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1.  Development and evaluation of a one step reverse transcription-loop mediated isothermal amplification assay (RT-LAMP) for rapid detection of foot and mouth disease virus in India 
Virusdisease  2014;25(3):358-364.
A simple, rapid and sensitive diagnostic assay for Foot-and-mouth disease (FMD) is required for deployment in the field. In this study, development of Reverse Transcription-Loop Mediated Isothermal Amplification (RT-LAMP) assay based on the 3D polymerase gene for specific and rapid detection FMD virus (FMDV) was carried out. The assay was optimised with viral RNA extracted from serotype O, A and Asia 1 FMDV vaccine strains, which resulted a reliable amplification at 65 °C for 60 min. The amplified RT-LAMP products were identified by agarose gel electrophoresis with ethidium bromide staining or observation by naked eye for the presence of turbidity and colour change following the addition of hydroxyl naphthol blue (HNB). The specificity of the assay was demonstrated by the absence of amplification of genome extracted from other viruses or cellular origin. With respect to analytical sensitivity the developed RT-LAMP assay was found more sensitive than routinely used multiplex PCR (mPCR). Further, the assay was evaluated with RNA extracted from cell cultured isolates (n = 50), tongue epithelial samples (n = 150) and semen samples from infected bulls (n = 13). In conclusion, RT-LAMP with HNB dye was shown to be simple, specific and sensitive assay for rapid diagnosis of FMDV infection. Further, the assay has the potential for field deployment and use for rapid FMDV surveillance in India.
Electronic supplementary material
The online version of this article (doi:10.1007/s13337-014-0211-2) contains supplementary material, which is available to authorized users.
PMCID: PMC4188206
Foot and mouth disease; FMD virus; Diagnosis; Loop mediated isothermal amplification assay; mPCR
2.  Dynalign II: common secondary structure prediction for RNA homologs with domain insertions 
Nucleic Acids Research  2014;42(22):13939-13948.
Homologous non-coding RNAs frequently exhibit domain insertions, where a branch of secondary structure is inserted in a sequence with respect to its homologs. Dynamic programming algorithms for common secondary structure prediction of multiple RNA homologs, however, do not account for these domain insertions. This paper introduces a novel dynamic programming algorithm methodology that explicitly accounts for the possibility of inserted domains when predicting common RNA secondary structures. The algorithm is implemented as Dynalign II, an update to the Dynalign software package for predicting the common secondary structure of two RNA homologs. This update is accomplished with negligible increase in computational cost. Benchmarks on ncRNA families with domain insertions validate the method. Over base pairs occurring in inserted domains, Dynalign II improves accuracy over Dynalign, attaining 80.8% sensitivity (compared with 14.4% for Dynalign) and 91.4% positive predictive value (PPV) for tRNA; 66.5% sensitivity (compared with 38.9% for Dynalign) and 57.0% PPV for RNase P RNA; and 50.1% sensitivity (compared with 24.3% for Dynalign) and 58.5% PPV for SRP RNA. Compared with Dynalign, Dynalign II also exhibits statistically significant improvements in overall sensitivity and PPV. Dynalign II is available as a component of RNAstructure, which can be downloaded from
PMCID: PMC4267632  PMID: 25416799
3.  SWIFT—Scalable Clustering for Automated Identification of Rare Cell Populations in Large, High-Dimensional Flow Cytometry Datasets, Part 2: Biological Evaluation 
Cytometry  2014;85(5):422-433.
A multistage clustering and data processing method, SWIFT (detailed in a companion manuscript), has been developed to detect rare subpopulations in large, high-dimensional flow cytometry datasets. An iterative sampling procedure initially fits the data to multidimensional Gaussian distributions, then splitting and merging stages use a criterion of unimodality to optimize the detection of rare subpopulations, to converge on a consistent cluster number, and to describe non-Gaussian distributions. Probabilistic assignment of cells to clusters, visualization, and manipulation of clusters by their cluster medians, facilitate application of expert knowledge using standard flow cytometry programs. The dual problems of rigorously comparing similar complex samples, and enumerating absent or very rare cell subpopulations in negative controls, were solved by assigning cells in multiple samples to a cluster template derived from a single or combined sample. Comparison of antigen-stimulated and control human peripheral blood cell samples demonstrated that SWIFT could identify biologically significant subpopulations, such as rare cytokine-producing influenza-specific T cells. A sensitivity of better than one part per million was attained in very large samples. Results were highly consistent on biological replicates, yet the analysis was sensitive enough to show that multiple samples from the same subject were more similar than samples from different subjects. A companion manuscript (Part 1) details the algorithmic development of SWIFT. © 2014 The Authors. Published by Wiley Periodicals Inc.
