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Search Results: 1 - 10 of 660 matches for " Farhad Hormozdiari "
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Integrating Functional Data to Prioritize Causal Variants in Statistical Fine-Mapping Studies
Gleb Kichaev,Wen-Yun Yang,Sara Lindstrom,Farhad Hormozdiari,Eleazar Eskin,Alkes L. Price,Peter Kraft,Bogdan Pasaniuc
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004722
Abstract: Standard statistical approaches for prioritization of variants for functional testing in fine-mapping studies either use marginal association statistics or estimate posterior probabilities for variants to be causal under simplifying assumptions. Here, we present a probabilistic framework that integrates association strength with functional genomic annotation data to improve accuracy in selecting plausible causal variants for functional validation. A key feature of our approach is that it empirically estimates the contribution of each functional annotation to the trait of interest directly from summary association statistics while allowing for multiple causal variants at any risk locus. We devise efficient algorithms that estimate the parameters of our model across all risk loci to further increase performance. Using simulations starting from the 1000 Genomes data, we find that our framework consistently outperforms the current state-of-the-art fine-mapping methods, reducing the number of variants that need to be selected to capture 90% of the causal variants from an average of 13.3 to 10.4 SNPs per locus (as compared to the next-best performing strategy). Furthermore, we introduce a cost-to-benefit optimization framework for determining the number of variants to be followed up in functional assays and assess its performance using real and simulation data. We validate our findings using a large scale meta-analysis of four blood lipids traits and find that the relative probability for causality is increased for variants in exons and transcription start sites and decreased in repressed genomic regions at the risk loci of these traits. Using these highly predictive, trait-specific functional annotations, we estimate causality probabilities across all traits and variants, reducing the size of the 90% confidence set from an average of 17.5 to 13.5 variants per locus in this data.
Minerals profile of forages for grazing ruminants in Pakistan  [PDF]
Farhad Mirzaei
Open Journal of Animal Sciences (OJAS) , 2012, DOI: 10.4236/ojas.2012.23019
Abstract: The current research was carried out at Rakh Khaire Wala, which is well known as one of the most developed animal husbandry in Punjab, Pakistan. This location in the arid region, where sheep farming is a common practice, was selected for this study. The aim of the study was to determine and collect data on the mineral contents of forages or feedstuffs that are harvested and used in animal nutrition in the region, in order to gain information on the deficiency and/or excess of mineral levels for ruminants grazing therein, fed mainly with these feedstuffs. These pastures were visited twice during the study, in summer and winter, to collect samples in order to determine the effect of seasonal changes on the mineral contents of forages. In each location, samples from the available forages were collected. Forage samples were analyzed in order to determine the Ca, Mg, Na, K, Fe, Cu, Zn and Mn levels using an Atomic Absorption Spectrophotometer. These results show that pasture grasses/forages had sufficient levels of K, Ca, Mg, Mn and Zn to meet requirements of ruminant animals, but the occurrence of marginal to deficient supplies of Na, and Cu appear very likely. There is an urgent requirement for experimentation on supplementation regimes involving these minerals, so that appropriate recommendations can be formulated.
Wool characteristics of crossbred Baghdadi wild ram and Iran native sheep  [PDF]
Nosratollah Taherpour, Farhad Mirzaei
Agricultural Sciences (AS) , 2012, DOI: 10.4236/as.2012.32021
Abstract: Twenty mid side wool samples of crossbred sheep were collected and their characteristics were determined. Data analyzed by SAS software and Duncan’s multiple range tests was used for comparison of mean wool characteristics. Average fleece weight, yield, wool diameter, Fine fiber and staple length were: 431.59 ± 38.95 gr, 65.14%, 14.24 ± 0.67 μm, 48.67 ± 5.59, and 43.65 ± 4.15 mm respectively. Mean fleece weight was significantly affected (p < 0.05) by sex (female 259 gr and male 506.55) and age (248.25, 458.38 and 637.75 gr for 1, 2 and 3 yr old respectively). Mean wool diameter was significantly affected by sex (male 12.78 ± 0.49, female 15.33 ± 0.85 μm) and there was a significant difference (p < 0.05) between F1 and F2 generation 11.84 ± 0.58, 16.27 ± 0.72 μm respectively. There were effective differences among ages (12.55 ± 0.74, 14.47 ± 0.58 and 13.11 ± 0.64 μm for 1, 2 and 3 yr old respectively). Wool diameter of younger animals, males and F1 was so fine (12.55, 12.87 and 11.84 μm respectively). Staple length of F2 crosses was significantly longer than F1 crosses (p < 0.05). However wool diameter of F1 was significantly finer than F2, but length and down fiber percentage was less than second generation. As wild sheep shed his fiber in winter, the first filial crosses also shed their fibers from the end of winter to early spring. Shedding was seldom observed in F2 generations. It seems likely that wool from crossbred sheep could be used for those applications for which cashmere is suitable. This study indicates that, such crossbred sheep have a superfine wool and could be used in pure or blend for textile industry.
