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Articles by M. Singh
Total Records ( 11 ) for M. Singh
  Z Khan , J. S Bloom , L Kruglyak and M. Singh
 

Motivation: High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome–genome comparisons.

Results: We introduce a new algorithm for finding MEMs. The algorithm leverages a sparse suffix array (SA), a text index that stores every K-th position of the text. In contrast to a full text index that stores every position of the text, a sparse SA occupies much less memory. Even though we use a sparse index, the output of our algorithm is the same as a full text index algorithm as long as the space between the indexed suffixes is not greater than a minimum length of a MEM. By relying on partial matches and additional text scanning between indexed positions, the algorithm trades memory for extra computation. The reduced memory usage makes it possible to determine MEMs between significantly longer sequences.

  P. K Jodhka , P Kaur , W Underwood , J. P Lydon and M. Singh
 

Whereas hormone therapy is used for the treatment of menopausal symptoms, its efficacy in helping reduce the risk of other diseases such as Alzheimer’s disease has been questioned in view of the results of recent clinical trials that appeared inconsistent with numerous basic research studies that supported the beneficial effects of hormones. One possible explanation of this discrepancy may lie in the choice of hormone used. For example, we and others found that progesterone is neuroprotective whereas medroxyprogesterone acetate (MPA), the synthetic progestin used in hormone therapy, is not. Because our data suggest that progesterone-induced protection is associated with the induction of brain-derived neurotrophic factor (BDNF) levels and, importantly, can be blocked by inhibiting the neurotrophin signaling, we determined whether progesterone and medroxyprogesterone acetate differed in their ability to regulate BDNF levels in the explants of the cerebral cortex. We found that progesterone elicited an increase in both BDNF mRNA and protein levels, whereas medroxyprogesterone acetate did not. Furthermore, using both a pharmacological inhibitor of the progesterone receptor (PR) and PR knockout mice, we determined that the effects of progesterone were mediated by the classical PR. Our results underscore the fact that not all progestins have equivalent effects on the brain and suggest that the selection of the appropriate progestin may influence the success of hormone therapy formulations used in treating the menopause and/or reducing the risk for diseases associated with the postmenopausal period.

