Showing papers by "Gaurav Sharma published in 2011"

TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences.

Abstract: 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 http://rna.urmc.rochester.edu .

Platelet activity and cardiovascular risk in apparently healthy individuals: a review of the data

Abstract: Cardiovascular disease is a major cause of morbidity and mortality. Numerous risk scores exist to identify healthy individuals at increased risk of developing cardiovascular disease. Although platelets are a key mediator in the pathogenesis of cardiovascular disease, the role of platelet activity measurements and the incidence of cardiovascular disease are uncertain. Platelet aggregometry—the most well studied method of platelet function testing—is associated with risk factors for cardiovascular disease. However, data supporting platelet aggregation and incident cardiovascular disease is conflicting. Plasma markers of platelet activation are promising candidates. Soluble CD40L and P-selectin are easily measured with a standardized ELISA, and there is some data to suggest an association with cardiovascular disease, but further studies are required. While mean platelet volume is a promising candidate, platelet count and bleeding time are not specific for platelet activity nor are they associated with cardiovascular disease in a healthy population. For this field to progress, we recommend large-scale, prospective studies that measure a battery of these platelet function tests in individuals without cardiovascular disease to better understand the associations, if any, between platelet activity and cardiovascular disease.

Economic Analysis of Post-harvest Losses in Marketing of Vegetables in Uttarakhand §

Abstract: The study has examined the nature and extent of post-harvest losses in vegetable supply chain in the Kumaon division of Uttarakhand. Multistage cluster sampling has been used for selection of 80 vegetable growers, 40 farmers from the hilly region and 40 farmers from the bhabhar region. The sample has also included 25 market functionaries. Twelve major vegetables have been selected for the study. The maximum aggregate post-harvest losses have been found in tomato, followed by potato, brinjal, chilly, French bean and pea. The study has suggested that establishment of producer co-operatives to handle various activities relating to production and marketing of vegetables would help in reducing post-harvest losses.

High Capacity Color Barcodes: Per Channel Data Encoding via Orientation Modulation in Elliptical Dot Arrays

Abstract: We present a new high capacity color barcode. The barcode we propose uses the cyan, magenta, and yellow (C,M,Y) colorant separations available in color printers and enables high capacity by independently encoding data in each of these separations. In each colorant channel, payload data is conveyed by using a periodic array of elliptically shaped dots whose individual orientations are modulated to encode the data. The orientation based data encoding provides beneficial robustness against printer and scanner tone variations. The overall color barcode is obtained when these color separations are printed in overlay as is common in color printing. A reader recovers the barcode data from a conventional color scan of the barcode, using red, green, and blue (R,G,B) channels complementary, respectively, to the print C, M, and Y channels. For each channel, first the periodic arrangement of dots is exploited at the reader to enable synchronization by compensating for both global rotation/scaling in scanning and local distortion in printing. To overcome the color interference resulting from colorant absorptions in noncomplementary scanner channels, we propose a novel interference minimizing data encoding approach and a statistical channel model (at the reader) that captures the characteristics of the interference, enabling more accurate data recovery. We also employ an error correction methodology that effectively utilizes the channel model. The experimental results show that the proposed method works well, offering (error-free) operational rates that are comparable to or better than the highest capacity barcodes known in the literature.

US-guided Fine-Needle Aspiration of Major Salivary Gland Masses and Adjacent Lymph Nodes: Accuracy and Impact on Clinical Decision Making

Abstract: Our findings suggest that US-guided fine-needle aspiration represents a diagnostically adequate method for sampling lesions of the salivary glands and adjacent lymph nodes, with an accuracy similar to that of US-guided core needle biopsy.

