femoral deformity in post slipped capital femoral epiphysis (SCFE) hips has been implicated in the development of femoral acetabular impingement, little has been studied about the acetabular side. The purpose of our study was to determine the frequency of morphologic changes suggestive of acetabular retroversion in patients who have sustained a SCFE.
Methods
IRB approval was obtained and the records of patients from 1975 to 2010 were searched for ICD-9 codes for SCFE. A total of 188 patients were identified for the study. Two observers evaluated AP radiographs for evidence of acetabular retroversion as characterized by the presence of either an ischial spine sign or a crossover sign. Demographic data, date of onset, and treatment were recorded. For analysis, the right hip was used in patients with bilateral involvement.
Results
Of the 188 patients identified, 5 patients had an incorrect diagnosis and 41 patients had missing or inadequate films, leaving 142 patients (284 hips) for review. 57 patients (114 hips) had bilateral SCFE and 85 patients had unilateral SCFE. 79 % (n = 45) of the right hips with bilateral SCFE and 82 % (n = 70) of the unilateral involved hips had at least one sign of retroversion. Uninvolved hips had at least one sign of retroversion 76 % (n = 65) of the time.
Conclusions
When compared to previously published values for normal patients, patients with SCFE appear to have an increased incidence of acetabular retroversion.
doi:10.1007/s11832-013-0481-z
PMCID: PMC3593012  PMID: 24432064
Slipped capital femoral epiphysis; SCFE; FAI; Retroversion; Pincer lesion; Cam lesion
15.  A Multi-Omic Systems-Based Approach Reveals Metabolic Markers of Bacterial Vaginosis and Insight into the Disease 
PLoS ONE  2013;8(2):e56111.
Background
Bacterial vaginosis (BV) is the most common vaginal disorder of reproductive-age women. Yet the cause of BV has not been established. To uncover key determinants of BV, we employed a multi-omic, systems-biology approach, including both deep 16S rRNA gene-based sequencing and metabolomics of lavage samples from 36 women. These women varied demographically, behaviorally, and in terms of health status and symptoms.
Principal Findings
16S rRNA gene-based community composition profiles reflected Nugent scores, but not Amsel criteria. In contrast, metabolomic profiles were markedly more concordant with Amsel criteria. Metabolomic profiles revealed two distinct symptomatic BV types (SBVI and SBVII) with similar characteristics that indicated disruption of epithelial integrity, but each type was correlated to the presence of different microbial taxa and metabolites, as well as to different host behaviors. The characteristic odor associated with BV was linked to increases in putrescine and cadaverine, which were both linked to Dialister spp. Additional correlations were seen with the presence of discharge, 2-methyl-2-hydroxybutanoic acid, and Mobiluncus spp., and with pain, diethylene glycol and Gardnerella spp.
Conclusions
The results not only provide useful diagnostic biomarkers, but also may ultimately provide much needed insight into the determinants of BV.
doi:10.1371/journal.pone.0056111
PMCID: PMC3566083  PMID: 23405259
17.  Bariatric Surgery versus Intensive Medical Therapy in Obese Patients with Diabetes 
The New England Journal of Medicine  2012;366(17):1567-1576.
BACKGROUND
Observational studies have shown improvement in patients with type 2 diabetes mellitus after bariatric surgery.
METHODS
In this randomized, nonblinded, single-center trial, we evaluated the efficacy of intensive medical therapy alone versus medical therapy plus Roux-en-Y gastric bypass or sleeve gastrectomy in 150 obese patients with uncontrolled type 2 diabetes. The mean (±SD) age of the patients was 49 ± 8 years, and 66% were women. The average glycated hemoglobin level was 9.2 ± 1.5%. The primary end point was the proportion of patients with a glycated hemoglobin level of 6.0% or less 12 months after treatment.
RESULTS
Of the 150 patients, 93% completed 12 months of follow-up. The proportion of patients with the primary end point was 12% (5 of 41 patients) in the medical-therapy group versus 42% (21 of 50 patients) in the gastric-bypass group (P = 0.002) and 37% (18 of 49 patients) in the sleeve-gastrectomy group (P = 0.008). Glycemic control improved in all three groups, with a mean glycated hemoglobin level of 7.5 ± 1.8% in the medical-therapy group, 6.4 ± 0.9% in the gastric-bypass group (P<0.001), and 6.6 ± 1.0% in the sleeve-gastrectomy group (P = 0.003). Weight loss was greater in the gastric-bypass group and sleeve-gastrectomy group (−29.4 ± 9.0 kg and −25.1 ± 8.5 kg, respectively) than in the medical-therapy group (−5.4 ± 8.0 kg) (P<0.001 for both comparisons). The use of drugs to lower glucose, lipid, and blood-pressure levels decreased significantly after both surgical procedures but increased in patients receiving medical therapy only. The index for homeostasis model assessment of insulin resistance (HOMA-IR) improved significantly after bariatric surgery. Four patients underwent reoperation. There were no deaths or life-threatening complications.
