Fpga-Based Accelerator for The Generation of Pseudo-Amino Acid Composition

Pengurangan jurang antara bilangan protein baru yang belum dicirikan dan yang telah dikenali di dalam bank data protein telah muncul sebagai salah satu cabaran terbesar era pasca genomik. Permintaan kian meningkat untuk teknik-teknik yang dapat meramal ciri-ciri protein dengan cekap dan tepat berdasarkan maklumat urutan protein sahaja. Komposisi Asid Amino Pseudo (PseAAC) telah muncul sebagai teknik pemodelan yang berupaya menggabungkan maklumat urutan protein terpilih dalam model diskret. PseAAC telah digunakan secara meluas dalam ujikaji protein melalui pelbagai perisian penjana PseAAC. Oleh sebab penjanaan PseAAC lazimnya melibatkan pemprosesan data berskala besar, tempoh pemprosesan amat penting. Prospek untuk mengurangkan tempoh tersebut terhad kerana proses perisian lazimnya berjujukan. Maka, perkakasan yang boleh diaturcara seperti Field Programmable Gate Array (FPGA) muncul sebagai alternatif baru dengan keupayaan pemprosesan selari yang dapat mempercepat penghitungan PseAAC. Dalam penyelidikan ini, suatu pemecut berasaskan FPGA untuk penjanaan PseAAC telah diperkenalkan. Penjana tersebut terdiri daripada beberapa modul. Untuk mempercepat proses, dua modul yang paling intensif dalam penghitungan, iaitu Sum-of-Small-T dan T-u-minus-20, direka untuk pelaksanaan secara selari. Penjana tersebut direalisasikan melalui FPGA Altera Cyclone III. Proses berjaya dipercepat sehingga 31.5 kali ganda berbanding suatu penjana PseAAC berasaskan perisian Perl. Kesimpulannya, pengurangan tempoh penghitungan yang ketara telah dicapai melalui rekabentuk penjana PseAAC yang menggunakan kebolehan pemprosesan selari FPGA. ________________________________________________________________________________________________________________________ One of the biggest challenges in protein prediction post genomic age is narrowing the gap between the number of newly discovered and uncharacterized proteins and the number of known proteins in protein data banks. This leads to increased demand for efficient techniques to accurately predict protein attributes based solely on its sequence-order information. The Pseudo-Amino Acid Composition (PseAAC) is a modeling technique that incorporates, selectively, sequence-order information of a protein into a discrete model. PseAAC has been applied in numerous protein-related researches using various software-based PseAAC generators. Since this often involves large-scale data processing, computation time is of the essence. The prospect of further reducing computation time of the software is limited due to the sequential nature of software execution. Alternative platform such as programmable hardware has emerged as a solution to this bottleneck. Programmable hardware such as Field Programmable Gate Array (FPGA) enables parallel processing that speeds up computation of PseAAC. In this research, an FPGA-based PseAAC generator architecture is proposed. The architecture consists of several modules. To speed up computation, the two most computation-heavy modules of the architecture, the Sum-of-Small-T and T-u-minus-20, are designed to run in parallel. The generator is realized on the Altera Cyclone III FPGA and achieves computation speed increase of up to 31.5 times over a Perl-based PseAAC generator. In conclusion, significant computation speed improvement is achieved by designing the PseAAC generator to capitalize on the parallel processing capability of the FPGA

