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1.  Association of Naso-Oro-Pharyngeal Structures with the Sleep Architecture in Suspected Obstructive Sleep Apnea 
The study was conducted to find out the association of various naso-oro-pharyngeal structures with sleep macro-architecture in suspected obstructive sleep apnea subjects. Study included 51 subjects with suspected obstructive sleep apnea. Subjects with possible central apnea and those consuming any substance that can affect sleep architecture were excluded. Level I polysomnography was performed after thorough physical examination. Overnight study was scored in 30 s epochs to find out the polysomnographic variables. Surgical treatment was offered wherever indicated. Subjects with moderate to severe obstructive sleep apnea were manually titrated on CPAP with the polysomnogram. SPSS v 17.0 was used for statistical analysis. We did not find any difference in the sleep architecture between genders. Sleep Efficiency was better in subjects with dental overjet, dental attrition, high tongue base, macroglossia, lesser oral cavity volume, edematous uvula, increased submental fat, hypertrophied facial muscles and Mallampatti grade III–IV. Shorter Sleep Latency was seen in subjects with tender TMJ and Mallampatti Gr III–IV. REM latency was shorter in subjects with high tongue base, macroglossia and hypertrophied muscles of mastication. Increased REM was observed in subjects with high tongue base, edematous uvula and tender TMJ. Enlarged tonsils had reversed effect with poor sleep efficiency, increased REM latency and decreased REM. CPAP therapy (N = 20) lessened awake time, decreased N2 and increased REM. Oro-pharyngeal structures affect the sleep architecture in suspected OSA subjects. Nasal structures do not affect the sleep architecture in these subjects and enlarged tonsils have opposite effect. Sleep architecture changes on the titration night with CPAP.
doi:10.1007/s12070-011-0326-3
PMCID: PMC3918340  PMID: 24533364
Sleep-architecture; Sleep-apnea; Oro-naso-pharyngeal anatomy
2.  MgrA Activates Expression of Capsule Genes, but Not the α-Toxin Gene in Experimental Staphylococcus aureus Endocarditis 
The Journal of Infectious Diseases  2013;208(11):1841-1848.
Background. Staphylococcus aureus produces numerous virulence factors but little is known about their in vivo regulation during an infection.
Methods. The production of capsule and α-toxin, and the expression of their respective genes, cap5 and hla, were analyzed by comparing CYL11481 (derivative of Newman) and its isogenic regulatory mutants in vitro. The temporal expression of cap5 and hla and the regulatory genes in vivo was carried out using a rat infective endocarditis model.
Results. In vitro analyses showed that capsule was positively regulated by MgrA, Agr, Sae, ArlR, and ClpC, and negatively by CodY and SbcDC. The α-toxin was positively regulated by MgrA, Agr, Sae, ArlR, and SbcDC but negatively by ClpC and CodY. In vivo analyses showed that cap5 expression correlated best with mgrA expression, whereas hla expression correlated best with sae expression. Mutation in mgrA drastically reduced cap5 expression in vivo.
Conclusions. Our results suggest that, in vitro, Agr is the most important regulator for capsule and α-toxin production, as well as for cap5 transcription, but SaeR is the most critical for hla transcription. However, in vivo, MgrA is the major transcriptional regulator of capsule, but not α-toxin, whereas saeR expression correlates best with hla expression.
doi:10.1093/infdis/jit367
PMCID: PMC3814835  PMID: 23901087
Staphylococcus aureus; virulence; infective endocarditis model; mgrA; capsule; α-toxin
3.  Navigated pedicle screw placement using computed tomographic data in dorsolumbar fractures 
Indian Journal of Orthopaedics  2014;48(6):555-561.
Background:
Computed tomographic (CT) based navigation is a technique to improve the accuracy of pedicle screw placement. It is believed to enhance accuracy of pedicle screw placement, potentially avoiding complications arising due to pedicle wall breach. This study aims to assess the results of dorsolumbar fractures operated by this technique.
Materials and Methods:
Thirty consecutive skeletally mature patients of fractures of dorsolumbar spine (T9–L5) were subjected to an optoelectronic navigation system. All patients were thoroughly examined for neurological deficit. The criterion for instability were either a tricolumnar injury or presence of neurological deficit or both. Patients with multilevel fractures and distorted spine were excluded from study. Time taken for insertion of each pedicle screw was recorded and placement assessed with a postoperative CT scan using Laine's grading system.