CONCLUSIONS
In obese patients with uncontrolled type 2 diabetes, 12 months of medical therapy plus bariatric surgery achieved glycemic control in significantly more patients than medical therapy alone. Further study will be necessary to assess the durability of these results. (Funded by Ethicon Endo-Surgery and others; ClinicalTrials.gov number, NCT00432809.)
doi:10.1056/NEJMoa1200225
PMCID: PMC3372918  PMID: 22449319
18.  Identification of Novel Mutations in HEXA Gene in Children Affected with Tay Sachs Disease from India 
PLoS ONE  2012;7(6):e39122.
Tay Sachs disease (TSD) is a neurodegenerative disorder due to β-hexosaminidase A deficiency caused by mutations in the HEXA gene. The mutations leading to Tay Sachs disease in India are yet unknown. We aimed to determine mutations leading to TSD in India by complete sequencing of the HEXA gene. The clinical inclusion criteria included neuroregression, seizures, exaggerated startle reflex, macrocephaly, cherry red spot on fundus examination and spasticity. Neuroimaging criteria included thalamic hyperdensities on CT scan/T1W images of MRI of the brain. Biochemical criteria included deficiency of hexosaminidase A (less than 2% of total hexosaminidase activity for infantile patients). Total leukocyte hexosaminidase activity was assayed by 4-methylumbelliferyl-N-acetyl-β-D-glucosamine lysis and hexosaminidase A activity was assayed by heat inactivation method and 4-methylumbelliferyl-N-acetyl-β-D-glucosamine-6-sulphate lysis method. The exons and exon-intron boundaries of the HEXA gene were bidirectionally sequenced using an automated sequencer. Mutations were confirmed in parents and looked up in public databases. In silico analysis for mutations was carried out using SIFT, Polyphen2, MutationT@ster and Accelrys Discovery Studio softwares. Fifteen families were included in the study. We identified six novel missense mutations, c.340 G>A (p.E114K), c.964 G>A (p.D322N), c.964 G>T (p.D322Y), c.1178C>G (p.R393P) and c.1385A>T (p.E462V), c.1432 G>A (p.G478R) and two previously reported mutations. c.1277_1278insTATC and c.508C>T (p.R170W). The mutation p.E462V was found in six unrelated families from Gujarat indicating a founder effect. A previously known splice site mutation c.805+1 G>C and another intronic mutation c.672+30 T>G of unknown significance were also identified. Mutations could not be identified in one family. We conclude that TSD patients from Gujarat should be screened for the common mutation p.E462V.
doi:10.1371/journal.pone.0039122
PMCID: PMC3377590  PMID: 22723944
19.  A Rare Form of Melanoma Masquerading as a Diabetic Foot Ulcer: A Case Report 
Case Reports in Endocrinology  2012;2012:502806.
Background. Acral lentiginous melanoma (ALM) is a less-common form of melanoma in US, and it accounts for about 5% of all diagnosed melanomas in US. ALM is often overlooked until it is well advanced because of the lesion's location and its atypical appearance in the early stages. We present a case of ALM initially presented as a diabetic foot ulcer. Case Report. An 81-year-old man initially presented to the primary care clinic with a right foot diabetic ulcer. There was a large plantar, dark-colored ulcer that bled easy. Initial excision biopsy revealed Clark's Level IV ALM. Subsequent definitive wide excision and sentinel node biopsy confirmed ALM with metastasis to inguinal lymph nodes (stage IIIb). The treatment included wide margin excision of the lesion with en bloc amputations of 4th and 5th toes, followed by adjuvant chemotherapy. Discussion. The development of ALM may potentially relate to diabetes as a reported higher prevalence of diabetes with ALM patients. Conclusion. The difficulty in early diagnosing of ALM remains as a formidable challenge particularly in diabetic patients who commonly develop plantar foot ulcers due to the diabetic neuropathy. This case reiterates the importance of a thorough foot exam in such patients.