Thoraco-Abdominal Pressure Gradients During the Phases of Respiration Contribute to Gastroesophageal Reflux Disease

Abstract: Exaggerated pressure fluctuation between the thorax and abdomen during exercise or with pulmonary disease may challenge the gastroesophageal barrier and allow reflux of gastric juice into the esophagus. The aim of this study was to investigate the pressure differentials in the region of the gastroesophageal junction to better understand the relationship between the thoraco-abdominal pressure gradient and the lower esophageal sphincter (LES) barrier function. We reviewed the esophageal motility and 24-h pH studies in 151 patients with a manometrically normal lower esophageal sphincter who did not have pulmonary disease, history of anti-reflux surgery, hiatal hernia, or ineffective esophageal motility (IEM). Intra-abdominal gastric and intra-thoracic esophageal pressure fluctuations with respiration were measured and the thoraco-abdominal pressure gradients were calculated during both inspiratory and expiratory phases of the respiratory cycle. Predictive factors for an abnormal composite pH score were identified by multivariable analysis. An inspiratory thoraco-abdominal pressure gradient that was higher than the resting LES pressure was found in 27 patients. In 23 of these patients (85.2%) there was increased esophageal acid exposure (OR 13.5, 95% CI 4.4–41.8). An abnormal composite pH score was predicted by a high inspiratory thoraco-abdominal pressure gradient (P < 0.001), greater fluctuation between inspiratory and expiratory thoracic pressure (P = 0.023), lower LES resting pressure (P = 0.049) and a decreased residual pressure after a swallow induced relaxation (P = 0.002). The gastroesophageal barrier function of the LES can be overcome during times when the inspiratory thoraco-abdominal pressure gradient is increased, leading to reflux of gastric juice into the esophagus. This implies that exaggerated ventilatory effort, as occurs with exercise or in respiratory disease, can result in gastroesophageal reflux.

Role of Sacrum in Sexual Dimorphism-A Morphometric Study

Abstract: The sacrum has always attracted the attention of the medico-legal experts for establishing the sex, because of its contribution to pelvic girdle and associated functional sex differences. The present study was performed to evaluate the reliability of the various parameters of sacrum in this regard. The material for the study comprised of 50 adult sacra (M: F= 40:10), obtained from the Department of Anatomy, Govt. Medical College, Amritsar. Different parameters viz. Midventral straight length, Midventral curved length, Ventral straight breadth, Transverse diameter of base, Transverse diameter of body of S1, Antero-posterior diameter of body of S1, Breadth of alae were measured and indices viz. Sacral index, Longitudinal curvature index and Corporobasal index were calculated and statistically analyzed.

Neurotoxic and Medicinal Properties of Datura stramonium L. – Review

Abstract: The troublesome weed, jimson weed (Datura stramonium L.) is a plant with both poisonous and medicinal properties. The neurotoxicity is attributed to the presence of tropane alkaloids which contain a methylated nitrogen atom (N-CH 3 ) and include the anticholinergic drugs atropine, and scopolamine, as well as the narcotic cocaine. A wide range of medicinal values of this plant have contributed in scientific field and also in ethnomedicine. The phytochemical, ethnomedicinal and toxicological works on D.stramonium has given a better assessment and information of this particular plant. The present paper presents an exclusive review work on the neurotoxic properties of D. stramonium.

Synthesis of a Broadly Absorbing Modified PCBM and Application As Electron Acceptor with Poly(3-Hexylthiophene) As Electron Donor in Efficient Bulk Heterojunction Solar Cells

Abstract: A simple and effective modification of PCBM was carried out by a two-step reaction. The modified PCBM, i.e., A was obtained as a mixture of monoadduct and multiadducts arising from the Prato reaction and was soluble in THF. It showed broader and stronger absorption in the visible region of the solar spectrum than PCBM due to the presence of a cyanovinylene 4-nitrophenyl segment. The lowest occupied molecular energy level (LUMO) of A was measured and found that it is higher than that of PCBM by 0.15 eV. The polymer solar cell (PSC) based on the P3HT as the electron donor with A as the electron acceptor shows an open circuit voltage (Voc) of 0.80 V, a short-circuit current (Jsc) of 9.0 mA/cm2, and a power conversion efficiency (PCE) of 3.88%, which are higher than those for the PSC based on P3HT:PCBM. The higher PCE for the PSC based on P3HT:A accounts for the increase in both Jsc and Voc, due to the increased absorption of A in the visible region and its higher LUMO level. The PCE of the PSC has been furth...