Results:
Only one screw out of a total of 118 screws was misplaced with a Laine's Grade 5 placement, showing a misplacement rate of 0.847%. Average time for matching was 7.8 min (range 5-12 min). Average time taken for insertion of a single screw was 4.19 min (range 2-8 min) and total time for all screws after exposure was 34.23 min (range 24-45 min) for a four screw construct. No neurovascular complications were seen in any of the patients postoperatively and in subsequent followup of 1-year duration.
Conclusion:
CT-based navigation is effective in improving accuracy of pedicle screw placement in traumatic injuries of dorsolumbar spine (T9-L5), however additional cost of procuring CT scan to the patient and cost of equipment is of significant concern in developing countries. Reduced radiation exposure and lowered ergonomic constraints around the operation table are its additional benefits.
doi:10.4103/0019-5413.144216
PMCID: PMC4232823  PMID: 25404766
Dorso lumbar spine; Laine's grading; navigation; paired point matching; Spine; spinal fractures; bone screws; neuronavigation; tomography
4.  What patients do to counteract the symptoms of Willis-Ekbom disease (RLS/WED): Effect of gender and severity of illness 
Objectives:
This study was carried out to assess different counteracting strategies used by patients with idiopathic Willis-Ekbom disease (RLS/WED). Whether these strategies were influenced by gender or disease severity was also assessed.
Materials and Methods:
A total of 173 patients of idiopathic RLS/WED were included in this study. Their demographic data was recorded. Details regarding the RLS/WED and strategies that they used to counteract the symptoms were asked. The severity of RLS/WED was measured with the help of the Hindi version of international restless legs syndrome severity rating scale. They were asked to provide the details regarding the relief obtained from all the strategies they used on three-point scale: no relief, some relief, and complete relief.
Results:
Of the patients, 72% were females. Mean age of the subjects in this study was 39.6 ± 12.6 years, and male subjects were older than females. Four common strategies were reported by the patients to counter the sensations of RLS/WED: moving legs while in bed (85.5%), asking somebody to massage their legs or massaging legs themselves (76.9%), walking (53.2%), and tying a cloth/rope tightly on the legs (39.3%). Of all the patients who moved their legs, 6.7% did not experience any relief, 64.2% reported some relief, and 28.4% reported complete relief. Similarly, of all the patients who used “walking” to counteract symptoms, 50% reported complete relief, 44.5% reported some relief, and the rest did not experience any relief. Many of these patients reported that massage and tying a cloth/rope on legs brought greater relief than any of these strategies. Tying cloth on the leg was more common among females as compared to males (45.9% females vs. 23.5% males; χ2 = 7.54; P = 0.006), while patients with moderately severe to severe RLS/WED reported “moving legs in bed” (79.3% in mild to moderate RLS/WED; 91.8% in severe to very severe RLS; χ2 = 5.36; P = 0.02).
Conclusion:
Patients with RLS/WED use a variety of strategies to counteract symptoms. These strategies may be influenced by gender, disease severity, and cultural practices.
doi:10.4103/0972-2327.144010
PMCID: PMC4251013  PMID: 25506161
Counter-acting strategies; gender; severity; Willis-Ekbom disease (RLS/WED)
5.  Sports injury pattern in school going children in Union Territory of Chandigarh☆ 
Objective
To determine incidence of various types of sport injuries and other associated factors, among competitive sports playing school children of Chandigarh.
Design
This study is a survey based study, and spanned for a period of one year. School going students in age group 11–18 years of Chandigarh (Union Territory) India, who were in competitive sports, were included for this survey after taking informed consent from concerned school authorities. 33 schools consisting of 36.165 students were analysed in the study, 7230 students were found to participate in 40 different categories of sports.
Results
Total of 246 filled questionnaires were analyzed making it an injury frequency of 3.40% among 7230 participating young athletes in 12 months study duration. Estimated incidence rate, considering hours of exposure in practice, came out to be 48.07 injuries per 1000 h of exposure in practice among 246 injured cases.
40.2% of the injured children (99/246) attributed their injury to poor ground condition while other 30.5% (75/246) to faulty techniques. Rest attributed their injuries to poor fitness levels, improper use of equipment and other reasons. Of the 33 schools surveyed, 27.3% (9/33) had a doctor as health professional, 9.1% (2/33) had a physiotherapist while 66.6% of the schools (22/33) had no health care professional.
Conclusion
The incidence of sports injuries in the region is high as compared to the global data. The findings has highlighted the need for a nationwide surveillance system and then taking appropriate measures for future injury prevention and appropriate management.
doi:10.1016/j.jcot.2014.07.004
PMCID: PMC4264560
Sports injuries; School children; Indian; Epidemiology
6.  Whole Genome Sequencing and Analysis of Plant Growth Promoting Bacteria Isolated from the Rhizosphere of Plantation Crops Coconut, Cocoa and Arecanut 
PLoS ONE  2014;9(8):e104259.
Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.
doi:10.1371/journal.pone.0104259
PMCID: PMC4146471  PMID: 25162593
7.  Neglected post burns contracture of hand in children: Analysis of contributory socio-cultural factors and the impact of neglect on outcome☆ 
Background
No study has ever evaluated the causes and effect of neglect on the outcome of post burns contractures of hand in children.
Methods
66 hands in 61 children (mean age 12.22 years) with a mean neglect of 11.6 years (range 5–17 years) were assessed for the causes of neglect and the outcome of surgery. Average follow up was 6.6 years. The results were assessed in two groups of 5–10 years neglect as group I and >10 years neglect as group II.
Results
In a total number of 134 contracted rays in 66 hands, the surgical procedures included local Z/V-Y flap (51 rays), cross finger flap (48 rays), full thickness graft (35 rays). Additional external fixator with a distracter was used in 3 patients treated at a delay of 14, 16 and 17 years.
50 (81.96%) patients belonged to rural and slum areas. The reasons for delayed treatment included poverty – 33 patients, lack of awareness of surgical treatment – 16 patients; and indifference of parents – 12 patients. 44 (72.13%) children were illiterates. With treatment the average DASH score improved from 65.10 to 36.90 (p < .000) and from 68.14 to 45.93 (p < .000) in group I and II respectively. The results were significantly superior in group I (p < .000).
Conclusion
The main factors for neglect in treatment of post burns contracture include poverty, lack of awareness and illiteracy. All the patients showed significant improvement in function after the surgery. Contractures with higher neglect had significantly inferior outcome.
doi:10.1016/j.jcot.2014.07.011
PMCID: PMC4263997
Neglected; Post burn; Hand contractures; Surgical outcome; Pediatric
8.  Correlation of Molecular Markers, Pfmdr1-N86Y and Pfcrt-K76T, with In Vitro Chloroquine Resistant Plasmodium falciparum, Isolated in the Malaria Endemic States of Assam and Arunachal Pradesh, Northeast India 
PLoS ONE  2014;9(8):e103848.
The mechanism of chloroquine (CQ) resistance in Plasmodium falciparum is not clearly understood. However, CQ resistance has been shown to be associated with point mutations in Pfcrt and Pfmdr1. These genes encode for digestive vacuole transmembrane proteins Pfcrt and Pgh1, respectively. The present study was carried out to analyze the association of Pfcrt-K76T and Pfmdr1-N86Y mutations with CQ resistance in Northeast Indian P. falciparum isolates. 115 P. falciparum isolates were subjected to in vitro CQ sensitivity testing and PCR-RFLP analysis for the Pfmdr1-N86Y and Pfcrt-K76T mutations. 100 isolates of P. falciparum were found to be resistant to CQ by the in vitro susceptibility test (geometric mean EC50 2.21 µM/L blood) while 15 were found to be CQ sensitive (geometric mean EC50 0.32 µM/L blood). All the CQ resistant isolates showed the presence of Pfmdr1 and Pfcrt mutations. CQ sensitive isolates were negative for these mutations. Strong linkage disequilibrium was observed between the alleles at these two loci (Pfmdr1-N86Y and Pfcrt-K76T). The results indicate that Pfmdr1-N86Y and Pfcrt-K76T mutations can be used as molecular markers to identify CQ resistance in P. falciparum. The result necessitates the evaluation of CQ in vivo therapeutic efficacy in endemic areas for more effective malaria control strategies.
doi:10.1371/journal.pone.0103848
PMCID: PMC4126653  PMID: 25105963
9.  The Draft Genome and Transcriptome of Amaranthus hypochondriacus: A C4 Dicot Producing High-Lysine Edible Pseudo-Cereal 
Grain amaranths, edible C4 dicots, produce pseudo-cereals high in lysine. Lysine being one of the most limiting essential amino acids in cereals and C4 photosynthesis being one of the most sought-after phenotypes in protein-rich legume crops, the genome of one of the grain amaranths is likely to play a critical role in crop research. We have sequenced the genome and transcriptome of Amaranthus hypochondriacus, a diploid (2n = 32) belonging to the order Caryophyllales with an estimated genome size of 466 Mb. Of the 411 linkage single-nucleotide polymorphisms (SNPs) reported for grain amaranths, 355 SNPs (86%) are represented in the scaffolds and 74% of the 8.6 billion bases of the sequenced transcriptome map to the genomic scaffolds. The genome of A. hypochondriacus, codes for at least 24,829 proteins, shares the paleohexaploidy event with species under the superorders Rosids and Asterids, harbours 1 SNP in 1,000 bases, and contains 13.76% of repeat elements. Annotation of all the genes in the lysine biosynthetic pathway using comparative genomics and expression analysis offers insights into the high-lysine phenotype. As the first grain species under Caryophyllales and the first C4 dicot genome reported, the work presented here will be beneficial in improving crops and in expanding our understanding of angiosperm evolution.