  M. Singh and P.K. Suri
  This study present a QoS based predictive Max-Min, Min-Min Switcher (QPSMax-Min<>Min-Min) algorithm for scheduling jobs in a grid. The algorithm makes an appropriate selection among the QoS based Max-Min or QoS based Min-Min algorithm on the basis of heuristic applied, before scheduling the next job. The effect on the execution time of grid jobs due to non-dedicated property of resources has also been considered. The algorithm uses the history information about the execution of jobs to predict the performance of non-dedicated resources. Simulation demonstrates that (QPSMax-Min<>Min-Min) outweighs the traditional QoS guided algorithms a lot in makespan.
  R. Taliyan , M. Singh and P.L. Sharma
  The present study was designed to investigate the effect of cyclosporine on hyperglycemia induced decrease antinociceptive effect of morphine in rats. Streptozotocin (STZ) (50 mg kg-1, i.p., once) was administered to induce experimental diabetes in the rats. Pain sensitivity was measured using tail-flick and paw withdrawal test. Urinary and serum nitrite concentration was estimated using Greiss reagent. Spleen Homogenate Supernatant (SHS) was prepared from spleen of 28th day diabetic rats and administered to normal rats (400 μL. i.v.) for 28 days. Experimental diabetes significantly decreased paw withdrawal latency to thermal stimuli on day 28 as compared to age matched control rats, indicating that diabetic rats exhibit thermal hyperalgesia. Moreover, analgesic effect of morphine (4 and 8 mg kg-1 s.c.), was progressively decreased in diabetic and SHS treated non diabetic rats. Further, the levels of nitric oxide were also elevated in 28th day diabetic and SHS treated non diabetic rats. However, administration of Cyclosporine (12.5 and 25 mg kg-1 i.p.), an IL-2 inhibitor and splenectomy attenuated diabetes and SHS induced decrease in nociceptive threshold and increase in serum and urinary nitrite levels. It is concluded that cyclosporine have beneficial effect in diabetic neuropathy and also improved the analgesic effect of morphine.
  D.M. Paiva , M. Singh , K.S. Macklin , S.B. Price , J.B. Hess and D.E. Conner
  Salmonella is an important foodborne pathogen often associated with poultry and highly prevalent in poultry processing plants. The objective of this study was to determine the efficacy of a commercial grade concrete sealant (BioSealed for ConcreteTM) to prevent bacterial attachment, colonization and antimicrobial effects against multiple strains of Salmonella (S. enteritidis, S. Kentucky, S. Typhimurium, S. Senftenberg and S. Heidelberg) on concrete blocks. Individual strains of Salmonella spp. were inoculated onto the concrete blocks and divided into 4 different treatment groups: (A) Bricks which were not treated with BioSealed for ConcreteTM (B) Bricks which were treated with BioSealed for ConcreteTM before inoculation (C) Bricks which were treated with BioSealed for ConcreteTM after inoculation and (D) Bricks which were treated with BioSealed for ConcreteTM before and after inoculation. External and internal surfaces of the treated concrete blocks were swabbed, serially diluted and plated onto XLD agar. Reductions of survival counts were enumerated and recorded as log10 CFU/cm2. Significantly (p<0.05) lower viable counts were observed following treatments C and D as compared to treatments A and B. However, no significant differences (p>0.05) in the survival populations of Salmonella were observed between treatments A and B for all five strains tested and between treatments C and D for any of the strains tested. This indicates that BioSealed for ConcreteTM proved to be a potent antimicrobial against multiple strains of Salmonella and can be used as an alternative method to control this pathogen in processing plant environments.
  D.M. Paiva , M. Singh , K.S. Macklin , S.B. Price , J.B. Hess and D.E. Conner
  This study was conducted to determine the efficiency of BioSealed for ConcreteTM against C. perfringens and B. subtilis on concrete blocks. Concrete blocks were divided into four different treatments: A) No Biosealed application; B) Biosealed applied before inoculation; C) Biosealed applied after inoculation; or D) Biosealed applied before and after inoculation with C. perfringens and B. subtilis individually (Ca. 109 CFU/mL). The C. perfringens inoculated concrete blocks were then incubated at 37oC for 48 h anaerobically; while the B. subtilis inoculated concrete blocks were incubated at 37oC for 24 h aerobically. External and internal surfaces of the treated concrete blocks were swabbed for microbiological analysis. Significantly lower (p<0.05) populations of both microorganisms were observed for treatment groups C and D as compared to A and B on the external surface of the concrete blocks whereas, no significant differences (p>0.05) were observed between treatment groups A, B and C on the internal surfaces of the concrete blocks. No significant differences (p>0.05) were found when comparing groups A and B, while a dual application of Biosealed for ConcreteTM; pre- and post-inoculation showed the greatest reduction (p<0.05) on the external and internal surfaces of the concrete blocks. Results from this study indicated that Biosealed for ConcreteTM has an immediate bactericidal effect on C. perfringens and B. subtilis and has the potential to be used in combination with other GMP’s and sanitation practices to control bacterial colonization on concrete surfaces in a poultry processing plant.
  B. Saenmahayak , M. Singh , S.F. Bilgili and J.B. Hess