PMCID: PMC4238823  PMID: 24532172
SWIFT; EM algorithm; flow cytometry clustering; ground truth data; automated analysis
4.  SWIFT—Scalable Clustering for Automated Identification of Rare Cell Populations in Large, High-Dimensional Flow Cytometry Datasets, Part 1: Algorithm Design 
Cytometry  2014;85(5):408-421.
We present a model-based clustering method, SWIFT (Scalable Weighted Iterative Flow-clustering Technique), for digesting high-dimensional large-sized datasets obtained via modern flow cytometry into more compact representations that are well-suited for further automated or manual analysis. Key attributes of the method include the following: (a) the analysis is conducted in the multidimensional space retaining the semantics of the data, (b) an iterative weighted sampling procedure is utilized to maintain modest computational complexity and to retain discrimination of extremely small subpopulations (hundreds of cells from datasets containing tens of millions), and (c) a splitting and merging procedure is incorporated in the algorithm to preserve distinguishability between biologically distinct populations, while still providing a significant compaction relative to the original data. This article presents a detailed algorithmic description of SWIFT, outlining the application-driven motivations for the different design choices, a discussion of computational complexity of the different steps, and results obtained with SWIFT for synthetic data and relatively simple experimental data that allow validation of the desirable attributes. A companion paper (Part 2) highlights the use of SWIFT, in combination with additional computational tools, for more challenging biological problems. © 2014 The Authors. Published by Wiley Periodicals Inc.
PMCID: PMC4238829  PMID: 24677621
automated multivariate clustering; rare subpopulation detection; Gaussian mixture models; weighted sampling; ground truth data
5.  An Information Transmission Measure for the Analysis of Effective Connectivity among Cortical Neurons 
We present a methodology for detecting effective connections between simultaneously recorded neurons using an information transmission measure to identify the presence and direction of information flow from one neuron to another. Using simulated and experimentally-measured data, we evaluate the performance of our proposed method and compare it to the traditional transfer entropy approach. In simulations, our measure of information transmission outperforms transfer entropy in identifying the effective connectivity structure of a neuron ensemble. For experimentally recorded data, where ground truth is unavailable, the proposed method also yields a more plausible connectivity structure than transfer entropy.
PMCID: PMC4216183  PMID: 21096617
6.  Comparative iron oxide nanoparticle cellular dosimetry and response in mice by the inhalation and liquid cell culture exposure routes 
Toxicity testing the rapidly growing number of nanomaterials requires large scale use of in vitro systems under the presumption that these systems are sufficiently predictive or descriptive of responses in in vivo systems for effective use in hazard ranking. We hypothesized that improved relationships between in vitro and in vivo models of experimental toxicology for nanomaterials would result from placing response data in vitro and in vivo on the same dose scale, the amount of material associated with cells.
Balb/c mice were exposed nose-only to an aerosol (68.6 nm CMD, 19.9 mg/m3, 4 hours) generated from of 12.8 nm superparamagnetic iron oxide particles (SPIO). Target cell doses were calculated, histological evaluations conducted, and biomarkers of response were identified by global transcriptomics. Representative murine epithelial and macrophage cell types were exposed in vitro to the same material in liquid suspension for four hours and levels of nanoparticle regulated cytokine transcripts identified in vivo were quantified as a function of measured nanoparticle cellular dose.
Target tissue doses of 0.009-0.4 μg SPIO/cm2 in lung led to an inflammatory response in the alveolar region characterized by interstitial inflammation and macrophage infiltration. In vitro, higher target tissue doses of ~1.2-4 μg SPIO/ cm2 of cells were required to induce transcriptional regulation of markers of inflammation, CXCL2 & CCL3, in C10 lung epithelial cells. Estimated in vivo macrophage SPIO nanoparticle doses ranged from 1-100 pg/cell, and induction of inflammatory markers was observed in vitro in macrophages at doses of 8-35 pg/cell.
