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At least 253 records · Page 14Linked to original sources
PubMed2002

Assessment of the status of work zone air environment due to opencast coal mining.

In India coal production will have to be increased to meat the energy demand at a very high rate. By 2000 AD the cool production from opencast (O/C) mining will rise to 250 Mt. which will be about 70%of the total coal production. The increasing trend of O/C mining leads to cause air pollution problem. A survey was conducted to assess the status of work zone air envimment due to opencast coal mining in Jharia Coalfield. Keeping in view of place of dust generation air quality monitoring stations were selected. Methodology adapted for sampling and analysis of air pollutants have been described. Four season data revealed that maximum concentration of SPM was observed at dragline section and the next high concentration was at haul roads. At all the locations SPM and RPM concentrations exceeded the permissible limits specified by Indian Pollution Control Board. Shift wise and location wise analysis for getting higher concentration of SO2 and NOx, have been discussed. Wind velocity and directions, mixing heights, ventilation coefficient of the area have been analyzed. Huge dust generation creates vision problem to HEMM operators. The methodology adopted may be utilised on industrial scale for various sites.

Air Pollutants↗
PubMed1999

The cornea swells in the posterior direction under hydrogel contact lenses.

Two mathematical models were developed to describe the topographical corneal swelling response to hydrogel contact lenses and the effect of these changes on refractive error. In one, corneal thickness changes resulted in deformation of the anterior corneal surface. In the other, the posterior surface only was deformed. Refractive error, corneal thickness and corneal shape were monitored in a sample of adapted contact lens wearers with one eye patched for 4 h while wearing a soft contact lens. The experimental data were most consistent with the model in which the posterior surface only was deformed.

Contact Lenses, Hydrophilic↗
PubMed2004

On the efficient path integral evaluation of thermal rate constants within the quantum instanton approximation.

We present an efficient path integral approach for evaluating thermal rate constants within the quantum instanton (QI) approximation that was recently introduced to overcome the quantitative deficiencies of the earlier semiclassical instanton approach [Miller, Zhao, Ceotto, and Yang, J. Chem. Phys. 119, 1329 (2003)]. Since the QI rate constant is determined solely by properties of the (quantum) Boltzmann operator (specifically, by the zero time properties of the flux-flux and delta-delta correlation functions), it can be evaluated by well-established techniques of imaginary time path integrals even for quite complex chemical reactions. Here we present a series of statistical estimators for relevant quantities which can be evaluated straightforwardly with any nonlinear reaction coordinates and general Hamiltonians in Cartesian space. To facilitate the search for the optimal dividing surfaces required by the QI approximation, we introduce a two-dimensional quantum free energy surface associated with the delta-delta correlation function and describe how an adaptive umbrella sampling can be used effectively to construct such a free energy surface. The overall computational procedure is illustrated by the application to a hydrogen exchange reaction in gas phase, which shows excellent agreement of the QI rates with those obtained from quantum scattering calculations.

Journal Article↗
PubMed2005

Alchemical free energy calculations and multiple conformational substates.

Thermodynamic integration (TI) was combined with (adaptive) umbrella sampling to improve the convergence of alchemical free energy simulations in which multiple conformational substates are present. The approach, which we refer to as non-Boltzmann TI (NBTI), was tested by computing the free energy differences between three five-atomic model systems, as well as the free energy difference of solvation between leucine and asparagine. In both cases regular TI failed to give converged results, whereas the NBTI results were free from hysteresis and had standard deviations well below +/-0.7 kcal/mole. We also present theoretical considerations that make it possible to compute free energy differences between simple molecules, such as the five-atomic model systems, by numerical integration of the partition functions at the respective end points.

Journal Article↗
PubMed2006

Effects of tea saponins on in vitro ruminal fermentation and growth performance in growing Boer goat.