doi:10.1093/dnares/dsu021
PMCID: PMC4263292  PMID: 25071079
Caryophyllales; grain amaranth; Amaranthus hypochondriacus; lysine biosynthesis; C4 photosynthesis
10.  Transcriptome Profiling Reveals Higher Vertebrate Orthologous of Intra-Cytoplasmic Pattern Recognition Receptors in Grey Bamboo Shark 
PLoS ONE  2014;9(6):e100018.
From an immunologist perspective, sharks are an important group of jawed cartilaginous fishes and survey of the public database revealed a great gap in availability of large-scale sequence data for the group of Chondrichthyans the elasmobranchs. In an attempt to bridge this deficit we generated the transcriptome from the spleen and kidney tissues (a total of 1,606,172 transcripts) of the shark, Chiloscyllium griseum using the Illumina HiSeq2000 platform. With a cut off of > = 300 bp and an expression value of >1RPKM we used 43,385 transcripts for BLASTX analysis which revealed 17,548 transcripts matching to the NCBI nr database with an E-value of < = 10−5 and similarity score of 40%. The longest transcript was 16,974 bases with matched to HECT domain containing E3 ubiqutin protein ligase. MEGAN4 annotation pipeline revealed immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway to be highly expressed in spleen, while different metabolism pathways such as amino acid metabolism, carbohydrate metabolism, lipid metabolism and xenobiotic biodegradation were highly expressed in kidney. Few of the candidate genes were selected to analyze their expression levels in various tissues by real-time PCR and also localization of a receptor by in-situ PCR to validate the prediction. We also predicted the domains structures of some of the identified pattern recognition receptors, their phylogenetic relationship with lower and higher vertebrates and the complete downstream signaling mediators of classical dsRNA signaling pathway. The generated transcriptome will be a valuable resource to further genetic and genomic research in elasmobranchs.
doi:10.1371/journal.pone.0100018
PMCID: PMC4067322  PMID: 24956167
12.  ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing 
Cell  2013;153(3):575-589.
SUMMARY
Adenosine deaminases acting on RNA (ADARs) are involved in RNA editing that converts adenosine residues to inosine specifically in double-stranded RNAs. In this study, we investigated the interaction of the RNA editing mechanism with the RNA interference (RNAi) machinery and found that ADAR1 forms a complex with Dicer through direct protein-protein interaction. Most importantly, ADAR1 increases the maximum rate (Vmax) of pre-microRNA (miRNA) cleavage by Dicer and facilitates loading of miRNA onto RNA-induced silencing complexes, identifying a new role of ADAR1 in miRNA processing and RNAi mechanisms. ADAR1 differentiates its functions in RNA editing and RNAi by formation of either ADAR1/ADAR1 homodimer or Dicer/ADAR1 heterodimer complexes, respectively. As expected, expression of miRNAs is globally inhibited in ADAR1−/− mouse embryos, which in turn alters expression of their target genes and might contribute to their embryonic lethal phenotype.
doi:10.1016/j.cell.2013.03.024
PMCID: PMC3651894  PMID: 23622242
13.  Refolding of β-Stranded Class I Chitinases of Hippophae rhamnoides Enhances the Antifreeze Activity during Cold Acclimation 
PLoS ONE  2014;9(3):e91723.