Application of target tissue dosimetry revealed good correspondence between target cell doses triggering inflammatory processes in vitro and in vivo in the alveolar macrophage population, but not in the epithelial cells of the alveolar region. These findings demonstrate the potential for target tissue dosimetry to enable the more quantitative comparison of in vitro and in vivo systems and advance their use for hazard assessment and extrapolation to humans. The mildly inflammogentic cellular doses experienced by mice were similar to those calculated for humans exposed to the same material at the existing permissible exposure limit of 10 mg/m3 iron oxide (as Fe).
Electronic supplementary material
The online version of this article (doi:10.1186/s12989-014-0046-4) contains supplementary material, which is available to authorized users.
PMCID: PMC4200214  PMID: 25266609
Magnetic particle detection; Nano-aerosol; In vivo testing; Lung deposition; Nanoparticle; Dosimetry; Extrapolation
7.  Association of facet tropism with lumbar disc herniation 
European Spine Journal  2012;22(5):1045-1052.
Facet tropism is defined as asymmetry between left and right facet joints and is postulated as a possible cause of disc herniation. In the present study, the authors used a 3-T MRI to investigate the association between facet tropism and lumbar disc herniation at a particular motion segment. They also examined whether the disc herniated towards the side of the more coronally oriented facet joint.
Sixty patients (18–40 years) with single level disc herniation (L3–L4, L4–L5, or L5–S1) were included in the study. Facet angles were measured using MRI of 3-T using the method described by Karacan et al. Facet tropism was defined as difference of 10° in facet joint angles between right and left sides. Normal disc adjacent to the herniated level was used as control. We also examined if disc herniated towards the side of more coronally oriented facet.
Twenty-five herniations were at L4–L5 level and 35 at L5–S1. Statistical analysis was performed using the Fischer Exact Test. At L4–L5 level, 6/25 cases had tropism compared to 3/35 controls (p = 0.145). At L5–S1 level, 13/35 cases had tropism as compared to 1/21 controls (p = 0.0094). Of 19 cases having tropism, the disc had herniated towards the coronally oriented facet in six (p = 0.11).
The findings of the study suggest that facet tropism is associated with lumbar disc herniation at the L5–S1 motion segment but not at the L4–L5 level.
PMCID: PMC3657057  PMID: 23242621
Facet tropism; Lumbar disc herniation; Facet asymmetry; Magnetic resonance imaging
8.  Draft Genome Sequence of Kocuria palustris PEL 
Genome Announcements  2014;2(1):e01261-13.
We report the 2.9-Mb draft genome sequence of an actinobacterium, Kocuria palustris PEL, of the family Micrococcaceae.
PMCID: PMC3916494  PMID: 24504000
9.  Microwave induced synthesis of graft copolymer of binary vinyl monomer mixtures onto delignified Grewia optiva fiber: application in dye removal 
Grafting method, through microwave radiation technique is very effective in terms of time consumption, cost effectiveness and environmental friendliness. Via this method, delignified Grewia optiva identified as a waste biomass, was graft copolymerized with methylmethacrylate (MMA) as an principal monomer in a binary mixture of ethyl methacrylate (EMA) and ethyl acrylate (EA) under microwave irradiation (MWR) using ascorbic acid/H2O2 as an initiator system. The concentration of the comonomer was optimized to maximize the graft yield with respect to the primary monomer. Maximum graft yield (86.32%) was found for dGo-poly(MMA-co-EA) binary mixture as compared to other synthesized copolymer. The experimental results inferred that the optimal concentrations for the comonomers to the optimized primary monomer was observed to be 3.19 mol/L × 10−1 for EMA and 2.76 mol/L × 10−1 for EA. Delignified and graft copolymerized fiber were subjected to evaluation of physicochemical properties such as swelling behavior and chemical resistance. The synthesized graft copolymers were characterized with Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and X-ray diffraction techniques. Thermal stability of dGo-poly(MMA-co-EA) was found to be more as compared to the delignified Grewia optiva fiber and other graft copolymers. Although the grafting technique was found to decrease percentage crystallinity and crystallinity index among the graft copolymers but there was significant increase in their acid/base and thermal resistance properties. The grafted samples have been explored for the adsorption of hazardous methylene dye from aqueous system.