Sorption and Degrading Parameters for Modeling Nematicide Fate in Soil

Since the ban of the traditional fumigants, DBCP and EDB, for nematode control in pineapple, there has been considerable interest in a non-volatile organosphosphorus nematicide, fenamiphos [Nemacur®, ethyl 3-methyl-4-(methylthio)phenyl (1-methylethyl) phosphoramidate]. The fate of fenamiphos is unknown in diverse field soils in Hawaii. The ability of mathematical simulation models to predict movement and persistence of fenamiphos in soils from key input parameters associated with mathematical descriptions of degradation, sorption and leaching, will aid us in designing optimum management strategies to achieve maximum efficacy and minimize environmental contamination. In view of the proposed modeling efforts, experiments were conducted to evaluate the errors and uncertainties in measurements of two important processes, sorption and degradation. Fenamiphos sorption measurements were conducted by the conventional batch method on Molokai and Pane soils under aerobic conditions. The impact on measured sorption by (1) degradation of fenamiphos during equilibration, (2) variable moisture status of soils before measurements and (3) equilibration time were evaluated. Apparent sorption and sorption corrected for degradation at both 4 and 24 hours equilibration on both soils increased in the following order: field-moist < prewetted < air-dried. Degradation of fenamiphos to fen. sulfoxide during batch equilibration occured at all moisture treatments, and the impact of degradation (45% of fenamiphos degraded) on sorption measurement was significant on the Pane soil. On the Molokai soil however, the impact was negligible because less than 20% of fenamiphos degraded. Competition of water molecules with fenamiphos for sorption sites and fenamiphos degradation during equilibration probably accounted for the differences in sorption due to pre-sorption moisture status. The percentage differences in fenamiphos sorption betweet. air-dried and field-moist soils after 24 hours equilibration were 34 % and 37% for Pane and Molokai soils, respectively. The effect of initial moisture on sorption measurements may not be of practical importance when we consider that the average coefficient of variation of fenamiphos and fen. sulfoxide sorption determined on soils obtained from nine fields was 35% and 46%, respectively. In the degradation study, the reliability of using laboratory-generated degradation rates for fenamiphos and fen. sulfoxide to predict degradation of these nematicides under field conditions was evaluated. Field and laboratory methods of determining fenamiphos degradation were compared at six locations within two cropped pineapple fields on the Oahu Dole and Del Monte plantations: the methods were compared using first-order degradation rates and the quantity of fenamiphos residue remaining at a given time. A similar comparison with fen. sulfoxide was performed on the Del Monte field. In field experiments, nematicides were applied to insitu field cores contained in aluminum cylinders (inserted into the tilled layer of pineapple beds) at six locations per field. Laboratory experiments were performed by application of 14C-labeled nematicides to soils collected from the same locations as the field tests; treated soils were incubated under controlled temperature and moisture. On the Del Monte field, the field and laboratory degradation data were fit reasonably well by first-order kinetics. First-order degradation rates determined from laboratory and field methods were similar. Fenamiphos degradation data from the Dole field generally deviated statistically from first-order kinetics; the better statistical resolution of deviations from first-order kinetics on the Dole field was largely due to q much lower overall standard error for this field. The difference, however, between laboratory and field measured fenamiphos residues on the Dole field was within a factor of 1.4. In view of the uncertainties in degradation measurements contributed from field soil variability and analytical techniques, this differrence is tolerable. Degradation rates of fenamiphos and fen. sulfoxide determined from laboratory methods are therefore considered reliable estimates for modeling persistence of these chemicals in field soils under pineapple cultivation

Leader Reinforcement Behaviors And Employee Work Outcomes: The Mediating Role Of Leader-Member Exchange

Pimpinan adalah salah satu tajuk yang paling dikaji dalam sastera pengurusan. Leadership is one of the most widely studied topics in the management literature

National Culture and the Preference for Management Controls: An exploratory Study of the Firm- Labor Market Interface

Abstract This study uses Hofstede's taxonomy of work-related national cultural dimensions to analyze preferences for specific management controls at the interface between the organization and the external labor market. Four experiments were conducted with samples of last-semester Japanese and U.S. MBA students. Most of the results did not provide support for the four hypotheses. These findings used as the basis for suggesting potential directions for future empirical refinements and theory construction

The Effects of Management Controls and National Culture on Manufacturing Performance: an Experimental Investigation

The increasing dominance of Asian manufacturing firms in the global economy has raised an important issue: whether these firms' superior manufacturing performance is caused by their management control systems, the national culture of their employees, or the interaction of these two factors. This experimental study provides a direct test of the effects of national culture and management control system on manufacturing performance. The dimension of national culture studied was individualism ( vs collectivism )because this work-related attribute has been noted as a major difference between Asian and Western cultures. In turn, the focus on cultural individualism motivated a study of two aspects of management controls: work flow interdependence and pay interdependence. The results are consistent with cultural individualism and management controls having independent, but not interactive, effects on manufacturing performance. The potential implications of these findings and suggestions for future research are discussed

Linking Value Chain Costs To Products And Customers: Survey And Evaluation Of Large U.S. Manufacturing Firms’ Current Practices

Success in a competitive environment requires effectively selecting an optimal mix of value chain activities. Despite the fact that corporate executives need to understand the costs and benefits of supporting particular products and customers, little empirical evidence is available on how, and how well, companies are linking their value chain costs to these two cost objects. The results of this study, based on responses to a survey of 120 large U.S. manufacturing companies, indicate that firms tend to link their value chain costs to products/product lines more than to customers/customer classes. For both cost objects, most of the cost allocation bases used is volume-based. These findings suggest that while there is attention to the value chain costs, there is room for increasing the proportion of costs traced to products and customers and for expanding the use of non-volume allocation bases

An Exploratory Study on Benifits and Success Factors of Information Technology Applications

This paper aims first, to explore the extent of benefits at different levels of IT applications in developing nations have realized. Second, this paper identifies those factors and/or processes associated with relative success and failure. This study collected data from fifty-seven firms in Taiwan using the mail survey method. Based on the Venkatraman’s (1994) levels of IT applications, six archetypes were developed to measure IT implementation (the first three stages represent evolutionary levels, while the last three represent revolutionary levels). Results indicated that a majority of firms are at the evolutionary levels of IT applications but over ninety percent of sample firms advanced IT applications within a three-year time frame. Despite the transformation, respondents perceived a low degree of variation in the realized benefits from IT applications and no significant differences existed between benefits derived from evolutionary and revolutionary levels of IT applications. Exceptions to this were benefits derived from reengineering the mix of internal value chain activities and IT applications on operations. Results from regression analysis indicated that success of IT applications was best determined by behavioral and organizational variables rather than by technical variables