  Influence of complexed zinc supplementation on growth performance and meat quality of broiler chickens were assessed at 49 d of age. A total of 960 male broilers were assigned to four dietary treatments: negative control (C), positive control (C + IZn; 40 ppm ZnSO4), C + 40 ppm complexed Zn (C + OZn) and C + IZn + 40 ppm complexed Zn added to the positive control (C + IZn + OZn). Each treatment feed was provided in a three-stage feeding program. No differences (p>0.05) were observed in the body weight, feed conversion, carcass and component yields due to any of the dietary treatments. However, drip loss was significantly (p<0.05) increased in fillets from birds fed organic trace minerals when measured at 24 h post deboning. Overall, fillet color (L*, a* and b* measurements) did not differ significantly (p>0.05) but after 28 d of storage, fillets from birds with high levels of zinc showed increased (p<0.05) redness (a* value). Breast fillet quality and microbial profile over a 28 d storage period under refrigeration (4oC) were not different (p>0.05) due to any of the dietary treatments.
  A. Morey , M. Singh and S.R. McKee
  This study evaluated the effect of manufacturer-recommended microwave times on Listeria monocytogenes in Ready-to-Eat (RTE) poultry products. Three chicken products including battered and breaded chicken patties, fully cooked chicken breast fillets (both frozen) and chicken sausages (refrigerated) were inoculated with streptomycin-resistant (1500 μg/ml) L. monocytogenes (Brie 1) at low (ca. ~4 log10 CFU/ml) and high (ca. ~9 log10 CFU /ml) levels. Following 12 h of either frozen or refrigerated storage, random samples (n = 3 of each product) were individually microwaved for recommended time, undercooked and overcooked. Survival of L. monocytogenes after microwaving was determined by spread plating the samples and enumerating bacterial colonies on BHIA+streptomycin (1500 μg/ml). Analysis of variance with Duncans’ grouping was conducted to determine significant differences in survival (α = 0.05). Microwaving the chicken patties inoculated with high levels of bacteria for a recommended time of 1 min increased surface temperature to 64°C-74°C leading to approximately 1-log reduction (p<0.05) of L. monocytogenes. Chicken breast samples and sausages microwaved at 1100 W according to manufacturer’s instruction reduced L. monocytogenes populations below detection limit at high as well as low levels. Although, recommended microwaving times might not always be effective in eliminating L. monocytogenes, its efficacy will depend upon factors such as product type and the level of L. monocytogenes contamination. Reconstitution of RTE foods below recommended times can make them a potential source of Listeria.
  R. Goyal , B. Ravishankar , V.J. Shukla and M. Singh
  Background: Rohitaka ghrita an ayurvedic formulation is recommended to use in various clinical conditions including jaundice, cirrhosis and cholestasis etc. The study was designed to investigate the hepatoprotective activity of Rohitaka ghrita using paracetamol intoxication model in rats. Wistar albino rats (180-240 g) were employed into the study. Material and Methods: Rohitaka ghrita was administered at the dose of 3.6 and 7.2 g kg-1, p.o. daily. Liver damage was induced by the administering paracetamol (3 g kg-1, p.o.). Silymarin was used as standard. Results: Paracetamol intoxication caused marked increase in SGPT, SGOT, ALP and bilirubin levels. It further impaired the hepatic antioxidant system as evidenced by increased lipid peroxidation; decreased glutathione, catalase levels and also Na+K+ATPase level. Moreover, the liver histopathology revealed central vein dilation, infiltration and fatty degeneration due to PCM intoxication. However, treatment with Rohitaka ghrita (3.6 and 7.2 g kg-1) and silymarin (25 mg kg-1) markedly reversed the effects of PCM in rat. Rohitaka ghrita have a significant hepatoprotective potential against paracetamol induced hepatocellular damage in rats. Conclusion: The present study provides a scientific rationale for its traditional and commercial uses in the management of liver diseases.
  M. Singh , A.K. Pandey , R.J. Butcher and N.K. Singh
  Two novel Ni(II) complexes {[Ni(en)2(pot)2]0.5CHCl3} (3) {pot=5-phenyl-1,3,4-oxadiazole-2-thione} (1) and [Ni(en)2](3-pytol)2 (4) {3-pytol=5-(3-pyridyl)-1,3,4-oxadiazole-2-thiol} (2) have been synthesized using en as coligand. The metal complexes have been characterized by physical and analytical techniques and also by single crystal X-ray studies. The complexes 3 and 4 crystallize in monoclinic system with space group P21/a and P121/c, respectively. The complex 3 has a slightly distorted octahedral geometry with trans (pot) ligands while 4 has a square planar geometry around the centrosymmetric Ni(II) center with ionically linked trans (3-pytol) ligands. The π...π (face to face) interaction plays an important role along with hydrogen bondings to form supramolecular architecture in both complexes.
  M. Chaturvedi , M. Singh , Chugh R. Man and S. Pandey
  A comparative study on the production of extra cellular lipase by Solid State Fermentation (SSF) using Bacillus subtilis with various substrates has been made. Different parameters such as temperature, pH, different substrates and effect of incubation time of the medium were optimized for maximum yield. The maximum extracellular lipase activity of 4.5 units per gram of dry fermented substrates (U g dS-1) was observed with ground nut oil cake after 48 h of fermentation with 70% initial moisture content of the substrate and suitable growth of bacterial mass culture was for maximum yield of lipase at pH 8 was observed.
 
 
 
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