Two experiments were conducted to investigate the effects of tea saponins (TS) on in vitro ruminal fermentation and growth performance in growing Boer goats. In Experiment 1, the Reading Pressure Technique (RPT) system was used to investigate the effect of addition of TS (0, 0.2, 0.4 and 0.8 mg/ml) on the ruminal fermentation in vitro. The 24h gas production and methane emission were significantly decreased when 0.4 or 0.8mg TS was included, suggesting that the TS could inhibit the release of methane. Compared to the control, the TS had little effect on pH values and the concentration of total volatile fatty acids in the ruminal fluids. However, the fermentation patterns were changed, with lower acetate and higher proportions of propionate when TS was added. Ammonia-N concentration and protozoal counts were significantly reduced, while microbial protein yield was increased by the TS addition, suggesting that the TS could modify the ruminal fermentation. In Experiment 2, 27 growing Boer goats were used to evaluate the effects of the TS addition on growth performance. The animals received the same basal diets, and added TS at levels of 0 (C), 3 g (T1) and 6 g (T2) per day. The experiment lasted for 60 days with the first 15 days for adaptation. Blood samples were obtained by jugular venipuncture before the morning feeding on the final day of the experiment. During the whole periods, dry matter intake, average daily gain and feed efficiency in T1 were higher than in the other two. Serum total protein, albumin, high density lipoprotein cholesterol, Ca and P and alkaline phosphatase levels were higher in group T1 than in C and T2, whereas the blood urea nitrogen, creatinine and total cholesterol were lower in the TS-added groups. The concentrations of glucose, glutamic-oxaloacetic transaminase and glutamic-pyruvic transaminase were not affected by the TS. From the results obtained in this study, it is inferred that the TS could modify the ruminal fermentation and that proper doses of TS may have potential in improving the animal growth performance, whereas at high doses, it may have adverse effects on animal production.

Animals↗
PubMed1988

Influence of dietary niacin on volatile fatty acids in rumen liquid of sheep and rumen dry matter degradability of untreated and ammonia-treated wheat straw.

Three rumen fistulated sheep were fed with roughage (1200 g artificially dried grass) or a concentrate/roughage diet (600 g concentrate, 400 g artificially dried grass per animal and day). The diets were unsupplemented or 0.5, 1 and 2 g niacin per animal and day were added. After a 14-day adaptation period samples of rumen liquid were taken 0, 1, 2, 3, 4 and 6 h after morning feeding. In a second experiment untreated and NH3-treated wheat straw were incubated in nylon bags for 6, 12, 24, 48 and 72 h in the rumen of 5 sheep fed with 1.2 kg artificially dried grass and unsupplemented or supplemented with 1 g niacin per day. Niacin did not significantly influence the total concentration of volatile fatty acids, acetate and branched chain fatty acids in both types of diet (P less than 0.05). 0.5 and 1 g niacin in the roughage and 0.5 g niacin in concentrate/roughage diet increased the propionic acid concentration and reduced the butyric acid concentration in rumen liquid of sheep (P less than 0.05). Niacin resulted in a small decrease (P greater than 0.05) of dry matter degradability in rumen. After 48 h incubation time, the dry matter disappearance of untreated and NH3-treated wheat straw amounted to 35.4 and 46.2% resp. The effects of niacin on rumen fermentation may be useful in avoiding ketogenic situations in dairy cows.

Ammonia↗
PubMed2006

Development of a genetic assay to distinguish between Leishmania viannia species on the basis of isoenzyme differences.

