Optimizing I/O cost and managing memory for composition vector method based on correlation matrix calculation in bioinformatics

The generation of a correlation matrix for set of genomic sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. Each sequence may be millions of bases long and there may be thousands of such sequences which we wish to compare, so not all sequences may fit into main memory at the same time. Each sequence needs to be compared with every other sequence, so we will generally need to page some sequences in and out more than once. In order to minimize execution time we need to minimize this I/O. This paper develops an approach for faster and scalable computing of large-size correlation matrices through the maximal exploitation of available memory and reducing the number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different bioinformatics problems with different correlation matrix sizes. The significant performance improvement of the approach over previous work is demonstrated through benchmark examples.

An improved method for undertaking limiting dilution assays for in vitro cloning of Plasmodium falciparum parasites

Background Obtaining single parasite clones is required for many techniques in malaria research. Cloning by limiting dilution using microscopy-based assessment for parasite growth is an arduous and labor-intensive process. An alternative method for the detection of parasite growth in limiting dilution assays is using a commercial ELISA histidine-rich protein II (HRP2) detection kit. Methods Detection of parasite growth was undertaken using HRP2 ELISA and compared to thick film microscopy. An HRP2 protein standard was used to determine the detection threshold of the HRP2 ELISA assay, and a HRP2 release model was used to extrapolate the amount of parasite growth required for a positive result. Results The HRP2 ELISA was more sensitive than microscopy for detecting parasite growth. The minimum level of HRP2 protein detection of the ELISA was 0.11ng/ml. Modeling of HRP2 release determined that 2,116 parasites are required to complete a full erythrocytic cycle to produce sufficient HRP2 to be detected by the ELISA. Under standard culture conditions this number of parasites is likely to be reached between 8 to 14 days of culture. Conclusions This method provides an accurate and simple way for the detection of parasite growth in limiting dilution assays, reducing time and resources required in traditional methods. Furthermore the method uses spent culture media instead of the parasite-infected red blood cells, enabling culture to continue.

Synthesis of diketopyrrolopyrrole based copolymers via the direct arylation method for p-channel and ambipolar OFETs

In this paper, we have synthesized two novel diketopyrrolopyrrole (DPP) based donor-acceptor (D-A) copolymers poly{3,6-dithiophene-2-yl-2,5-di(2-octyl)- pyrrolo[3,4-c]pyrrole-1,4-dione-alt-1,5-bis(dodecyloxy)naphthalene} (PDPPT-NAP) and poly{3,6-dithiophene-2-yl-2,5-di(2-butyldecyl)-pyrrolo[3,4-c]pyrrole-1,4- dione-alt-2-dodecyl-2H-benzo[d][1,2,3]triazole} (PDPPT-BTRZ) via direct arylation organometallic coupling. Both copolymers contain a common electron withdrawing DPP building block which is combined with electron donating alkoxy naphthalene and electron withdrawing alkyl-triazole comonomers. The number average molecular weight (Mn) determined by gel permeation chromatography (GPC) for polymer PDPPT-NAP is around 23 400 g mol-1 whereas for polymer PDPPT-BTRZ it is 18 600 g mol-1. The solid state absorption spectra of these copolymers show a wide range of absorption from 400 nm to 1000 nm with optical band gaps calculated from absorption cut off values in the range of 1.45-1.30 eV. The HOMO values determined for PDPPT-NAP and PDPPT-BTRZ copolymers from photoelectron spectroscopy in air (PESA) data are 5.15 eV and 5.25 eV respectively. These polymers exhibit promising p-channel and ambipolar behaviour when used as an active layer in organic thin-film transistor (OTFT) devices. The highest hole mobility measured for polymer PDPPT-NAP is around 0.0046 cm2 V-1 s-1 whereas the best ambipolar performance was calculated for PDPPT-BTRZ with a hole and electron mobility of 0.01 cm2 V-1 s-1 and 0.006 cm2 V-1 s-1.

A new method of interfacing battery/supercapacitor energy storage systems for distributed energy sources

Battery-supercapacitor hybrid energy storage systems can achieve better power and energy performances compared to their individual use. These hybrid systems require separate dc-dc converters, or at least one dc-dc converter for the supercapacitor bank, to connect them to the dc-link of the grid connecting inverter. However, the use of such dc-dc converters introduces additional cost and power losses. Therefore, the possibility of direct connection of energy storage systems, to the dc-link of a diode clamped 3-level inverter is investigated in this paper. Even though the proposed topology does not use dc-dc converters, a vector selection method is proposed to produce a similar control flexibility that is found in the separate dc-dc converter topology. The major issue with the proposed system is the imminent imbalance of the neutral point potential. A PWM technique with modified carriers is used to solve this problem. Simulations are carried out using MATLAB/SIMULINK to verify the efficacy of the proposed system.