Color QR Codes: Increased Capacity Via Per-Channel Data Encoding and Interference Cancellation.

Abstract: Monochrome 2-D barcodes have recently become extremely popular in mobile imaging applications. To accommodate higher data rates, we present a methodology for extending these barcodes to color. We use independent per channel data encoding in cyan, magenta, and yellow print colorant channels and decode the information in the complementary red, green, and blue channels used in capture, effectively increasing the data rate by a factor of three. To overcome unavoidable inter-channel interference, our framework utilizesadaptive thresholding and model-based interference cancellation at the decoder which are facilitated by an intelligent barcode design that allows estimation of parameters required for thresholding and cancellation. We present the framework by constructing and evaluating the performance for a color version of the QR code, the most commonly deployed monochrome barcode in mobile applications. Experimental results demonstrate that the framework is effective and allows recovery of embedded data with low bit error rates, which can be readily handled by the builtin error correction withinthe QRcode standard.

State of Maternal, Newborn and Child Health Programmes in Nepal: What May a Continuum of Care Model Mean for More Effective and Efficient Service Delivery?

Abstract: The cost-effective interventions exist across the continuum of maternal to child survival at each level of the health system that can contribute to achieve the Millennium Development Goals 4 and 5. However, implementation inefficiency, low coverage and equity gaps along this continuum remain a serious challenge to Nepal's efforts to achieve these goals. This paper proposes a continuum of care model; discusses the readiness of policy and programs to provide high impact interventions across the continuum; identifies existing gaps in MNCHN programs; and recommends policy and program actions to improve coverage, equity, effectiveness and efficiency along the continuum of MNCHN service delivery in Nepal. The literature review includes systematic desk review, followed by discussions and deliberations amongst a group of professionals and MNCH experts in Nepal. Within the government health system in Nepal, a continuum of care approach is feasible, as policies and plans exist to ensure an integrated approach across the maternal to child care continuum. However, health programs largely remain vertically oriented. Achieving integration across the maternal to child continuum of care remains a challenge at each level of health system. An integrated system of program management for maternal, newborn and child health would be a feasible solution to enable an efficient and effective delivery of intervention packages. A collaborative and partnership approach to strengthen health systems, building managerial capacity, improving governance and engaging the private and civil sectors remains vital to achieve effective coverage and improve equity across the continuum of care.

Genetic correlates influencing immunopathogenesis of HIV infection

Abstract: 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.

Efficient Bulk Heterojunction Solar Cells Based on a Broadly Absorbing Phenylenevinylene Copolymer Containing Thiophene and Pyrrole Rings

Abstract: A novel low band gap alternating phenylenevinylene copolymer, P, containing thiophene and pyrrole rings was synthesized by Heck polycondensation. It was soluble in common organic solvents and showed a long-wavelength absorption maximum at 596−635 nm and an optical band gap of 1.65 eV. The electrochemical properties and electronic energy levels of P were studied by cyclic voltammetry. The highest occupied molecular orbital (HOMO) level of P is deeper than that of poly(3-hexylthiophene) (P3HT). The polymer solar cells (PSCs) based on P with a modified 1-(3-methoxycarbonyl)propyl-1-phenyl-[6,6]-C-61 (PCBM) (i.e., F) as an electron acceptor shows higher open circuit voltage (Voc) than that for the device based on P3HT. The power conversion efficiency (PCE) for the devices P−F and P−PCBM processed from tetrahydrofuran (THF) solvent is approximately 2.42% and 1.50%, respectively. The enhanced PCE is attributed to the higher value of both Voc and short circuit current (Jsc). The PCE of the devices based on P−F p...

Transmigration of Mandibular Canine: Report of Four Cases and Review of Literature

Abstract: 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.