PMCID: PMC4127470  PMID: 25157348
comonomer; microwave; delignified Grewia optiva fiber; physicochemical properties; methylene blue
10.  Clinical Implications of Referral Bias in the Diagnostic Performance of Exercise Testing for Coronary Artery Disease 
Exercise testing with echocardiography or myocardial perfusion imaging is widely used to risk‐stratify patients with suspected coronary artery disease. However, reports of diagnostic performance rarely adjust for referral bias, and this practice may adversely influence patient care. Therefore, we evaluated the potential impact of referral bias on diagnostic effectiveness and clinical decision‐making.
Methods and Results
Searching PubMed and EMBASE (1990–2012), 2 investigators independently evaluated eligibility and abstracted data on study characteristics and referral patterns. Diagnostic performance reported in 4 previously published meta‐analyses of exercise echocardiography and myocardial perfusion imaging was adjusted using pooled referral rates and Bayesian methods. Twenty‐one studies reported referral patterns in 49 006 patients (mean age 60.7 years, 39.6% women, and 0.8% prior history of myocardial infarction). Catheterization referral rates after normal and abnormal exercise tests were 4.0% (95% CI, 2.9% to 5.0%) and 42.5% (36.2% to 48.9%), respectively, with odds ratio for referral after an abnormal test of 14.6 (10.7 to 19.9). After adjustment for referral, exercise echocardiography sensitivity fell from 84% (80% to 89%) to 34% (27% to 41%), and specificity rose from 77% (69% to 86%) to 99% (99% to 100%). Similarly, exercise myocardial perfusion imaging sensitivity fell from 85% (81% to 88%) to 38% (31% to 44%), and specificity rose from 69% (61% to 78%) to 99% (99% to 100%). Summary receiver operating curve analysis demonstrated only modest changes in overall discriminatory power but adjusting for referral increased positive‐predictive value and reduced negative‐predictive value.
Exercise echocardiography and myocardial perfusion imaging are considerably less sensitive and more specific for coronary artery disease after adjustment for referral. Given these findings, future work should assess the comparative ability of these and other tests to rule‐in versus rule‐out coronary artery disease.
PMCID: PMC3886773  PMID: 24334965
coronary artery disease; diagnostic performance; echocardiography; exercise testing; myocardial perfusion imaging
11.  Genomic architecture of HIV-1 infection: Current status & challenges 
Studies on host genomics have revealed the existence of identifiable HIV-1 specific protective factors among infected individuals who remain naturally resistant viraemia controllers with little or no evidence of virus replication. These factors are broadly grouped into those that are immune associated (MHC, chemokines, cytokines, CTLs and others), linked to viral entry (chemokine co-receptors and ligands), act as post-entry restriction elements (TRIM5a, APOBEC3) and those associated with viral replication (cytokines and others). These features have been identified through multiple experimental approaches ranging from candidate gene approaches, genome wide association studies (GWAS), expression analysis in conjunction with functional assays in humans to primate based models. Several studies have highlighted the individual and population level gross differences both in the viral clade sequences as well as host determined genetic associations. This review collates current information on studies involving major histocompatibility complex (MHC) as well as non MHC genes in the context of HIV-1 infection and AIDS involving varied ethnic groups. Special focus of the review is on the genetic studies carried out on the Indian population. Further challenges with regard to therapeutic interventions based on current knowledge have been discussed along with discussion on documented cases of stem cell therapy and very early highly active antiretroviral therapy (HAART) interventions.
PMCID: PMC3928698  PMID: 24434320
AIDS; chemokine; elite controllers; genes; HIV-1; HLA; restriction; viraemia
12.  Evaluation of buspirone for relapse-prevention in adults with cocaine dependence: An efficacy trial conducted in the real world 
Contemporary clinical trials  2012;33(5):993-1002.