doi:10.1155/2012/502806
PMCID: PMC3420798  PMID: 22937296
20.  Size- and charge-dependent non-specific uptake of PEGylated nanoparticles by macrophages 
The assessment of macrophage response to nanoparticles is a central component in the evaluation of new nanoparticle designs for future in vivo application. This work investigates which feature, nanoparticle size or charge, is more predictive of non-specific uptake of nanoparticles by macrophages. This was investigated by synthesizing a library of polymer-coated iron oxide micelles, spanning a range of 30–100 nm in diameter and −23 mV to +9 mV, and measuring internalization into macrophages in vitro. Nanoparticle size and charge both contributed towards non-specific uptake, but within the ranges investigated, size appears to be a more dominant predictor of uptake. Based on these results, a protease-responsive nanoparticle was synthesized, displaying a matrix metalloproteinase-9 (MMP-9)-cleavable polymeric corona. These nanoparticles are able to respond to MMP-9 activity through the shedding of 10–20 nm of hydrodynamic diameter. This MMP-9-triggered decrease in nanoparticle size also led to up to a six-fold decrease in nanoparticle internalization by macrophages and is observable by T2-weighted magnetic resonance imaging. These findings guide the design of imaging or therapeutic nanoparticles for in vivo targeting of macrophage activity in pathologic states.
doi:10.2147/IJN.S28531
PMCID: PMC3284223  PMID: 22359457
macrophage targeting; poly(ethylene glycol) (PEG); poly(propylene sulfide) (PPS); iron oxides; opsonization
22.  Trials of large group teaching in Malaysian private universities: a cross sectional study of teaching medicine and other disciplines 
BMC Research Notes  2011;4:337.
Background
This is a pilot cross sectional study using both quantitative and qualitative approach towards tutors teaching large classes in private universities in the Klang Valley (comprising Kuala Lumpur, its suburbs, adjoining towns in the State of Selangor) and the State of Negeri Sembilan, Malaysia. The general aim of this study is to determine the difficulties faced by tutors when teaching large group of students and to outline appropriate recommendations in overcoming them.
Findings
Thirty-two academics from six private universities from different faculties such as Medical Sciences, Business, Information Technology, and Engineering disciplines participated in this study. SPSS software was used to analyse the data. The results in general indicate that the conventional instructor-student approach has its shortcoming and requires changes. Interestingly, tutors from Medicine and IT less often faced difficulties and had positive experience in teaching large group of students.
Conclusion
However several suggestions were proposed to overcome these difficulties ranging from breaking into smaller classes, adopting innovative teaching, use of interactive learning methods incorporating interactive assessment and creative technology which enhanced students learning. Furthermore the study provides insights on the trials of large group teaching which are clearly identified to help tutors realise its impact on teaching. The suggestions to overcome these difficulties and to maximize student learning can serve as a guideline for tutors who face these challenges.
doi:10.1186/1756-0500-4-337
PMCID: PMC3224573  PMID: 21902839
23.  Anti-HSP90 autoantibodies in sera of infertile women identify a dominant, conserved epitope EP6 (380-389) of HSP90 beta protein 
Background
We earlier reported a simple specific test for detection of anti-ovarian antibodies in infertile women and identified number of specific molecular and cellular targets of which human heat shock protein 90-beta (HSP90 beta) was found to be the most immunodominant. The present study focuses on prediction and validation of the immunodominant epitope/s of this protein using sera from infertile women having anti-HSP90 autoantibodies.
Methods
Delineation of the immunodominant epitopes of HSP90 beta was done by using epitope prediction algorithms and 10 peptides (EP1-EP10) were custom synthesized. Their immunoreactivity was measured by ELISA using sera from patients and controls. To determine the most immunodominant epitope, the results were subjected to statistical analysis. The immunoreactivity of the immunodominant peptides were confirmed by dot blots using sera from patients. A rabbit polyclonal antibody against the immunodominant epitope was generated and its immunoreactivity to the parent protein in ovarian extracts as well in oocytes and embryos was investigated.
Results
Experimentally and statistically, peptide EP6 (380-389) seems to be the major antigenic epitope for the serum antibody binding followed by EP1 (1-12) and EP8 (488-498). Predicted 3D structures of these peptides demonstrated that they exist in the loop conformation which is the most mobile part of the protein. Also, analysis of the sequences of HSP90 beta across several species reveals that EP6 peptide forms a part of a well conserved motif. The polyclonal antibody generated to the immunodominant epitope- EP6 confirms similar biochemical and cellular immunoreactivity as seen with the patients' sera having anti-HSP90 autoantibodies.