Adaptive color visualization for dichromats using a customized hierarchical palette

Abstract: We propose a user-centric methodology for displaying digital color documents, that optimizes color representations in an observer specific and adaptive fashion. We apply our framework to situations involving viewers with common dichromatic color vision deficiencies, who face challenges in perceiving information presented in color images and graphics designed for color normal individuals. For situations involving qualitative data visualization, we present a computationally efficient solution that combines a customized observer-specific hierarchical palette with "display time" selection of the number of colors to generate renderings with colors that are easily discriminated by the intended viewer. The palette design is accomplished via a clustering algorithm, that arranges colors in a hierarchical tree based on their perceived differences for the intended viewer. A desired number of highly discriminable colors are readily obtained from the hierarchical palette via a simple truncation. As an illustration, we demonstrate the application of the methodology to Ishihara style images.

Design and Development of Multi-Die Laterally Placed and Vertically Stacked Embedded Micro-Wafer-Level Packages

Abstract: Two embedded micro-wafer-level packages (EMWLP) with 1) laterally placed and 2) vertically stacked thin dies are designed and developed. Three-dimensional stacking of thin dies is demonstrated as progressive miniaturization driver for multi-chip EMWLP. Both the developed packages have dimensions of 10 mm × 10 mm × 0.4 mm and solder ball pitch of 0.4 mm. As part of the development several key processes like thin die stacking, 8-in wafer encapsulation using compression molding, low-temperature dielectric with processing temperature less than 200°C have been developed. The EMWLP components success fully pass 1000 air to air thermal cycling (-40°C to 125°C), unbiased highly accelerated stress testing (HAST) and moisture sensitivity level (MSL3) tests. Developed EMWLP also show good board level TC (>; 1000 cycles) and drop test reliability results. Integration of thin film passives like inductors and capacitors are also demonstrated on EMWLP platform. Developed thin film passives show a higher Q-factor when compared to passives on high resistivity silicon platform. Thermo-mechanical simulation studies on developed EMWLP demonstrate that systemic control over die, RDL, and package thicknesses can lead to designs with improved mechanical reliability.

In-Car Service Interval Adjustment Device

Abstract: Disclosed is a device and method for providing service interval notifications to a vehicle operator, and to incorporate relevant vehicle operating conditions which most directly impact the longevity of engine lubrication and other wear prone components of vehicles. Wear prone conditions which are determined include city driving, frequency of “cold” starts, frequency of “winter” “cold” starts, and high load high grade travel. The device and method utilize as a primary input a location aware sensor device and as a secondary input a source for the ambient temperature either retrieved from an Internet source or a local ambient temperature sensor. No direct vehicle sensor is utilized for the service interval adjustment performed by the device and method.

Ultrasound-guided fine needle aspiration of major salivary gland masses and adjacent lymph nodes.

Abstract: Ultrasound has an established role in the detection of masses in the major salivary glands and potentially malignant adjacent lymph nodes. Because there is overlap in their sonographic features, tissue diagnosis plays an important role in management. This review assesses ultrasound-guided fine needle aspiration biopsy as a diagnostic tool in the characterization of these lesions. The literature, and the authors' experience, suggests that ultrasound-guided fine needle aspiration is a safe and accurate technique, with definable implications for management, when performed in conjunction with cytopathologic expertise.

High capacity image barcodes using color separability

Abstract: Two-dimensional barcodes are widely used for encoding data in printed documents. In a number of applications, the visual appearance of the barcode constitutes a fundamental restriction. In this paper, we propose high capacity color image barcodes that encode data in an image while preserving its basic appearance. Our method aims at high embedding rates and sacrifices image fidelity in favor of embedding robustness in regions where these two goals conflict with each other. The method operates by utilizing cyan, magenta, and yellow printing channels with elongated dots whose orientations are modulated in order to encode the data. At the receiver, by using the complementary sensor channels to estimate the colorant channels, data is extracted in each individual colorant channel. In order to recover from errors introduced in the channel, error correction coding is employed. Our simulation and experimental results indicate that the proposed method can achieve high encoding rates while preserving the appearance of the base image.

