Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation and Function of Versatile Aerobic and Anaerobic Respiratory Metabolism in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a ubiquitously distributed opportunistic pathogen that inhabits soil and water as well as animal-, human-, and plant-host-associated environments. The ubiquity would be attributed to its very versatile energy metabolism. P. aeruginosa has a highly branched respiratory chain terminated by multiple terminal oxidases and denitrification enzymes. Five terminal oxidases for aerobic respiration have been identified in the P. aeruginosa cells. Three of them, the cbb3-1 oxidase, the cbb3-2 oxidase, and the aa3 oxidase, are cytochrome c oxidases and the other two, the bo3 oxidase and the cyanide-insensitive oxidase, are quinol oxidases. Each oxidase has a specific affinity for oxygen, efficiency of energy coupling, and tolerance to various stresses such as cyanide and reactive nitrogen species. These terminal oxidases are used differentially according to the environmental conditions. P. aeruginosa also has a complete set of the denitrification enzymes that reduce nitrate to molecular nitrogen via nitrite, nitric oxide (NO), and nitrous oxide. These nitrogen oxides function as alternative electron acceptors and enable P. aeruginosa to grow under anaerobic conditions. One of the denitrification enzymes, NO reductase, is also expected to function for detoxification of NO produced by the host immune defense system. The control of the expression of these aerobic and anaerobic respiratory enzymes would contribute to the adaptation of P. aeruginosa to a wide range of environmental conditions including in the infected hosts. Characteristics of these respiratory enzymes and the regulatory system that controls the expression of the respiratory genes in the P. aeruginosa cells are overviewed in this article.
Vulnerable regions and enterprise policy: SMEs and technological change

European integration has prompted considerable interest in the adjustment capacities of small and medium enterprises in vulnerable regions characterised by high levels of unemployment and lower than average incomes. At issue, in these circumstances, is the extent to which competitiveness can be enhanced by increased rates of technological change and by policies adopted by European and national governments. Drawing on survey data from a recently completed EU Fifth Framework study, this paper focuses upon the adjustment strategies of firms in four labour intensive industries open to global and European competition in the UK, Ireland, Greece, Spain and Italy. The results of the surveys provide econometric and statistical analyses that demonstrate the commonalities and differences apparent in small and mediumsized firms’ responses to changing market competition. We tested hypotheses having to do with the significance of firm, country and industry effects in determining the employment consequences of competitive strategies. We found that there are significant variations in firms’ responses to global competition that can be attributed to country and industry of origin. The particular variations that this paper examines are investment strategies; technology adoption; labour and technological change and the relevance and usefulness of existing regional, national and EU policy instruments.
PID-PSO control for Takagi-Sugeno Fuzzy model

In this paper, a novel design method for determining the optimal proportional-integral-derivative (PID) controller parameters of nonlinear system of Takagi-Sugeno Fuzzy model using the particle swarm optimization (PSO) algorithm is presented. This paper demonstrated in detail how to employ the PSO method to search efficiently the optimal PID controller parameters of a nonlinear system. The proposed approach had superior features, including easy implementation, stable convergence characteristic, and good computational efficiency. Fast tuning of optimum PID controller parameters yields high-quality solution. In order to assist estimating the performance of the proposed PSO-PID controller. Compared with the method of pole placement, the proposed method was indeed more efficient and robust in improving the response of a nonlinear system for Takagi-Sugeno Fuzzy model.
Investment dynamics of the Western and Central Pacific Ocean US purse seine fleet

Understanding fisher decision making in a competitive but changing market is becoming increasingly important when developing management plans for sustainable fisheries. In the Western and Central Pacific, catches of tuna by weight are dominated by the purse seine fleet. To investigate the key drivers that influence the behaviour of the US purse seine fleet operating in the complex Western Central Pacific Ocean tuna fishery, multivariate methods were applied to identify candidate predictor variables in 2 separate 7 year periods and the 14 year time series to be applied in a discrete choice multinomial model. By integrating available cost data, interest rates and other factors that were likely to influence future anticipated benefits or losses, it was possible to identify key important drivers influencing whether operators chose to enter (invest in), remain (stay and continue fishing) or exit (tie‐up for a period or remain under a different flag) the US fleet. Results show the importance of capturing the changes of the fisher dynamics over the time period. Early years show that vessel engine power was an important factor (a proxy for capital investment) in contrast to the later time period where vessel tonnage was of greater importance potentially due to fuel prices increases (cost), a drop in interest rates (financing decisions), increased revenues (net benefits) to offset the increase in costs. Fishers Willingness To Pay (WTP) estimated by the 3 models estimates increased from US$29 to US$7290 per day, which shows the perceived value placed on the fishery by fishers wanting to invest in. These models may assist fisheries managers when considering potential strategic long‐term policies for balancing licence sales, and hence revenues for pacific island nations without displacing large amounts of capacity.
DSWE: A Grid-enabled Domain Specific Workflow Engine for Aircraft MDO

