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Search Results: 1 - 10 of 7630 matches for " Feroz Khan "
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The Generation of Large Networks from Web-of-Science Data
Loet Leydesdorff,Gohar Feroz Khan,Lutz Bornmann
Computer Science , 2014,
Abstract: During the 1990s, one of us developed a series of freeware routines (http://www.leydesdorff.net/indicators) that enable the user to organize downloads from the Web-of-Science (Thomson Reuters) into a relational database, and then to export matrices for further analysis in various formats (for example, for co-author analysis). The basic format of the matrices displays each document as a case in a row that can be attributed different variables in the columns. One limitation to this approach was hitherto that relational databases typically have an upper limit for the number of variables, such as 256 or 1024. In this brief communication, we report on a way to circumvent this limitation by using txt2Pajek.exe, available as freeware from http://www.pfeffer.at/txt2pajek/.
Crystallization, Transport and Magnetic Properties of the Amorphous (Fe1–xMnx)75P15C10 Alloys  [PDF]
Md. Kamruzzaman, Md. Abu Sayem Karal, Dilip Kumar Saha, Feroz Alam Khan
Journal of Crystallization Process and Technology (JCPT) , 2012, DOI: 10.4236/jcpt.2012.23013
Abstract: The amorphous (Fe1-xMnx)75P15C10 (0 ≤ x ≥ 0.30) alloys were prepared by the standard melt spinning technique and investigated their crystallization, thermal, transport and magnetic properties. Crystallization was observed from 400℃ to 650℃ with an interval 50℃within 30 minutes annealing time by XRD. The as-cast samples were amorphous in nature. Annealing 400℃ to 450℃ samples showed the mixed bcc Fe and amorphous structures. The lattice parameter ‘a’ was varied from 2.855 to 2.859 ? but above 450℃, samples contained hexagonal, FeP and FeC structures. The lattice parameters ‘a’ and ‘c’ were varied from (5.016-5.036) ? and (13.575-13.820) ? , respectively. Average crystallite size was found to vary from 8 to 48 nm. Crystallization temperature and weight change were observed by differential thermal analysis and thermogravimetric analysis, respectively. Crystallization temperature was increased with increasing Mn content. Resistivity was increased above and bellows the Curie temperature. Real permeability remained almost constant upto around 106 Hz for of all samples after that it was decreased with increasing frequency and it was also decreased with Mn, whereas imaginary permeability was increased sharply above frequency 107 Hz. The value of saturation magnetization was found to decrease with increment Mn.
D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs
Naresh Sen,Manoj Mishra,Feroz Khan,Abha Meena
Bioinformation , 2009,
Abstract: Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network.
Phylogenetics of an antibiotic producing Streptomyces strain isolated from soil
Vineeta Singh,Vandana Praveen,Chandra Kant Mani Tripathi,Feroz Khan
Bioinformation , 2009,
Abstract: Traditional methods of species classification and identification of the organism are based on morphological, physiological, biochemical, developmental and nutritional characteristics. Accurate assignment of taxonomic status to the new biologically active microbial isolates through existing bioinformatics methods is now very essential and also helpful in chemical characterization of the active molecule produced by microorganisms. The bacterial strain M4 (ckm7) was isolated from the pre-treated soil sample collected from the agricultural field of Eastern Uttar Pradesh (U.P.), India and was found to be producing antibacterial and antifungal antibiotics. Taxonomic identification of the isolate belongs to the genus Streptomyces which was done with the help of sequence analysis and later confirmed by biological activity. Sequence comparison study of ckm7 showed 98% identical similarity with 16S rRNA gene sequences of Streptomyces spinichromogenes, Streptomyces triostinicus and Streptomyces capoamus. On the basis of both biological activity and phylogenetic analysis of ckm7, it was concluded that the isolated strain is a new variant of S. triostinicus.
Prediction of MHC class I binding peptides using probability distribution functions
S. S. Soam,B. N. Mishra,Feroz Khan,B. Bhasker
Bioinformation , 2009,
Abstract: Binding of peptides to specific Major Histo-compatibility Complex (MHC) molecule is important for understanding immunity and has applications to vaccine discovery and design of immunotherapy. Artificial neural networks (ANN) are widely used by predictions tools to classify the peptides as binders or non-binders (BNB). However, the number of known binders to a specific MHC molecule is limited in many cases, which poses a computational challenge for prediction of BNB and hence, needs improvement in learning of ANN. Here, we describe, the application of probability distribution functions to initialize the weights and biases of the artificial neural network in order to predict HLA-A*0201 binders and non-binders. The 10-fold cross validation has been used to validate the results. It is evident from the results that the AROC for 90% of test cases for Weibull, Uniform and Rayleigh distributions is in the range 0.90-1.0. Further, the standard deviation for AROC was minimum for Weibull distribution, and may be used to train the artificial neural network for HLA-A*0201 MHC Class-I binders and non-binders prediction.
Pharmacovigilance: Effects of herbal components on human drugs interactions involving Cytochrome P450
Akansha Saxena,Kumar Parijat Tripathi,Sudeep Roy,Feroz Khan
Bioinformation , 2008,
Abstract: Cytochrome P450 (CYP P450) enzymes are a superfamily of mono-oxygenases that are found in all kingdoms of life. The CYP P450 enzymes constitute a large superfamily of haem-thiolate proteins involved in the metabolism of a wide variety of both exogenous and endogenous compounds. The CYP activities have been shown to be involved in numerous interactions especially between drugs and herbal constituents. The majority of serious cases of drug interactions are as a result of the interference of the metabolic clearance of one drug by yet another co-administered drug, food or natural product. Gaining mechanistic knowledge towards such interactions has been accepted as an approach to avoid adverse reactions. The inductions and inhibition of CYP enzymes by natural products in the presence of a prescribed drug has led to adverse effects. Herbal medicines such as St. John’s wort (Hypericum perforatum), garlic (Allium sativa), piperine (from Piper sp.), ginseng (Ginseng sp.), gingko (Gingko biloba), soya beans (Glycine max), alfalfa (Medicago sativa) and grape fruit juice show clinical interactions when co-administered with medicines. This review documents the involvement of CYP enzymes in the metabolism of known available drugs and herbal products. We also document the interactions between herbal constituents & CYP enzymes showing potential drug-herb interactions. Data on CYP450 enzymes in activation (i.e. induction or inhibition) with natural constituents is also reviewed.