Class I chitinases hydrolyse the β-1,4-linkage of chitin and also acquire antifreeze activity in some of the overwintering plants during cold stress. Two chitinases, HrCHT1a of 31 kDa and HrCHT1b of 34 kDa, were purified from cold acclimated and non-acclimated seabuckthorn seedlings using chitin affinity chromatography. 2-D gels of HrCHT1a and HrCHT1b showed single spots with pIs 7.0 and 4.6 respectively. N-terminal sequence of HrCHT1b matched with the class I chitinase of rice and antifreeze proteins while HrCHT1a could not be sequenced as it was N-terminally blocked. Unlike previous reports, where antifreeze activity of chitinase was cold inducible, our results showed that antifreeze activity is constitutive property of class I chitinase as both HrCHT1a and HrCHT1b isolated even from non-acclimated seedlings, exhibited antifreeze activity. Interestingly, HrCHT1a and HrCHT1b purified from cold acclimated seedlings, exhibited 4 and 2 times higher antifreeze activities than those purified from non-acclimated seedlings, suggesting that antifreeze activity increased during cold acclimation. HrCHT1b exhibited 23–33% higher hydrolytic activity and 2–4 times lower antifreeze activity than HrCHT1a did. HrCHT1b was found to be a glycoprotein; however, its antifreeze activity was independent of glycosylation as even deglycosylated HrCHT1b exhibited antifreeze activity. Circular dichroism (CD) analysis showed that both these chitinases were rich in unusual β-stranded conformation (36–43%) and the content of β-strand increased (∼11%) during cold acclimation. Surprisingly, calcium decreased both the activities of HrCHT1b while in case of HrCHT1a, a decrease in the hydrolytic activity and enhancement in its antifreeze activity was observed. CD results showed that addition of calcium also increased the β-stranded conformation of HrCHT1a and HrCHT1b. This is the first report, which shows that antifreeze activity is constitutive property of class I chitinase and cold acclimation and calcium regulate these activities of chitinases by changing the secondary structure.
doi:10.1371/journal.pone.0091723
PMCID: PMC3953593  PMID: 24626216
14.  Attenuation of quorum sensing controlled virulence of Pseudomonas aeruginosa by cranberry 
Background & objectives:
Emergence of antimicrobial resistance in Pseudomonas aeruginosa has led to the search for alternative agents for infections control. Natural products have been a good alternative to present antibiotics. The present study was undertaken to evaluate the effectiveness of cranberry in attenuation of virulence of P. aeruginosa in experimental urinary tract infection (UTI) in mouse model. Efforts were also directed to explore the action of cranberry towards virulence of P. aeruginosa through quorum sensing (QS) inhibition.
Methods:
Efficacy of cranberry was evaluated in an experimental UTI mouse model and on production of QS signals, alginate, pyochelin, haemolysin, phospholipase-C, cell-surface hydrophobicity, uroepithelial cell-adhesion assay and biofilm formation by already standardized methods.
Results:
Presence of cranberry showed significant decline in the production of QS signals, biofilm formation and virulence factors of P. aeruginosa in vitro (P<0.001). Further, cranberry was found to be useful in prevention of experimental UTI in mouse model as indicated by reduced renal bacterial colonization and kidney tissues destruction.
Interpretation & conclusions:
The findings of the present study indicated that cranberry inhibited QS and hence elaboration of virulence factors of P. aeruginosa. It also affected the adherence ability of this pathogen. This approach can lead to the discovery of new category of safe anti-bacterial drugs from dietary sources such as cranberry with reduced toxicity without the risk of antibiotic resistance.
PMCID: PMC4069740  PMID: 24820840
Biofilm; cranberry; P. aeruginosa; quorum sensing; virulence factors
15.  Prevalence and Correlates of Insomnia and Obstructive Sleep Apnea in Chronic Kidney Disease 
Background:
Poor sleep quality, insomnia, and restless legs syndrome (RLS) and sleep apnea are common in patients with chronic kidney disease (CKD). Clinical correlates of these problems are poorly understood.
Aims:
This study was to find out the prevalence and correlates of insomnia and subjects with ‘high risk for obstructive sleep apnea (OSA)’ in adults with chronic kidney disease.
Materials and Methods:
One hundred and four adults with CKD were included. Their demographic data, details regarding kidney disease and hemodialysis (HD) were recorded. Presence of insomnia and its severity was assessed. They were screened for sleep apnea using a validated questionnaire.
Results:
Average age was 54.17 (± 12.96) years. 89.4% had stage 5 nephropathy and 78.8% subjects were on regular HD. Males outnumbered females. Insomnia was reported by 35.5%. Among these, 50% had chronic insomnia. Insomnia subjects had higher prevalence of diabetes (P = 0.01) and depression (P < 0.001). Fifty-one percent subjects were at “high risk for sleep apnea”. They had higher prevalence of diabetes (P < 0.001), coronary disease (P = 0.02), insomnia (P = 0.008), and experienced daytime symptoms of insomnia (P < 0.001). However, in the logistic regression, only male gender (odds ratio, OR = 13.59) and daytime symptoms of insomnia (OR = 7.34) were found to be associated with “higher risk for sleep apnea”.
Conclusion:
Insomnia was prevalent in CKD. Nearly half of these patients are at high risk for sleep apnea and a third of them suffer from insomnia. Hence, these patients should be screened for sleep disorders.
doi:10.4103/1947-2714.122306
PMCID: PMC3877437  PMID: 24404542
Chronic kidney disease; Hemodialysis; Insomnia; Obstructive sleep apnea
16.  CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation 
Nucleic Acids Research  2013;42(2):774-789.
CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF’s binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18th position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site.
doi:10.1093/nar/gkt910
PMCID: PMC3902912  PMID: 24121688
17.  Prevalence of obstructive sleep apnea in surgical patients presenting to a tertiary care teaching hospital in India: A preliminary study 
Saudi Journal of Anaesthesia  2013;7(2):155-159.
Background:
Obstructive sleep apnea (OSA) is often not diagnosed in patients presenting for surgical procedures thereby increasing the incidence of adverse perioperative course. Early diagnosis of this disease is important in modifying anesthetic management as well as utilizing specific means which may decrease the complications and improve the patient outcome.
Methods:
Patients greater than eighteen years of age, ASA I-III scheduled for elective surgical procedures under anesthesia were randomly selected. Their demographic data, diagnosis and nature of surgery were noted in a semi-structured performa. They were then screened for the presence of OSA with the help of a STOP BANG questionnaire.
Results:
This study included two hundred four patients randomly selected. Slight female predominance was seen in this sample (55.4%). Mean age of the subjects was 42.7 years (SD=15.08). 24.5% subjects were at high risk for OSA (STOP-BANG>3) with a male predominance (72% versus 37% in low risk group; X2=18.62; P<0.001). High risk OSA subjects had higher prevalence of cardiovascular risk factors (57% vs. 11.7% in low risk group; X2=33.35; P<0.001). Similarly, this group had a higher prevalence of asthma and chronic obstructive pulmonary disease (COPD) (14% versus 3.8% in low risk group; X2=6.54; P=0.03). Prevalence of diabetes mellitus (22%) and hypothyroidism (6%) was also higher in this group (5.2% and 1.9% in low risk group respectively; X2=15.42; P<0.001).
Conclusion:
High degree of suspicion and knowledge of association of OSA and medical diseases may help in detection of such cases and decrease the rate of perioperative complications thus improving patients safety.
doi:10.4103/1658-354X.114072
PMCID: PMC3737691  PMID: 23956715
Anaesthesia; complication; obstructive sleep apnea; STOP BANG
18.  Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling 
Frontiers in Genetics  2012;3:239.
mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the expressions at isoform level. In this paper our objective would be use the mRNA-Seq data to infer expression at isoform level, where splicing patterns of a gene is assumed to be known. A Bayesian latent variable based modeling framework is proposed here, where the parameterization enables us to infer at various levels. For example, expression variability of an isoform across different conditions; the model parameterization also allows us to carry out two-sample comparisons, e.g., using a Bayesian t-test, in addition simple presence or absence of an isoform can also be estimated by the use of the latent variables present in the model. In this paper we would carry out inference on isoform expression under different normalization techniques, since it has been recently shown that one of the most prominent sources of variation in differential call using mRNA-Seq data is the normalization method used. The statistical framework is developed for multiple isoforms and easily extends to reads mapping to multiple genes. This could be achieved by slight conceptual modifications in definitions of what we consider as a gene and what as an exon. Additionally proposed framework can be extended by appropriate modeling of the design matrix to infer about yet unknown novel transcripts. However such attempts should be made judiciously since the input date used in the proposed model does not use reads from splice junctions.
doi:10.3389/fgene.2012.00239
PMCID: PMC3536024  PMID: 23293650
mRNA-Seq; isoform expression; Bayesian latent variable modeling; multi-sample comparison; Bayesian t-test; spike-n-slab method
19.  Sequencing and analysis of a South Asian-Indian personal genome 
BMC Genomics  2012;13:440.
Background
With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala.
Results
We identified over 3.4 million SNPs in this genome including over 89,873 private variations. Comparison of the SAIF genome with several published personal genomes revealed that this individual shared ~50% of the SNPs with each of these genomes. Analysis of the SAIF mitochondrial genome showed that it was closely related to the U1 haplogroup which has been previously observed in Kerala. We assessed the SAIF genome for SNPs with health and disease consequences and found that the individual was at a higher risk for multiple sclerosis and a few other diseases. In analyzing SNPs that modulate drug response, we found a variation that predicts a favorable response to metformin, a drug used to treat diabetes. SNPs predictive of adverse reaction to warfarin indicated that the SAIF individual is not at risk for bleeding if treated with typical doses of warfarin. In addition, we report the presence of several additional SNPs of medical relevance.