The effect of trade openness on deforestation: empirical analysis for 142 countries

This study explores the effect of trade openness on deforestation. Previous studies do not find a clear effect of trade openness on deforestation. We use updated data on the annual rate of deforestation for 142 countries from 1990 to 2003, treat trade and income as endogenous, and take into consideration an adjustment process by applying a dynamic model. We find that an increase in trade openness increases deforestation for non-OECD countries while slowing down deforestation for OECD countries. There is a possibility that both capital-labor and environmental-regulation effects have a negative impact on deforestation in developing countries, whereas the opposite holds in developed countries. © 2012 Springer Japan.

A novel dc-link voltage regulation method for single source hybrid multilevel inverters

This paper presents a novel dc-link voltage regulation technique for a hybrid inverter system formed by cascading two 3-level inverters. The two inverters are named as “bulk inverter” and “conditioning inverter”. For the hybrid system to act as a nine level inverter, conditioning inverter dc link voltage should be maintained at one third of the bulk inverter dc link voltage. Since the conditioning inverter is energized by two series connected capacitors, dc-link voltage regulation should be carried out by controlling the capacitor charging/discharging times. A detailed analysis of conditioning inverter capacitor charging/discharging process and a simplified general rule, derived from the analysis, are presented in this paper. Time domain simulations were carried out to demonstrate efficacy of the proposed method on regulating the conditioning inverter dc-link voltage under various operating conditions.

Decomposition analysis of air pollution abatement in China: empirical study for ten industrial sectors from 1998 to 2009

This study analyzes the management of air pollutant substance in Chinese industrial sectors from 1998 to 2009. Decomposition analysis applying the logarithmic mean divisia index is used to analyze changes in emissions of air pollutants with a focus on the following five factors: coal pollution intensity (CPI), end-of-pipe treatment (EOP), the energy mix (EM), productive efficiency change (EFF), and production scale changes (PSC). Three pollutants are the main focus of this study: sulfur dioxide (SO2), dust, and soot. The novelty of this paper is focusing on the impact of the elimination policy on air pollution management in China by type of industry using the scale merit effect for pollution abatement technology change. First, the increase in SO2 emissions from Chinese industrial sectors because of the increase in the production scale is demonstrated. However, the EOP equipment that induced this change and improvements in energy efficiency has prevented an increase in SO2 emissions that is commensurate with the increase in production. Second, soot emissions were successfully reduced and controlled in all industries except the steel industry between 1998 and 2009, even though the production scale expanded for these industries. This reduction was achieved through improvements in EOP technology and in energy efficiency. Dust emissions decreased by nearly 65% between 1998 and 2009 in the Chinese industrial sectors. This successful reduction in emissions was achieved by implementing EOP technology and pollution prevention activities during the production processes, especially in the cement industry. Finally, pollution prevention in the cement industry is shown to result from production technology development rather than scale merit. © 2013 Elsevier Ltd. All rights reserved.

Which industry is greener? An empirical study of nine industries in OECD countries

This study analyzed the relationship between the CO2 emissions of different industries and economic growth in OECD countries from 1970 to 2005. We tested an environmental Kuznets curve (EKC) hypothesis and found that total CO2 emissions from nine industries show an N-shaped trend instead of an inverted U or monotonic increasing trend with increasing income. The EKC hypothesis for sector-level CO2 emissions was supported in the (1) paper, pulp, and printing industry; (2) wood and wood products industry; and (3) construction industry. We also found that emissions from coal and oil increase with economic growth in the steel and construction industries. In addition, the non-metallic minerals, machinery, and transport equipment industries tend to have increased emissions from oil and electricity with economic growth. Finally, the EKC turning point and the relationship between GDP per capita and sectoral CO2 emissions differ among industries according to the fuel type used. Therefore, environmental policies for CO2 reduction must consider these differences in industrial characteristics. © 2013 Elsevier Ltd.

Corporate Environmental and Economic Performance of Japanese Manufacturing Firms: Empirical Study for Sustainable Development

This study examines the relationship between environmental performance and economic performance in Japanese manufacturing firms. The environmental performance indicators include CO2 emissions and the aggregate toxic risk associated with chemical emissions relative to sales. Return on assets (ROA) is used as an indicator of economic performance. We demonstrate that there is a significant inverted U-shaped relationship between ROA and environmental performance calculated by aggregated toxic risk. We also find that the environmental performance increases ROA through both returns on sales and improved capital turnover. However, we observe a significant positive relationship between financial performance and environmental performance based on CO2 emissions. These findings may provide evidence for the consequences of firms' environmental behavior and sustainable development. © 2012 John Wiley & Sons, Ltd and ERP Environment.