BACKGROUND: Tegumentary leishmaniasis in Latin America is caused mainly by Leishmania viannia braziliensis complex parasites. L. braziliensis and Leishmania viannia peruviana are the 2 predominant Leishmania species in Peru. L. braziliensis is more virulent, because it can cause mucocutaneous leishmaniasis, known as espundia, that results in severe facial destruction. Early identification of the species that causes the initial cutaneous infection would greatly help to prevent mucocutaneous leishmaniasis, because it would allow more aggressive treatment and follow-up. However, because of the close genetic similarity of L. braziliensis and L. peruviana, there currently exists no simple assay to distinguish between these species. METHODS: We cloned the mannose phosphate isomerase gene from both L. braziliensis and L. peruviana. It is the only known isoenzyme capable of differentiating between L. braziliensis and L. peruviana in multilocus enzyme electrophoresis. Interestingly, only a single nucleotide polymorphism was found between the mannose phosphate isomerase genes from L. braziliensis and L. peruviana, resulting in an amino acid change from threonine to arginine at amino acid 361. A polymerase chain reaction assay was developed to distinguish the single nucleotide polymorphism of the mannose phosphate isomerase gene to allow for the specific identification of L. braziliensis or L. peruviana. RESULTS: This assay was validated with 31 reference strains that were previously typed by multilocus enzyme electrophoresis, successfully applied to patient biopsy samples, and adapted to a real-time polymerase chain reaction assay. CONCLUSIONS: This innovative approach combines new genetic knowledge with traditional biochemical fundamentals of multilocus enzyme electrophoresis to better manage leishmaniasis in Latin America.

Amino Acid Sequence↗
PubMed2026

A token-pruning framework enables efficient representation of the human genome for RNA modification analysis.

MOTIVATION: Modelling long genomic sequences remains challenging due to extreme sequence length, high redundancy, and the need for biological interpretability. Although Transformer-based architectures have achieved strong performance across genomic tasks, their high computational cost and reliance on fixed tokenization strategies limit their scalability and ability to focus on biologically informative regions. RESULTS: We propose ATSFormer, a token-pruning Transformer framework for efficient and biologically informed genomic sequence modelling. ATSFormer incorporates an attention-guided and parameter-free Adaptive Token Sampling (ATS) module into Transformer layers. Guided by attention-derived importance scores, ATS dynamically retains informative tokens while probabilistically discarding redundant ones, thereby reducing sequence length, FLOPs, and memory usage without introducing additional learnable parameters or extra training procedures. Importantly, the retained tokens correspond to key contributors to model predictions, enabling ATSFormer to highlight biologically meaningful sites and sequence motifs. We evaluated ATSFormer on four benchmark RNA modification datasets derived from RMVar 2.0, covering A-to-I, m1A, m5C, and m7G. Experimental results show that ATSFormer consistently outperforms existing state-of-the-art methods while achieving substantial computational savings. Furthermore, structural analysis using AlphaFold3 supports the biological relevance of the motifs identified by ATSFormer. AVAILABILITY AND IMPLEMENTATION: The source data and code are freely available at GitHub (https://github.com/1gao2/ATSFormer) and Zenodo (https://doi.org/10.5281/zenodo.21813541).

Humans↗
PubMed1997

Comprehensive, rapid and sensitive detection of sequence variants of human mitochondrial tRNA genes.

In the present study, a comprehensive, rapid and sensitive method for screening sequence variation of the human mitochondrial tRNA genes has been developed. For this purpose, the denaturing gradient gel electrophoresis (DGGE) technique has been appropriately modified for simultaneous mutation analysis of a large number of samples and adapted so as to circumvent the problems caused by the anomalous electrophoretic behavior of DNA fragments encoding tRNA genes. Eighteen segments of mitochondrial DNA (mtDNA), each containing a single uniform melting domain, were selected to cover all tRNA-encoding regions using the computer program MELT94. All 18 segments were simultaneously analyzed by electrophoresis through a single broad range denaturing gradient gel under rigorously defined conditions, which prevent band broadening and other migration abnormalities from interfering with detection of sequence variants. All base substitutions tested, which include six natural mutations and 14 artificially introduced ones, have been detected successfully in the present study. Several types of evidence strongly suggest that the anomalous behavior in DGGE of tRNA gene-containing mtDNA fragments reflects their tendency to form temporary or stable alternative secondary structures under semi-denaturing conditions. The high sensitivity of the method, which can detect as low as 10% of mutant mtDNA visually, makes it valuable for the analysis of heteroplasmic mutations.

Cell Line↗
PubMed1978

Estimation of multiple relative risk functions in matched case-control studies.