Efficient Components on Livestock Products Export in Iran  [PDF]
Behnam Maleki, Farhad Mirzaei
Modern Economy (ME) , 2012, DOI: 10.4236/me.2012.38117
Abstract: Iran’s dependence on oil revenues has caused severe impact of commodity price fluctuations on the currency revenues and any reduction in export prices has led into a deficit in the country’s balance of payments. Accordingly, it was in the past years and especially the Second Development Plan that government included encouragement and reducing the country’s dependence on oil revenues in its agenda. The international agricultural exports, especially exports of live-stock and poultry country subdivision have a proper status due to its relative advantage. Therefore, in this study factors affecting the supply of exportable animal products are considered. For this purpose, factors affecting exports of live-stock products are studied by using Cointegration Analysis based on statistical intervals in 1984-2008. Experimental results showed that the value of income per capita importer countries of Iran and the real exchange rate had a positive effect on export demand and the added value and export price index had a negative impact on exports of livestock sector.
Designing a Full Adder Circuit Based on Quasi-Floating Gate  [PDF]
Sahar Bonakdarpour, Farhad Razaghian
Energy and Power Engineering (EPE) , 2013, DOI: 10.4236/epe.2013.53B012
Abstract:

Since in designing the full adder circuits, full adders have been generally taken into account, so as in this paper it has been attempted to represent a full adder cell with a significant efficiency of power, speed and leakage current levels. For this objective, a comparison between five full adder circuits has been provided. Applying floating gate technology and refresh circuits in the full adder cell lead to the reduction of leakage current on the gate node. The simulations were accomplished in this paper, through HSPICE software and 65 nm CMOS technology. The simulation results indicate the considerable efficiency of power consumption, speed and leakage current in the full adder cell rather than other cells.

An Overview of the Copyright Protection Laws in Bangladesh—A Critical Analysis of the Copyright Act, 2000 with Its Loopholes and Recommendations  [PDF]
Muhammad Farhad Hosen
Beijing Law Review (BLR) , 2017, DOI: 10.4236/blr.2017.82011
Abstract: Nowadays, it goes without saying copyright is one of the most significant field of Intellectual Property related to the exclusive monopoly rights in the arena of literature, dramatics, musical, artistic, cinematograph and sound recordings. Day by day the importance of copyright is increasing whereas the lacking of necessary measures to protect copyrights are going to be difficult because of our lack of enforcing mechanisms and insufficient laws and plagiarizing activities although we have Copyright Act 2000. To protect the rights and privileges of the author or the creator of Copyright works, footsteps and different measures of the Government should be increased and piracy must be stopped by establishing strong enforcement agency. To protect the copyrights of the creator especially of the author, the govt. should come forward to enforce the rules and regulations which have been incorporated in the Act of 2000 and some amendments are also required to enforce. By this research, the researcher tries to pick out the copyright status of Bangladesh, an overview of the Copyright Act 2000, and the common barriers and solutions of those barriers related to the copyright position in Bangladesh.
Coordination within International Manufacturing Networks: A Comparative Study of Three Industrial Practices  [PDF]
Farhad Norouzilame, Magnus Wiktorsson
American Journal of Industrial and Business Management (AJIBM) , 2018, DOI: 10.4236/ajibm.2018.86107
Abstract: The globalisation of manufacturing activities has led to the emergence of internationally dispersed manufacturing plants. Coordination of such networks is a complex task and entails several management challenges. The purpose of this paper is to increase the understanding regarding the coordination issues and how they could be managed in IMN environment. Using a multiple case study approach, data from three multi-plant manufacturing businesses were collected and analysed. The results include discussions on coordination aspects such as autonomy and mechanisms to conduct coordination. Furthermore, a model for assigning autonomy level to the plant in an IMN is suggested as well as mechanisms to conduct the coordination work.