Cocaine dependence is a significant public health problem for which there are currently no FDA-approved medications. Hence, identifying candidate compounds and employing an efficient evaluation process is crucial. This paper describes key design decisions made for a National Institute on Drug Abuse (NIDA) Clinical Trials Network (CTN) study that uses a novel two-stage process to evaluate buspirone (60 mg/day) for cocaine-relapse prevention. The study includes pilot (N=60) and full-scale (estimated N=264) trials. Both trials will be randomized, double-blind, and placebo-controlled and both will enroll treatment-seeking cocaine-dependent participants engaged in inpatient/residential treatment and scheduled for outpatient treatment post-discharge. All participants will receive contingency management in which incentives are given for medication adherence as evaluated by the Medication Events Monitoring System (MEMS). The primary outcome measure is maximum days of continuous cocaine abstinence, as assessed by twice-weekly urine drug screens (UDS) and self-report, during the 15-week outpatient treatment phase. Drug-abuse outcomes include cocaine use as assessed by UDS and self-report of cocaine use, other substance use as assessed by UDS and self-report of substance use (i.e., alcohol and/or illicit drugs), cocaine bingeing, HIV risk behavior, quality of life, functioning, and substance-abuse treatment attendance. Unique aspects of the study include conducting an efficacy trial in community treatment programs, a two-stage process to efficiently evaluate buspirone, and an evaluation of mediators by which buspirone might exert a beneficial effect on relapse prevention.
PMCID: PMC3408816  PMID: 22613054
cocaine; buspirone; relapse-prevention; contingency management
13.  One-Step Fabrication of Polymeric Janus Nanoparticles for Drug Delivery 
With its unique structure of two compartments, Janus particles inadequate, including to be used as a drug delivery system to deliver multiple payloads with widely different solubility. Here we report on a fluidic nanoprecipitation system (FNPS), capable of fabricating biocompatible Janus polymeric nanoparticles comprised of the FDA-approved polymer poly(lactic-co-glycolic acid) (PLGA). The FNPS contains dual inlets, one for each half of the particle, that insert into the precipitation stream. The system provides a one-step approach for production of Janus polymeric particles with submicrometer diameters and is likely amenable to substantial scale-up. To the best of our knowledge, this is the first demonstration of biocompatible Janus nanoparticles that encapsulate a hydrophobic drug (paclitaxel) on one side and a hydrophilic drug (doxorubicin hydrochloride) on the other.
PMCID: PMC3582348  PMID: 22251479
14.  Design considerations for a study to evaluate the impact of smoking cessation treatment on stimulant use outcomes in stimulant-dependent individuals 
Contemporary Clinical Trials  2011;33(1):197-205.
Cigarette smoking is prevalent in cocaine/methamphetamine-dependent patients and associated with significant morbidity and mortality, yet, the provision of smoking cessation treatment in conjunction with substance use disorder (SUD) treatment is not standard practice. This is due, in part, to clinician concern that combining smoking cessation treatment with SUD treatment could lead to poorer SUD outcomes. The NIDA Clinical Trials Network is conducting a 10-week, two-group, randomized trial to evaluate the impact of providing smoking cessation treatment (SCT) with SUD treatment as usual (TAU), compared to TAU alone, in smokers who are in outpatient treatment for cocaine or methamphetamine dependence. Approximately 528 participants, recruited from 12 community treatment programs, will be randomized into the trial. The present paper describes key design decisions made during protocol development. The trial is designed to evaluate the relationship between cigarette smoking and stimulant use, which prior research suggests is linked, and should contribute to our understanding of how best to address the co-occurring problems of nicotine dependence and cocaine/ methamphetamine-dependence. Unique aspects of the trial include the primary question of interest, which concerns the impact of providing SCT on SUD outcomes rather than on smoking outcomes, and the intensity of the SCT chosen, which includes bupropion, nicotine replacement, and two psychosocial interventions.
PMCID: PMC3253873  PMID: 22005174
cocaine; methamphetamine; smoking cessation; bupropion; contingency management
Nano LIFE  2010;1(3-4):207-214.