Metabolic pathway reconstruction of eugenol to vanillin bioconversion in Aspergillus niger
Suchita Srivastava,Suaib Luqman,Mahendra P. Darokar,Feroz Khan
Bioinformation , 2010,
Abstract: Identification of missing genes or proteins participating in the metabolic pathways as enzymes are of great interest. One such class of pathway is involved in the eugenol to vanillin bioconversion. Our goal is to develop an integral approach for identifying the topology of a reference or known pathway in other organism. We successfully identify the missing enzymes and then reconstruct the vanillin biosynthetic pathway in Aspergillus niger. The procedure combines enzyme sequence similarity searched through BLAST homology search and orthologs detection through COG & KEGG databases. Conservation of protein domains and motifs was searched through CDD, PFAM & PROSITE databases. Predictions regarding how proteins act in pathway were validated experimentally and also compared with reported data. The bioconversion of vanillin was screened on UV-TLC plates and later confirmed through GC and GC-MS techniques. We applied a procedure for identifying missing enzymes on the basis of conserved functional motifs and later reconstruct the metabolic pathway in target organism. Using the vanillin biosynthetic pathway of Pseudomonas fluorescens as a case study, we indicate how this approach can be used to reconstruct the reference pathway in A. niger and later results were experimentally validated through chromatography and spectroscopy techniques.
Radioactivity Measurements in River Sediments and Aquatic Organisms of Kanyakumari District
Eugin shaji. J,Kannan. C,Feroz Khan. M
Advanced Biotech , 2013,
Abstract: The present study was focused to assess the Natural radioactivity levels in river sediment samples and the associated organisms (fishes and molluscs) collected from Kanyakumari district. The gross and activity were measured using alpha scintillation counter and low beta counter. The natural radioactivity level is higher in sediment samples collected from Valliyar river near Eraniel and the level was minimum in sediments of Sittar. The radioactivity level of all the river sediments mainly depended upon the contents of silt and clay. The based on the radioactivity data the radiation hazard indices were calculated for fishes and molluscs and found lower than the recommended level of international agencies. Therefore, the data revealed no significant radiological threat to the environment.
Serological and Molecular Studies of a Novel Virus Isolate Causing Yellow Mosaic of Patchouli [Pogostemon cablin (Blanco) Benth]
Mohammad Zaim, Ashif Ali, Jomon Joseph, Feroz Khan
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0083790
Abstract: Here we have identified and characterized a devastating virus capable of inducing yellow mosaic on the leaves of Patchouli [Pogostemon cablin (Blanco) Benth]. The diagnostic tools used were host range, transmission studies, cytopathology, electron microscopy, serology and partial coat protein (CP) gene sequencing. Evidence from biological, serological and sequence data suggested that the causal virus belonged to genus Potyvirus, family Potyviridae. The isolate, designated as Patchouli Yellow Mosaic Virus (PaYMV), was transmitted through grafting, sap and the insect Myzus persicae (Sulz.). Flexuous rod shaped particles with a mean length of 800 nm were consistently observed in leaf-dip preparations from natural as well as alternate hosts, and in purified preparation. Cytoplasmic cylindrical inclusions, pinwheels and laminar aggregates were observed in ultra-thin sections of infected patchouli leaves. The purified capsid protein has a relative mass of 43 kDa. Polyclonal antibodies were raised in rabbits against the coat protein separated on SDS – PAGE; which were used in ELISA and western blotting. Using specific antibodies in ELISA, PaYMV was frequently detected at patchouli plantations at Lucknow and Bengaluru. Potyvirus-specific degenerate primer pair (U335 and D335) had consistently amplified partial CP gene from crude preparations of infected tissues by reverse transcription polymerase chain reaction (RT-PCR). Comparison of the PCR product sequence (290 bp) with the corresponding regions of established potyviruses showed 78–82% and 91–95% sequence similarity at the nucleotide and amino acid levels, respectively. The results clearly established that the virus under study has close homology with watermelon mosaic virus (WMV) in the coat protein region and therefore could share a common ancestor family. Further studies are required to authenticate the identity of PaYMV as a distinct virus or as an isolate of WMV.
Growth and Characterization of Holmium Oxalate Heptahydrate Crystals  [PDF]
Basharat Want, Feroz Dar
Journal of Crystallization Process and Technology (JCPT) , 2012, DOI: 10.4236/jcpt.2012.24019
Abstract: Single crystals of holmium oxalate heptahydrate are grown by gel diffusion method using organic agar gel as a medium of growth. The crystals grow in the agar gel with hexagonal morphology having well defined habit faces Powder X-ray diffraction results show that the crystals belong to monoclinic system bearing the space group P21/c with cell parameters; a = 12.197\"\"? \"\", b = 11.714 , c = 6.479 , α = 90°, β = 120.12°, γ = 90°, V = 799.6? 3. Fourier transform Infrared spectrum of the crystals shows the presence of water and other associated functional groups. Thermogravimetric analysis support the presence of 7 H2O molecules associated with holmium oxalate crystal lattice. The thermal decomposition in the nitrogen atmosphere leads to the formation of holmium oxide as the final product.
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