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1.  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
3.  Supratentorial primitive neuroectodermal tumor in an adult: a case report and review of the literature 
Introduction
Supratentorial primitive neuroectodermal tumors predominantly occur in children, and are rare in the adult population. Less than 100 cases of supratentorial primitive neuroectodermal tumor have been reported in adults internationally. Our case study reports this rare incident.
Case presentation
A 22-year-old Hispanic man presented with headaches, blurry vision, diplopia, intermittent vomiting, and grossly decreased vision. A magnetic resonance image showed a left posterior parietal heterogeneously enhancing mass measuring 4.2cm × 7.2cm × 7.0cm. After craniotomy for resection and decompression, the mass was histologically revealed to be a supratentorial primitive neuroectodermal tumor. Standardized immunohistochemical studies for this mass were carried out.
Conclusion
We have concluded that immunohistochemical and genetic workup should be included in the standardized pathological workup for primitive neuroectodermal tumors in order to provide more prognostic information. Based on our current literature review, we propose an immunohistochemical panel.
doi:10.1186/1752-1947-6-361
PMCID: PMC3492070  PMID: 23095172
4.  Bursa over K nail presenting as pseudo tumor in gluteal region 
We present a case of enlarged bursa with calcified/ossified walls presenting as pseudo tumor in the left gluteal region over an indwelling protruded tip of a K nail implanted 18 years back in a 35 years old male. The patient had received initial treatment from a quack and subsequently from a qualified physician before coming to us and was referred to us with a provisional diagnosis of some soft tissue tumor. Removal of the nail and the bursa resulted in complete recovery and full function.
doi:10.1016/j.jcot.2012.09.008
PMCID: PMC3872806
Gluteal region; Bursa; K nail; Intramedullary nail; Pseudo tumor
5.  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
6.  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
7.  Adult rumination syndrome: Differentiation from psychogenic intractable vomiting 
Indian Journal of Psychiatry  2012;54(3):283-285.
Rumination syndrome is known to exist in infants and mentally retarded adults since long time. In past few years, some reports appeared that showed its existence in adult patients also. It is frequently confused with the intractable vomiting in adults and misdiagnosis leads to delay in appropriate management. We are here describing the case of a female patient with rumination syndrome where specific points in the history delineated the presence of this illness and helped in appropriate management. The patient became symptom free soon after the diagnosis was reached.
doi:10.4103/0019-5545.102434
PMCID: PMC3512372  PMID: 23226859
Psychogenic; intractable vomiting; rumination
8.  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
9.  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
10.  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

Results 1-10 (10)