Macrophage foam cells are key components of atherosclerotic plaque and play an important role in the progression of atherosclerosis leading to plaque rupture and thrombosis. Foam cells are emerging as attractive targets for therapeutic intervention and for imaging the progression of disease. Therefore, designing nanoparticles (NPs) targeted to macrophage foam cells in plaque is of considerable therapeutic significance. Here we report the construction of an oligonucleotide functionalized NP system with high affinity for foam cells. Nanoparticles functionalized with a 23-mer poly-Guanine (polyG) oligonucleotide are specifically recognized by the scavenger receptors on lipid-laden foam cells in vitro and ex vivo. The enhanced uptake of polyG-functionalized NPs by foam cells is inhibited in the presence of acetylated-LDL, a known ligand of scavenger receptors. Since polyG oligonucleotides are stable in serum and are unlikely to induce an immune response, their use for scavenger receptor-mediated targeting of macrophage foam cells provides a strategy for targeting atherosclerotic lesions.
PMCID: PMC3484886  PMID: 23125876
Atherosclerosis; Nanoparticles; polyG; foam cells; scavenger receptors
17.  Mucosal fixed drug eruption in a patient treated with ornidazole 
Therapeutic drugs have been observed to cause a wide spectrum of adverse oral effects such as dry mouth, gingival enlargement, taste disturbance, oral mucosal ulceration, halitosis, etc.
A rare case of intra-oral fixed drug eruption (FDE) induced by ornidazole presenting on the hard palate, an extremely rare site for FDE, in a 40-year-old male is reported.
Ornidazole is a relatively newer 5-nitroimidazole derivative commonly prescribed for Amoebic dysentery in developing countries. FDE is a rare adverse drug effect characterized by onset of round/oval, erythematous macules on the skin or mucosa that can be associated with itching and burning sensation. The exact mechanism causing FDE is unknown.
PMCID: PMC3322106  PMID: 22514586
drug-induced; mucous; oral; ornidazole
18.  Integration of digital gross pathology images for enterprise-wide access 
Sharing digital pathology images for enterprise- wide use into a picture archiving and communication system (PACS) is not yet widely adopted. We share our solution and 3-year experience of transmitting such images to an enterprise image server (EIS).
Gross pathology images acquired by prosectors were integrated with clinical cases into the laboratory information system's image management module, and stored in JPEG2000 format on a networked image server. Automated daily searches for cases with gross images were used to compile an ASCII text file that was forwarded to a separate institutional Enterprise Digital Imaging and Communications in Medicine (DICOM) Wrapper (EDW) server. Concurrently, an HL7-based image order for these cases was generated, containing the locations of images and patient data, and forwarded to the EDW, which combined data in these locations to generate images with patient data, as required by DICOM standards. The image and data were then “wrapped” according to DICOM standards, transferred to the PACS servers, and made accessible on an institution-wide basis.
In total, 26,966 gross images from 9,733 cases were transmitted over the 3-year period from the laboratory information system to the EIS. The average process time for cases with successful automatic uploads (n=9,688) to the EIS was 98 seconds. Only 45 cases (0.5%) failed requiring manual intervention. Uploaded images were immediately available to institution- wide PACS users. Since inception, user feedback has been positive.
Enterprise- wide PACS- based sharing of pathology images is feasible, provides useful services to clinical staff, and utilizes existing information system and telecommunications infrastructure. PACS-shared pathology images, however, require a “DICOM wrapper” for multisystem compatibility.
PMCID: PMC3327039  PMID: 22530178
DICOM; digital image; LIS; PACS; pathology; wrapper
19.  Utility of saliva and hair follicles in donor selection for hematopoietic stem cell transplantation and chimerism monitoring 
Chimerism  2012;3(1):9-17.
Selection of an HLA identical donor is a critical pre-requisite for successful hematopoietic stem cell transplantation (HSCT). Most transplant centers utilize blood as the most common source of DNA for HLA testing. However, obtaining blood through phlebotomy is often challenging in patients with conditions like severe leucopenia or hemophilia, pediatric and elderly patients. We have used a simple in-house protocol and shown that HLA genotypes obtained on DNA extracted from saliva or hair are concordant with blood and hence can be used for selection of donors for HSCT or organ transplantation. Similarly, for post-HSCT chimerism monitoring, non-availability of pre-transplant DNA samples poses a major limitation of reference STR fingerprints. This study shows that DNA obtained post-HSCT from hair follicles can be used to generate pre-transplant patient specific fingerprints while the STR profiles obtained in saliva samples cannot as these display a mixed state of chimerism.