Genome Sequencing Highlights the Dynamic Early History of Dogs
Adam H. Freedman,Ilan Gronau,Rena M. Schweizer,Diego Ortega-Del Vecchyo,Eunjung Han,Pedro M. Silva,Marco Galaverni,Zhenxin Fan,Peter Marx,Belen Lorente-Galdos,Holly Beale,Oscar Ramirez,Farhad Hormozdiari,Can Alkan,Carles Vilà,Kevin Squire,Eli Geffen,Josip Kusak,Adam R. Boyko,Heidi G. Parker,Clarence Lee,Vasisht Tadigotla,Adam Siepel,Carlos D. Bustamante,Timothy T. Harkins,Stanley F. Nelson,Elaine A. Ostrander,Tomas Marques-Bonet,Robert K. Wayne ,John Novembre
PLOS Genetics , 2014, DOI: doi/10.1371/journal.pgen.1004016
Abstract: To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.
Genome Sequencing Highlights Genes Under Selection and the Dynamic Early History of Dogs
Adam H. Freedman,Rena M. Schweizer,Ilan Gronau,Eunjung Han,Diego Ortega-Del Vecchyo,Pedro M. Silva,Marco Galaverni,Zhenxin Fan,Peter Marx,Belen Lorente-Galdos,Holly Beale,Oscar Ramirez,Farhad Hormozdiari,Can Alkan,Carles Vilà,Kevin Squire,Eli Geffen,Josip Kusak,Adam R. Boyko,Heidi G. Parker,Clarence Lee,Vasisht Tadigotla,Adam Siepel,Carlos D. Bustamante,Timothy T. Harkins,Stanley F. Nelson,Elaine A. Ostrander,Tomas Marques-Bonet,Robert K. Wayne,John Novembre
Quantitative Biology , 2013,
Abstract: To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we analyzed novel high-quality genome sequences of three gray wolves, one from each of three putative centers of dog domestication, two ancient dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. We find dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow, which confounds previous inferences of dog origins. In dogs, the domestication bottleneck was severe involving a 17 to 49-fold reduction in population size, a much stronger bottleneck than estimated previously from less intensive sequencing efforts. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was far larger than represented by modern wolf populations. Conditional on mutation rate, we narrow the plausible range for the date of initial dog domestication to an interval from 11 to 16 thousand years ago. This period predates the rise of agriculture, implying that the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that surprisingly, none of the extant wolf lineages from putative domestication centers are more closely related to dogs, and the sampled wolves instead form a sister monophyletic clade. This result, in combination with our finding of dog-wolf admixture during the process of domestication, suggests a re-evaluation of past hypotheses of dog origin is necessary. Finally, we also detect signatures of selection, including evidence for selection on genes implicated in morphology, metabolism, and neural development. Uniquely, we find support for selective sweeps at regulatory sites suggesting gene regulatory changes played a critical role in dog domestication.
Relationship between insertion/deletion (indel) frequency of proteins and essentiality
Simon K Chan, Michael Hsing, Fereydoun Hormozdiari, Artem Cherkasov
BMC Bioinformatics , 2007, DOI: 10.1186/1471-2105-8-227
Abstract: We have investigated three species, Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae, for which high-quality protein essentiality data is available. Using these data, we demonstrated with t-test calculations that the mean indel frequencies in essential proteins were greater than that of non-essential proteins in the three proteomes. The abundance of indels in both types of proteins was also shown to be accurately modeled by the Weibull distribution. However, Receiver Operator Characteristic (ROC) curves showed that indel frequencies alone could not be used as a marker to accurately discriminate between essential and non-essential proteins in the three proteomes. Finally, we analyzed the protein interaction data available for S. cerevisiae and observed that indel-bearing proteins were involved in more interactions and had greater betweenness values within Protein Interaction Networks (PINs).Overall, our findings demonstrated that indels were not randomly distributed across the studied proteomes and were likely to occur more often in essential proteins and those that were highly connected, indicating a possible role of sequence insertions and deletions in the regulation and modification of protein-protein interactions. Such observations will provide new insights into indel-based drug design using bioinformatics and cheminformatics tools.Essential genes encode products that are required for the viability of an organism. There are two major reasons why there is considerable interest in determining the set of essential genes in an organism. Firstly, this will provide insights into the basic requirements needed to sustain a living cell. For example, the sequencing of the parasitic bacterium Mycoplasma genitalium [1] and the subsequent studies to determine its essential genes [2,3] have provided a more in-depth understanding of what constitutes a 'minimum genome.' Secondly, essential proteins in pathogens can potentially be excellent drug targets [4,5], as
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