A linear logistic model used to estimate multiple risk functions in both cohort and case-control studies is adapted for sampling plans wherein each case is matched with R controls. The resulting methodology substantially liberalizes current practice by permitting simultaneous analysis of multiple discrete and continuous risk factors. Interactions among risk factors, and between risk factors and matching variables, may be explored. Data from two studies of oesophageal cancer, one conducted among Singapore Chinese and the other on the Caspian littoral of Iran, illustrate the methods.

Epidemiologic Methods↗
PubMed1998

Endothelial cell density and contact lens-induced corneal swelling.

PURPOSE: To determine the relationships among endothelial morphometric variables and contact lens-induced corneal swelling in a homogeneous sample of adapted contact-lens wearers. METHODS: Fifteen male subjects ranging in age from 20 to 40 years, all adapted to daily wear of hydrogel lenses, wore uniform-thickness lenses (Dk/L = 5.78) under unilaterally patched eyes for 4 h. Unpatched fellow eyes served as controls. Central corneal thickness was measured with an optical pachometer. Central endothelial images were obtained with a Topcon SP-1000 Specular Microscope and analyzed by the Topcon IMAGEnet processing system. Thickness and morphometric data were collected on test and control eyes before and after the patching sessions. RESULTS: A strong correlation (r = -0.795; p < 0.001) was found between central corneal swelling and endothelial-cell density. Correlations between swelling and the coefficient of variation in cell area (r = 0.502; p < 0.06) and between swelling and the percentage of six-sided cells (r = -0.200; p < 0.48) were not significant. Correlations among the morphometric variables were not significant. Differences in the morphometric variables between test and control eyes were not significant before or immediately after the patching sessions. CONCLUSION: Endothelial-cell density is useful in explaining differences in corneal-swelling responses to closed-eye contact-lens wear among adapted wearers, whereas morphometric variables based on cell-size variability and shape are not.

Adult↗
PubMed2005

Color demosaicking via directional linear minimum mean square-error estimation.

Digital cameras sample scenes using a color filter array of mosaic pattern (e.g., the Bayer pattern). The demosaicking of the color samples is critical to the image quality. This paper presents a new color demosaicking technique of optimal directional filtering of the green-red and green-blue difference signals. Under the assumption that the primary difference signals (PDS) between the green and red/blue channels are low pass, the missing green samples are adaptively estimated in both horizontal and vertical directions by the linear minimum mean square-error estimation (LMMSE) technique. These directional estimates are then optimally fused to further improve the green estimates. Finally, guided by the demosaicked full-resolution green channel, the other two color channels are reconstructed from the LMMSE filtered and fused PDS. The experimental results show that the presented color demosaicking technique outperforms the existing methods both in PSNR measure and visual perception.

Algorithms↗
PubMed1999

A hierarchical Bayesian model for combining multiple 2 x 2 tables using conditional likelihoods.

This paper introduces a hierarchical Bayesian model for combining multiple 2 x 2 tables that allows the flexibility of different odds ratio estimates for different tables and at the same time allows the tables to borrow information from each other. The proposed model, however, is different from a full Bayesian model in that the nuisance parameters are eliminated by conditioning instead of integration. The motivation is a more robust model and a faster and more stable Gibbs algorithm. We work out a Gibbs scheme using the adaptive rejection sampling for log concave density and an algorithm for the mean and variance of the noncentral hypergeometric distribution. The model is applied to a multicenter ulcer clinical trial.

Algorithms↗
PubMed1986

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

Amino Acid Sequence↗
PubMed1999

Comparison of enzyme immunoassay and reverse transcriptase PCR for identification of serotype G9 rotaviruses.