Conclusions
This is the first study to report the complete whole genome sequence of a female from the state of Kerala in India. The availability of this complete genome and variants will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and assessing disease burden in the Indian population.
doi:10.1186/1471-2164-13-440
PMCID: PMC3534380  PMID: 22938532
Indian genome; Personal genomics; Whole genome sequencing
20.  Primary headaches in restless legs syndrome patients 
Annals of Indian Academy of Neurology  2012;15(Suppl 1):S104-S108.
Earlier studies conducted among migraineurs have shown an association between migraine and restless legs syndrome (RLS). We chose RLS patients and looked for migraine to exclude sample bias.
Materials and Methods:
99 consecutive subjects of idiopathic RLS were recruited from the sleep clinic during four months period. Physician diagnosis of headache and depressive disorder was made with the help of ICHD-2 and DSM-IV-TR criteria, respectively. Sleep history was gathered. Severity of RLS and insomnia was measured using IRLS (Hindi version) and insomnia severity index Hindi version, respectively. Chi-square test, one way ANOVA and t-test were applied to find out the significance.
Results:
Primary headache was seen in 51.5% cases of RLS. Migraine was reported by 44.4% subjects and other types of ‘primary headaches’ were reported by 7.1% subjects. Subjects were divided into- RLS; RLS with migraine and RLS with other headache. Females outnumbered in migraine subgroup (χ2=16.46, P<0.001). Prevalence of depression (χ2=3.12, P=0.21) and family history of RLS (χ2=2.65, P=0.26) were not different among groups. Severity of RLS (P=0.22) or insomnia (P=0.43) were also similar.
Conclusion:
Migraine is frequently found in RLS patients in clinic based samples. Females with RLS are prone to develop migraine. Depression and severity of RLS or insomnia do not affect development of headache.
doi:10.4103/0972-2327.100031
PMCID: PMC3444227  PMID: 23024558
Migraine; primary headache; restless legs syndrome
21.  Repair of the torn distal biceps tendon by endobutton fixation 
Indian Journal of Orthopaedics  2012;46(1):71-76.
Background:
A number of techniques have been described to reattach the torn distal biceps tendon to the bicipital tuberosity. We report a retrospective analysis of single incision technique using an endobutton fixation in sports persons.
Materials and Methods:
The present series include nine torn distal biceps tendons in eight patients, fixed anatomically to the radial tuberosity with an endobutton by using a single incision surgical technique; seven patients had suffered the injuries during contact sports. The passage of the endobutton was facilitated by using a blunt tipped pin in order to avoid injury to the posterior interosseous nerve. The patients were evaluated by Disabilities of the Arm, Shoulder and Hand (DASH) score and Mayo elbow score.
Results:
The average age of the patients was 27.35 years (range 21–42 years). Average follow-up was 41.5 months (range 24–102 months). The final average flexion extension arc was 0°–143°, while the average pronation and supination angles were 77° (range 70°–82°) and 81° (range 78°–85°), respectively at the last followup. All the patients had a Disabilities of the Arm, Shoulder and Hand (DASH) score of 0 and a Mayo elbow score of 100 each. All the seven active sports persons were able to get back to their respective game. There was no nerve injury or any other complication.
Conclusions:
The surgical procedure used by us is a simple, safe and reproducible technique giving minimal morbidity and better cosmetic results.
doi:10.4103/0019-5413.91638
PMCID: PMC3270609  PMID: 22345810
Autograft; biceps tendon; elbow; tendon repair; tendon rupture
22.  Antibiotic Resistance Pattern of Community Acquired Uropathogens at a Tertiary Care Hospital in Jaipur, Rajasthan 
Background:
Urinary tract infections (UTIs) are amongst the most common infections described in outpatients setting.
Objectives:
A study was conducted to evaluate the uropathogenic bacterial flora and its antimicrobial susceptibility profile among patients presenting to the out-patient clinics of a tertiary care hospital at Jaipur, Rajasthan.
Materials and Methods:
2012 consecutive urine specimens from symptomatic UTI cases attending to the outpatient clinics were processed in the Microbiology lab. Bacterial isolates obtained were identified using biochemical reactions. Antimicrobial susceptibility testing was performed by the Kirby-Bauer disc diffusion method. Extended spectrum beta lactamase (ESBL) production was determined by the double disk approximation test and the Clinical and Laboratory Standards Institute (formerly NCCLS) confirmatory method.
Results:
Pathogens were isolated from 346 (17.16%) of the 2012 patients who submitted a urine sample. Escherichia coli was the most frequently isolated community acquired uropathogen accounting for 61.84% of the total isolates. ESBL production was observed in 23.83% of E. coli strains and 8.69% of Klebsiella strains. With the exception of Nitrofurantoin, resistance to agents commonly used as empiric oral treatments for UTI was quite high.