Conclusions
The decapeptide EP6 is a major immunogenic epitope of HSP90 followed by EP1 and EP8. Knowledge of binding epitopes on the autoantigen is necessary to understand the subsequent pathologic events. The study might generate new tools for the detection of disease-inducing epitopes and a possible therapeutic intervention.
doi:10.1186/1477-7827-9-16
PMCID: PMC3039567  PMID: 21272367
24.  Comparative Genomics of Gardnerella vaginalis Strains Reveals Substantial Differences in Metabolic and Virulence Potential 
PLoS ONE  2010;5(8):e12411.
Background
Gardnerella vaginalis is described as a common vaginal bacterial species whose presence correlates strongly with bacterial vaginosis (BV). Here we report the genome sequencing and comparative analyses of three strains of G. vaginalis. Strains 317 (ATCC 14019) and 594 (ATCC 14018) were isolated from the vaginal tracts of women with symptomatic BV, while Strain 409-05 was isolated from a healthy, asymptomatic individual with a Nugent score of 9.
Principal Findings
Substantial genomic rearrangement and heterogeneity were observed that appeared to have resulted from both mobile elements and substantial lateral gene transfer. These genomic differences translated to differences in metabolic potential. All strains are equipped with significant virulence potential, including genes encoding the previously described vaginolysin, pili for cytoadhesion, EPS biosynthetic genes for biofilm formation, and antimicrobial resistance systems, We also observed systems promoting multi-drug and lantibiotic extrusion. All G. vaginalis strains possess a large number of genes that may enhance their ability to compete with and exclude other vaginal colonists. These include up to six toxin-antitoxin systems and up to nine additional antitoxins lacking cognate toxins, several of which are clustered within each genome. All strains encode bacteriocidal toxins, including two lysozyme-like toxins produced uniquely by strain 409-05. Interestingly, the BV isolates encode numerous proteins not found in strain 409-05 that likely increase their pathogenic potential. These include enzymes enabling mucin degradation, a trait previously described to strongly correlate with BV, although commonly attributed to non-G. vaginalis species.
Conclusions
Collectively, our results indicate that all three strains are able to thrive in vaginal environments, and therein the BV isolates are capable of occupying a niche that is unique from 409-05. Each strain has significant virulence potential, although genomic and metabolic differences, such as the ability to degrade mucin, indicate that the detection of G. vaginalis in the vaginal tract provides only partial information on the physiological potential of the organism.
doi:10.1371/journal.pone.0012411
PMCID: PMC2928729  PMID: 20865041
25.  A diagnostic PCR assay for the detection of an Australian epidemic strain of Pseudomonas aeruginosa 
Background
Chronic lung infection with the bacterium Pseudomonas aeruginosa is one of the hallmarks of cystic fibrosis (CF) and is associated with worsening lung function, increased hospitalisation and reduced life expectancy. A virulent clonal strain of P. aeruginosa (Australian epidemic strain I; AES-I) has been found to be widespread in CF patients in eastern Australia.
Methods
Suppression subtractive hybridization (SSH) was employed to identify genetic sequences that are present in the AES-I strain but absent from the sequenced reference strain PAO1. We used PCR to evaluate the distribution of several of the AES-I loci amongst a collection of 188 P. aeruginosa isolates which was comprised of 35 AES-I isolates (as determined by PFGE), 78 non-AES-I CF isolates including other epidemic CF strains as well as 69 P. aeruginosa isolates from other clinical and environmental sources.
Results
We have identified a unique AES-I genetic locus that is present in all 35 AES-I isolates tested and not present in any of the other 153 P. aeruginosa strains examined. We have used this unique AES-I locus to develop a diagnostic PCR and a real-time PCR assay to detect the presence of P. aeruginosa and AES-I in patient sputum samples.
Conclusions
We have developed diagnostic PCR assays that are 100% sensitive and 100% specific for the P. aeruginosa strain AES-I. We have also shown that Whatman FTA® Elute cards may be used with PCR-based assays to rapidly detect the presence of P. aeruginosa strains in CF sputum.
doi:10.1186/1476-0711-9-18
PMCID: PMC2912777  PMID: 20637114

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