Aircraft MDO (Multidisciplinary Design Optimization) needs Grid technology because of complex process and time-consuming design. Specifically, aircraft MDO can benefit from Grid computing in terms of massive computational capacity and resource sharing. However, determining how to manage aircraft MDO processes and how to effectively apply grid technology into aircraft MDO remain as problems, which address the demand of an effective domain specific workflow engine. Different previous works focus on universal workflow engines. In this paper, we propose a Grid-enabled DSWE (Domain Specific Workflow Engine) system for aircraft MDO, which highlights the requirements in aircraft MDO and provides a friendly interface for workflow construction. A practical prototype system of the DSWE has been implemented. We demonstrated the effectiveness of the Grid-enabled DSWE system from performance evaluation and testing results in the case study.
Cognitive Skills, Educational Attainment and Earnings -Evidence from the International Adult Literacy Survey

In this paper a rich and innovative dataset, the International Adult Literacy Survey, is used to examine the impact of cognitive skill/functional literacy earnings. The IALS surveys 12 OECD countries and sub-regions via a consistent questionnaire and includes a number of tests of numeracy and literacy, as well as basic labour market information. This paper examines the effect of these skills on labour market earnings for the Republic of Ireland, Northern Ireland, and for Great Britain.
Perspectives of Educators Engaged in Continuous Improvement Efforts Within A Rural Appalachian School Setting

This research study serves as an analysis of how educators in a rural Appalachian school district respond to change resulting from federal and state mandates for curriculum reform and initiatives secured through grant funding. Case study research was chosen as the methodology for this study in order to provide an intensive examination of a particular case specific to rural Appalachia. The research protocol included an on-line survey, interviews, and documentation review. The findings of this study provide evidence that systemic educational improvement can be effectively implemented in rural school districts; however, particular attention should be given to factors related to the culture of not only the schools, but also the community at large. The themes of management, collaboration, impact, and culture emerged within the framework of the Concerns Based Adoption Model and are supported by educational literature, yet the cultural element should be added to the Concerns Based Adoption Model if utilized for planning for systemic change. This study illuminates the importance of examining the cultural climate and institutional memories of any district prior to beginning any improvement activity as this may allow the culture of a district to inform the work of those leaders engaging in improvement efforts.
Design and Implementation of a Wearable ECG System

In this paper, we design and implement a wearable ECG (electrocardiogram) system with the smartphone for real-time monitoring, self-diagnosis and remote-diagnosis to the chronic heart disease patients before sudden outbreak. The smart shirt with ECG can be worn by inpatient or outpatient and monitored in real-time. Healthcare profession can access to patients' data in real time wirelessly with smartphone. Especially this system can useful for senior citizen who lives alone or has disability. Therefore, this system can be utilized for the remote medical system to assist the elderly patients as well as selftesting diagnostics or physicians to diagnose diseases of the circulatory system.
Analysis of Pattern Similarity between Choi-Williams Kernel and Born-Jordan Kernel

This paper analyzes the pattern similarity of two t ypes of kernels, Sinc kernel (i.e., Born-Jordan’s) and Choi Williams kernel (i.e., Gaussian’s). Correlation coefficients are used to characterize the dissimila rities between the two kernels. The correlation curve in t he sense of L2 between Born-Jordan kernel and ChoiWilliams kernel is carried out. The analysis result shows that the maximum correlation value is less than 0.6 . Hence, the curve may help us interpret the differen ces between the two kernels in quantitative.
Distinctive Subcellular Inhibition of Cytokine-Induced Src by Salubrinal and Fluid Flow

A non-receptor protein kinase Src plays a crucial role in fundamental cell functions such as proliferation, migration, and differentiation. While inhibition of Src is reported to contribute to chondrocyte homeostasis, its regulation at a subcellular level by chemical inhibitors and mechanical stimulation has not been fully understood. In response to inflammatory cytokines and stress to the endoplasmic reticulum (ER) that increase proteolytic activities in chondrocytes, we addressed two questions: Do cytokines such as interleukin 1 beta (IL1β) and tumor necrosis factor alpha (TNFα) induce location-dependent Src activation? Can cytokine-induced Src activation be suppressed by chemically alleviating ER stress or by applying fluid flow? Using live cell imaging with two Src biosensors (i.e., cytosolic, and plasma membrane-bound biosensors) for a fluorescence resonance energy transfer (FRET) technique, we determined cytosolic Src activity as well as membrane-bound Src activity in C28/I2 human chondrocytes. In response to TNFα and IL1β, both cytosolic and plasma membrane-bound Src proteins were activated, but activation in the cytosol occurred earlier than that in the plasma membrane. Treatment with salubrinal or guanabenz, two chemical agents that attenuate ER stress, significantly decreased cytokine-induced Src activities in the cytosol, but not in the plasma membrane. In contrast, fluid flow reduced Src activities in the plasma membrane, but not in the cytosol. Collectively, the results demonstrate that Src activity is differentially regulated by salubrinal/guanabenz and fluid flow in the cytosol and plasma membrane.
Human coordination dynamics with heterogeneous robots in a team