PMCID: PMC3370928  PMID: 22690267
chimerism; DNA; hair; HLA; saliva; transplantation
20.  Image microarrays derived from tissue microarrays (IMA-TMA): New resource for computer-aided diagnostic algorithm development 
Conventional tissue microarrays (TMAs) consist of cores of tissue inserted into a recipient paraffin block such that a tissue section on a single glass slide can contain numerous patient samples in a spatially structured pattern. Scanning TMAs into digital slides for subsequent analysis by computer-aided diagnostic (CAD) algorithms all offers the possibility of evaluating candidate algorithms against a near-complete repertoire of variable disease morphologies. This parallel interrogation approach simplifies the evaluation, validation, and comparison of such candidate algorithms. A recently developed digital tool, digital core (dCORE), and image microarray maker (iMAM) enables the capture of uniformly sized and resolution-matched images, with these representing key morphologic features and fields of view, aggregated into a single monolithic digital image file in an array format, which we define as an image microarray (IMA). We further define the TMA-IMA construct as IMA-based images derived from whole slide images of TMAs themselves.
Here we describe the first combined use of the previously described dCORE and iMAM tools, toward the goal of generating a higher-order image construct, with multiple TMA cores from multiple distinct conventional TMAs assembled as a single digital image montage. This image construct served as the basis of the carrying out of a massively parallel image analysis exercise, based on the use of the previously described spatially invariant vector quantization (SIVQ) algorithm.
Multicase, multifield TMA-IMAs of follicular lymphoma and follicular hyperplasia were separately rendered, using the aforementioned tools. Each of these two IMAs contained a distinct spectrum of morphologic heterogeneity with respect to both tingible body macrophage (TBM) appearance and apoptotic body morphology. SIVQ-based pattern matching, with ring vectors selected to screen for either tingible body macrophages or apoptotic bodies, was subsequently carried out on the differing TMA-IMAs, with attainment of excellent discriminant classification between the two diagnostic classes.
The TMA-IMA construct enables and accelerates high-throughput multicase, multifield based image feature discovery and classification, thus simplifying the development, validation, and comparison of CAD algorithms in settings where the heterogeneity of diagnostic feature morphologic is a significant factor.
PMCID: PMC3424658  PMID: 22934237
TMA; IMA; SIVQ; dCORE; iMAM; WSI; CAD; image analysis
21.  Genetic correlates influencing immunopathogenesis of HIV infection 
Variability to HIV infection, its progression as well as responsiveness to antiretroviral therapy (ART) is observed among individuals including viraemia controllers or exposed uninfected, rapid versus slow progressors and ART responders compared to non responders. This differential responsiveness/vulnerability to HIV-1 is governed by multiple host genetic factors that include HLA, cytokines, chemokines, their receptors and others. This review highlights the influence of these genetic factors on HIV/AIDS outcome; however, in India, the information in this area is very limited and most of these genetic studies have been conducted in Caucasian and South African populations. Considering, the population specific differences in the frequencies of protective or susceptibility favouring alleles and their influence on the disease outcome, it is of utmost importance to strengthen ongoing efforts towards defining largely unknown genetic propensity in Indian population, particularly by recruitment of large cohorts of well categorized exposed uninfected individuals, rapid, long term non progressors and elite viraemic controllers. Multi-parametric analysis of these potentially interactive immunogenetic variables in these cohorts may help to define potential targets for diagnostics and therapy in a population specific manner.
PMCID: PMC3284087  PMID: 22310811
Chemokines; cytokines; clades; exposed uninfected individuals; genetic correlates; genetic variants; HIV; HIV/AIDS; HLA; immunopathogenesis; rapid & slow progressors; viraemia controllers
22.  Polymer Particle Shape Independently Influences Binding and Internalization by Macrophages 
The interaction of macrophages with micro and nano particles (MNPs) is important because these cells clear particles from the circulation, and because they are potential therapeutic targets in inflammatory conditions, atherosclerosis and cancer. Therefore, an understanding of the features of MNPs that influence their interaction with macrophages may allow optimization of their properties for enhanced drug delivery. In this study, we show that particle shape impacts phagocytosis by macrophages, and more importantly, that particle shape and size separately impact attachment and internalization. The study provides methodology for further exploring how particle shape can be controlled to achieve desired attachment and internalization. The results of the study also give mechanistic guidance on how particle shape can be manipulated to design drug carriers to evade macrophages, or alternatively to target macrophages.