Environmental information provision, market valuation, and firm incentives: An empirical study of the Japanese PRTR system

The environmental performance of a listed firm could affect its level of investment in pollution prevention and its access to financial markets. Previous studies using Tobin's q that explore market response to environmental performance do not distinguish between the impact of performance on investment and market response, which may mislead conclusions. To overcome this problem, we simultaneously estimate the functions of the intangible asset, the replacement cost, and the toxic chemical risk. We find that the Japanese financial market does not value risk associated with toxic chemical releases. Nevertheless, even without market valuation, firms increase investment to reduce pollution. © 2010 by the Board of Regents of the University of Wisconsin System.

Total factor productivity growth and convergence in the petroleum industry : empirical analysis testing for convexity

While economic theory acknowledges that some features of technology (e.g., indivisibilities, economies of scale and specialization) can fundamentally violate the traditional convexity assumption, almost all empirical studies accept the convexity property on faith. In this contribution, we apply two alternative flexible production technologies to measure total factor productivity growth and test the significance of the convexity axiom using a nonparametric test of closeness between unknown distributions. Based on unique field level data on the petroleum industry, the empirical results reveal significant differences, indicating that this production technology is most likely non-convex. Furthermore, we also show the impact of convexity on answers to traditional convergence questions in the productivity growth literature.

Productivity measures and effects from subsidies and trade : an empirical analysis for Japan's forestry

Several techniques have been proposed in the literature to measure productivity. While allowing for inefficiency of the production unit, we provide a methodological comparison of alternative approaches to measure total factor productivity. This article evaluates the effects of unintended policy outcomes such as government subsidies and foreign trade. Empirically, we analyse the forest productivity of timber in Japan by using panel data on 46 regions. The results suggest substantial variation in productivity between these two techniques although average trends are similar. We find that subsidies impede competition since the government is ready to rescue a loss-making firm with subsidies rather than allow it to close. In contrast, trade is shown to have positive effects on productivity.

A review selection method using product feature taxonomy

As of today, online reviews have become more and more important in decision making process. In recent years, the problem of identifying useful reviews for users has attracted significant attentions. For instance, in order to select reviews that focus on a particular feature, researchers proposed a method which extracts all associated words of this feature as the relevant information to evaluate and find appropriate reviews. However, the extraction of associated words is not that accurate due to the noise in free review text, and this affects the overall performance negatively. In this paper, we propose a method to select reviews according to a given feature by using a review model generated based upon a domain ontology called product feature taxonomy. The proposed review model provides relevant information about the hierarchical relationships of the features in the review which captures the review characteristics accurately. Our experiment results based on real world review dataset show that our approach is able to improve the review selection performance according to the given criteria effectively.

Determinants of plant performance dynamics : empirical analysis of the manufacturing sector in Indonesia, 1990-2000

We identify determinants of plant dynamics and find their differences before, during, and after the Asian financial crisis. The results show that the distinction of the crisis is important and the effects of the crisis do not seem to persist after 1998. Furthermore, we reject Gibrat's law as the right functional form to describe plant growth. We are not able to support empirically the theoretical results that smaller and efficient plants tend to grow faster than larger and inefficient plants with the exception of the crisis period. The results reflect that there was a trickle down effect of economic development.

Adoption of accountable-eHealth systems by future healthcare professionals: An empirical research model based on the Australian context

This paper provides a first look at the acceptance of Accountable-eHealth systems, a new genre of eHealth systems, designed to manage information privacy concerns that hinder the proliferation of eHealth. The underlying concept of AeH systems is appropriate use of information through after-the-fact accountability for intentional misuse of information by healthcare professionals. An online questionnaire survey was utilised for data collection from three educational institutions in Queensland, Australia. A total of 23 hypothesis relating to 9 constructs were tested using a structural equation modelling technique. A total of 334 valid responses were received. The cohort consisted of medical, nursing and other health related students studying at various levels in both undergraduate and postgraduate courses. The hypothesis testing disproved 7 hypotheses. The empirical research model developed was capable of predicting 47.3% of healthcare professionals’ perceived intention to use AeH systems. A validation of the model with a wider survey cohort would be useful to confirm the current findings.