Clinico-Pathological Profile in Deaths Due To Burns

Abstract: Burn injuries occur universally and have plagued mankind since antiquity till the present day. Burns represent an extremely stressful experience for both the burn victims as well as their families. An extensive burn profoundly affects the patient's physique, psyche, financial situation and family. Patients with extensive burns frequently die, and for those with lesser injury, physical recovery is slow and painful. In addition to their dramatic physical effects, burn injuries frequently cause deleterious psychological complications. In all societies including developed or developing countries, burns constitute, a medical and psychological problem, but also have severe economic and social consequences not only to them, but also to their family and society ingeneral.24%cases were not hospitalized. 40%cases died within 24 hours of sustaining burns. 38%cases were unconscious before death. 66%cases had given dying declaration.Mechanical injuries were present in 10%cases.84%cases of total cases were alleged casesof accident. The major cause of death was Septicemic shock in 56%cases.

Impact of Mahatma Gandhi National Rural Employment Guarantee Act on Rubber Block Plantation Scheme in Tripura

Abstract: Among the various promotional schemes targeted for the promotion of rubber in Tripura, Block Plantation Scheme (BPS) has been introduced exclusively for the rehabilitation of scheduled tribes and scheduled castes BPS is a comprehensive scheme with the characteristic features of group/community approach in all spheres of operations up to primary processing and marketing and family labour participation as wage labour during the immature phase of the plantations spanning six years However, there has been a distortion in the uninterrupted supply of family labour to the scheme in the recent past due to growing popularity of employment opportunities under the Mahatma Gandhi National Rural Employment Guarantee Act, 2005 (MGNREGA) programme, which may eventually lead to a prolongation of immature phase and adversely affect the uniform and healthy growth of the rubber plants These factors in turn could affect the overall rubber yield and so suitable policies needed to be evolved to ensure adequate and timely availability of family labour to immature rubber plantation One of the options could be the inclusion of the developmental works required for the immature rubber plantations under the MGNREGA projects by the State Government of Tripura

Nevus of Ota with Rare Palatal Involvement: A Case Report with Emphasis on Differential Diagnosis

Abstract: 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.

Efficient Computation of Display Gamut Volumes in Perceptual Spaces.

Abstract: Gamut volume computations in perceptual spaces are useful for optimizing designs of color displays. We develop a useful representation of the gamut of an additive display that facilitates efficient numerical computation of the gamut volume. For three primary systems, our representation coincides with the obvious representation of a three-primary additive gamut, while for multiprimary systems, the representation we develop provides a partition of the device gamut as a disjoint union of displaced three primary gamuts thereby facilitating a computation of the overall gamut volume as the sum of these individual three primary gamut volumes. Based on our representation, we develop and evaluate several alternative numerical schemes for gamut volume computations in perceptual spaces, comparing their accuracy and computational requirements.

Distributed Estimation and Coding: A Sequential Framework Based on a Side-Informed Decomposition

Abstract: We propose a sequential framework for the distributed multiple-sensor estimation and coding problem that decomposes the problem into a series of side-informed source coding problems and enables construction of good codecs. Our construction relies on a separation result for the simplified scenario where information from one sensor is to be sent to the CP that already has information regarding the desired signal. We show that the optimal encoder decoder combination, in this setting, can be decomposed, without loss in performance, into two steps: A first preprocessing step to extract relevant information from the indirect observation with consideration of the side information, followed by a second step of side-informed encoding of the preprocessed output. A recursive exploit of the decomposition coupled with side-informed transform coding allows us to construct encoders by reusing scalar Wyner-Ziv codecs. We develop a numerical procedure for obtaining bounds delineating the best achievable performance for the proposed sequential framework and construct and demonstrate a practical codec in the proposed framework that achieves empirical performance close to the bound. Furthermore, we also compare the bounds for the sequential scheme against bounds for a number of alternate schemes-for some of which codec constructions are obvious and others for which codec constructions are inobvious. Our results show that, in most cases, our codec exceeds the performance bound of schemes offering obvious constructions. The achievable bound for our sequential framework is also shown to be close to a general nonconstructive distributed bound that does not impose the sequential constraint indicating that the sequential approach may not cause a significant performance compromise.