PMCID: PMC2975856  PMID: 20691741
23.  Nevus of Ota with Rare Palatal Involvement: A Case Report with Emphasis on Differential Diagnosis 
Case Reports in Dentistry  2011;2011:670679.
Nevus of Ota, a dermal melanocytic nevus, is rare in the Indian subcontinent. It presents as a brown, blue, or gray patch on the face and is within the distribution of the ophthalmic and maxillary branches of the trigeminal nerve. The oral cavity is infrequently involved in nevus of Ota. Only 11 cases have been documented in the English literature. We report a rare case of intraoral nevus of Ota in a 22-year-old male patient. This paper focuses on the differential diagnosis of oral manifestations of nevus of Ota to assist in proper followup to avert malignant transformation.
PMCID: PMC3335646  PMID: 22567445
24.  Transmigration of Mandibular Canine: Report of Four Cases and Review of Literature 
Case Reports in Dentistry  2011;2011:381382.
Transmigration of canine is a rare phenomenon. The prevalence of transmigration of mandibular canine has been found to be only 0.14%–0.31%. The treatment of impacted transmigrated canine is very complicated if it is diagnosed at a later stage. We report 4 cases of transmigration of mandibular canine and review the literature regarding the etiology and treatment. Panoramic radiograph should be taken during the mixed dentition period if the mandibular canine has not erupted from more than one year from its normal chronological age of eruption as intraoral periapical radiograph examination will not always detect an impacted or transmigrated canine.
PMCID: PMC3335525  PMID: 22570797
25.  TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences 
BMC Bioinformatics  2011;12:108.
The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence. The most accurate computational methods predict conserved structures for a set of homologous RNA sequences. These methods usually suffer from high computational complexity. In this paper, TurboFold, a novel and efficient method for secondary structure prediction for multiple RNA sequences, is presented.
TurboFold takes, as input, a set of homologous RNA sequences and outputs estimates of the base pairing probabilities for each sequence. The base pairing probabilities for a sequence are estimated by combining intrinsic information, derived from the sequence itself via the nearest neighbor thermodynamic model, with extrinsic information, derived from the other sequences in the input set. For a given sequence, the extrinsic information is computed by using pairwise-sequence-alignment-based probabilities for co-incidence with each of the other sequences, along with estimated base pairing probabilities, from the previous iteration, for the other sequences. The extrinsic information is introduced as free energy modifications for base pairing in a partition function computation based on the nearest neighbor thermodynamic model. This process yields updated estimates of base pairing probability. The updated base pairing probabilities in turn are used to recompute extrinsic information, resulting in the overall iterative estimation procedure that defines TurboFold.
TurboFold is benchmarked on a number of ncRNA datasets and compared against alternative secondary structure prediction methods. The iterative procedure in TurboFold is shown to improve estimates of base pairing probability with each iteration, though only small gains are obtained beyond three iterations. Secondary structures composed of base pairs with estimated probabilities higher than a significance threshold are shown to be more accurate for TurboFold than for alternative methods that estimate base pairing probabilities. TurboFold-MEA, which uses base pairing probabilities from TurboFold in a maximum expected accuracy algorithm for secondary structure prediction, has accuracy comparable to the best performing secondary structure prediction methods. The computational and memory requirements for TurboFold are modest and, in terms of sequence length and number of sequences, scale much more favorably than joint alignment and folding algorithms.
TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative analysis between sequences with the thermodynamic folding model. Unlike most other multi-sequence structure prediction methods, TurboFold does not enforce strict commonality of structures and is therefore useful for predicting structures for homologous sequences that have diverged significantly. TurboFold can be downloaded as part of the RNAstructure package at
PMCID: PMC3120699  PMID: 21507242

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