While only four globally important rotavirus G serotypes (1 to 4) have been documented, many studies suggest that serotype G9 viruses may be widely distributed and more important than previously recognized. We have evaluated 10 serotype G9 rotavirus-neutralizing monoclonal antibodies (MAbs) directed to VP7, which bound by direct enzyme immunoassay (EIA) to P1A[8], G9 rotaviruses F45, WI61, and AU32, for their ability to recognize the New Delhi G9 rotavirus 116E. Only one MAb (MAb F45:1) bound to P[11], G9 virus 116E to a high titer by EIA. This MAb was incorporated into an indirect EIA for G serotyping, which was validated with prototype cultivable human rotaviruses of G types 1 to 4 and 9. The EIA was compared with genotyping by reverse transcriptase PCR (RT-PCR) under code for the determination of the G types of rotaviruses obtained from neonates in New Delhi, India. The sensitivities of RT-PCR and EIA (after two additional freeze-thaw cycles) for the typing of G9 rotaviruses were 91 and 86%, respectively, for 24 culture-adapted rotavirus strains. The untypeable culture-adapted rotavirus samples also were unreactive with VP7 group antigen-reactive MAb 60. After two additional freeze-thaw cycles, only 26 of 42 (62%) of stools containing rotavirus typed as G9 by RT-PCR were positive for G9 rotavirus by EIA. Stools containing rotavirus untypeable by EIA contained significantly less MAb 60-reactive VP7 antigen (P = 0. 0001) than the stools containing typeable rotavirus. Thus, RT-PCR genotyping was the more sensitive method for determination of G9 type, but a serotype was readily determined in rotavirus samples containing MAb 60-reactive VP7 antigen by an EIA that incorporates MAb F45:1.

Antibodies, Monoclonal↗
PubMed1997

A simple integrative method for presenting head-contingent motion parallax and disparity cues on intel x86 processor-based machines.

Rogers and Graham (1979) developed a system to show that head-movement-contingent motion parallax produces monocular depth perception in random dot patterns. Their display system comprised an oscilloscope driven by function generators or a special graphics board that triggered the X and Y deflection of the raster scan signal. Replication of this system required costly hardware that is no longer on the market. In this paper the Rogers-Graham method is reproduced with an Intel processor based IBM PC compatible machine with no additional hardware cost. An adapted joystick sampled through the standard game-port can serve as a provisional head-movement sensor. Monitor resolution for displaying motion is effectively enhanced 16 times by the use of anti-aliasing, enabling the display of thousands of random dots in real-time with a refresh rate of 60 Hz or above. A color monitor enables the use of the anaglyph method, thus combining stereoscopic and monocular parallax on a single display without the loss of speed. The power of this system is demonstrated by a psychophysical measurement in which subjects nulled head-movement-contingent illusory parallax, evoked by a static stereogram, with real parallax. The amount of real parallax required to null the illusory stereoscopic parallax monotonically increased with disparity.

Computer Terminals↗
PubMed1998

A rapid assay for tyrosine hydroxylase activity, an indicator of chronic stress in laboratory and domestic animals.

Tyrosine hydroxylase (TH) (EC 1.14.16.2) activity has been frequently employed as a marker of adrenomedullar catecholamine-synthesizing capacity and, thus, as an indicator of chronic stress exposure in various animal species. We have developed a thin layer chromatography (TLC) procedure for its assay in adrenal glands of rats and large animals that reduces some of the drawbacks of currently employed methods, thereby facilitating routine use. Preparation of tissue samples was adapted for rats and pigs. The activity of the enzyme is expressed as the rate of the TH-catalysed tyrosine hydroxylation to 3,4-dihydroxyphenyl-alanine (DOPA) using tritium-labeled tyrosine, in the presence of cofactors and a DOPA decarboxylase inhibitor. The subsequent separation of the radioactive product (DOPA) from the substrate (tyrosine) is accomplished by TLC on silicagel plates, in a n-butanol/acetic acid/water solvent system (4:1:1). Radioactivity in the scraped zones, in which DOPA has been detected by means of an internal standard, is measured by beta-counting. An advantage of this procedure is its simplicity, reliability, and convenience for routine assays. Levels of endogenous adrenal tyrosine (HPLC assay) are considerably higher in pig (2.5-5 nmol/mg protein) than in rat (0.15 nmol/mg protein); their effects upon assay results being, in both cases, negligible. Michaelis constants estimated by this procedure amounted to 0.9 mmol l(-1) (at 0.7 mM DMPH4) for pig, and 1.1 mmol l(-1) (at 1.5 mM DMPH4) for rat.

Adrenal Medulla↗