Conclusion:
The study revealed E. coli as the predominant bacterial pathogen for the community acquired UTIs in Jaipur, Rajasthan. An increasing trend in the production ESBLs among UTI pathogens in the community was noted. Nitrofurantoin should be used as empirical therapy for primary, uncomplicated UTIs.
doi:10.4103/0970-0218.94023
PMCID: PMC3326806  PMID: 22529539
Urinary tract infection; outpatients; Escherichia coli
23.  Migraine: Clinical pattern and psychiatric comorbidity 
Industrial Psychiatry Journal  2012;21(1):18-21.
Background:
Migraine is a common disorder which has psychiatric sequelae.
Objective:
The objective of this study was to determine the clinical pattern and psychiatric comorbidity of migraine.
Materials and Methods:
100 cases of migraine seen over a period of one year were analysed to know the sociodemographic characteristics, clinical pattern and psychiatric morbidity.
Results:
Maximum patients were between 31-40 years of age group (40%), females (78.0%), married (76%) and housewives (56.0%). Family history of migraine was present in 12% cases. Average age of onset was 22 years. Unilateral and throbbing type of headache was most common. The commonest frequency was one to two per week. Migraine without aura was commonest sub-type (80%). Generalized anxiety disorder (F41.1) was the most common psychiatric disorder (34%), followed by mixed anxiety and depressive disorder (F41.2) (18%) and depressive episode (F32) (14%). In 22% cases, no psychiatric disorder could be elicited.
Conclusion:
The present study confirms that majority patients with migraine had psychiatric disorders. This needs timely detection and appropriate intervention to treat and control the migraine effectively.
doi:10.4103/0972-6748.110943
PMCID: PMC3678173  PMID: 23766573
Migraine; pattern; psychiatric comorbidity
24.  Papillary Carcinoma of the Breast: An Overview 
Papillary carcinoma of the breast represents approximately 0.5% of all newly diagnosed cases of breast cancer. The prevalence of both invasive and in situ papillary carcinoma seems to be greater older postmenopausal women, and -in relative terms-in males. Histologic features of the tumor include cellular proliferations surrounding fibrovascular cores, with or without invasion. In this review, characteristics of both in situ and invasive disease are outlined. Immunohistochemical analyses of papillary carcinoma suggest the utility of markers such as smooth muscle myosin heavy chain, calponin, p63 and high molecular weight keratins, which can characterize the myoepithelial cell layer. With respect to radiographic evaluation of papillary carcinoma, ultrasonography is the most extensively studied imaging modality, though magnetic resonance mammography has potential utility. Available data suggest improved outcome for papillary carcinoma as compared to invasive ductal carcinoma. Treatment-related information for patients with papillary carcinoma is limited, and patterns noted in available series suggest a variable approach to this disease. The scarcity of information underscores the need for further treatment- and outcome-related studies in papillary carcinoma of the breast.
doi:10.1007/s10549-010-0961-5
PMCID: PMC3244819  PMID: 20524058
papillary; breast carcinoma; male breast cancer; breast ultrasonography; breast magnetic resonance mammography
25.  Translation and validation of International Restless Leg Syndrome Study Group rating scale in Hindi language 
Objectives:
The objective of this study is to translate and validate the International Restless Leg Syndrome Study Group rating scale (IRLS) in Hindi language.
Materials and Methods:
Thirty one consecutive patients diagnosed of Restless Leg Syndrome (RLS) were included in the study. Control group comprised of 31 subjects not having any symptom of RLS. The scale was procured from MAPI research trust; and, permission for the translation was sought. The translation was done according to the guidelines provided by the publisher. After translation, final version of the scale was applied in both the groups to find out the reliability and clinical validity.
Results:
RLS group had a predominance of females, and they were younger than the male counterparts (Age=36.80 ± 10.46 years vs 45.18 ± 8.34 years; t=2.28; P=0.03). There was no difference in the mean age between groups (RLS=39.77 ± 10.44 years vs Non RLS=38.29 ± 11.29 years; t=-0.53; P=0.59). IRLS scores were significantly different between both groups on all items (P<0.001). Translated version showed high reliability (Cronbach's alpha=0.86). IRLS scores were significantly different between both groups on all items (P<0.001).
Conclusion:
Hindi version of IRLS is reliable and a clinically valid tool that can be applied in Hindi speaking population.
doi:10.4103/0972-2327.91939
PMCID: PMC3271463  PMID: 22346013
Hindi translation; International Restless Leg Syndrome Study Group rating scale; Restless Leg Syndrome; translation; validation

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