Robots with different behaviors will be a part of human-robot teams in the future and will impact the overall interaction patterns of teams. In this paper, we investigate how the presence of robots affect the coordination of human-robot teams when a single robot or multiple robots with the same or different behavior are the part of that team. We compare two different event anticipation methods for robots, and then extend those findings to assess its effects on the group coordination. Our results indicate that humans are significantly more synchronous as a group when they danced alone than with the robots. We also find that an addition of a robot with a different anticipation algorithm to a single robot team significantly reduces the group synchrony. This work will prove useful for the robotics community to build more fluent human-robot interactions in the future.
Mechanism of helicase translocation along nucleic acid

In cells, helicase translocation along nucleic acid is essential for many biological processes. However, so far, the mechanism of this translocation is not fully understood. Recent studies show that helicase might translocate through two processes, active process and passive process, with different translocation rate. In this study, a model including such two processes is presented. In which, each of these two processes consists of two sub-processes, chemical sub-process in which needed translocation factors are attached, and mechanochemical sub-process in which helicase makes a forward translocation step. Helicase can switch stochastically between these two processes with external force dependent rates. By this model, ribosome translocation along message RNA is detailed discussed. We found that, with the increase of external force, the mean translocation rate of ribosome increases from one lower limit to one upper limit, and both of these two limits increase with concentrations of the translocation factors. Under high external force, ribosome translocates mainly through active process. At saturating concentrations of translocation factors, the translocation is governed by mechanochemical sub-processes.
Introduction of Unleaded Gasoline in the EU Countries

This paper considers the phase-out process of leaded gasoline consumption in EU countries during 1985-1995. Leaded and unleaded gasoline demand models are specified and estimated assuming static as well as dynamic structures. The demand for gasoline is a function of prices, policy and other characteristic variables. The models include the features of the usual error component models. Different characteristics of the countries studied are used to compare and to explain the heterogeneity in the phase-out process. The effectiveness of various marketbased policy instruments in the adjustment towards desired unleaded gasoline consumption is analyzed. This is important in identificatio n of efficient policy instruments that can be implemented in achieving a desired reduction in consumption of leaded gasoline. The results are expected to emphasize the importance of studying specific characteristics of countries before implementing policy instrument.
A practical simulation method for generating phase noise of oscillators

In various electronic systems or equipment, phase noise has important research value as an important indicator existing and seriously affecting its performance. Thus it is significance to propose a correct and efficient simulation method for generating phase noise. In this paper, an effective and practical simulation method is put forward to generate the phase noise of oscillators built on the work and insight of predecessors. This novel method is described in detail and focuses on the generation processes of phase noise. In the novel method, FIR shaping filters are used to generate power-law noise components which are further processed to obtain the phase noise data consistent with specified noise coefficients in time domain, and the method is also validated in the frequency domain. All in all, the paper provides a theoretical basis and implementation method for the study of short-term frequency stability of frequency sources.
Appendix C Virtual Physical Link ( VPL ) Ontology to Support Virtual Models Linked with Physical Components

This appendix is a supplement to Paper I and Paper II and demonstrates how an ontology to support virtual models linked with physical components in construction can be developed. Ontology development methods, tools and recommendations are described and demonstrated by initialising the development of the ontology: “Virtual Physical Link”. It is also the author’s expectation that this appendix will inspire researchers and developers in the development of future ontologies for the construction industry (e.g. classification systems) to have focus on modern information and communication technology (ICT) usage rather than looking backwards for solutions to support outdated information handling methods.
A Review on Security Enhancement in WSN Using Neural Network

This paper presents an application of a neural netw ork in wireless sensor network to enhance the security. A multilayer perceptron (MLP) based media access cont rol protocol (MAC) can be used in wireless sensor netwo rk (WSN) against the denial-of-service (DOS) attacks. The MLP enhances the security of a WSN by constantly monitoring the parameters that exhibit unusual vari ations in case of DOS attack. The MLP shuts down the MAC laye r and the physical layer of the sensor node when the suspicion factor appears or the output of the MLP e xce ds a threshold level. Back propagation and Hopfield are us d for training the MLP. Hopfield network (HN) uses associ ative memory to store the pattern. The HN itself is robus t since it performs pattern completion in case of missing data and pattern correction in case of corrupted data due to the association ability.
Investigating Power-Reduction for a Reconfigurable Sensor Interface

The power consumption of different implementations of a sensor interface utilized for wireless sensor network nodes are investigated. Most sensor network nodes use a CPU to implement the main functionality in software. This maintains flexibility compared with a pure ASIC implementation. Unfortunately, to utilize the CPU for simple tasks as periodically controlling the data acquisition proved expensive in terms of energy consumption due to the wakeupoverhead and several waiting periods. As an alternative a special reconfigurable peripheral block is introduced into the WSN SoC. It is responsible for these measurements while the CPU stays in an inactive “sleep mode”. It is only activated if further processing is required (e.g. transmission of a notification packet via the wireless network if the measurement value has changed). A huge reduction of power consumption by a factor of 30 was achieved. The objective is to reduce power consumption while maintaining a high degree of flexibility for the implemented applications.1
Glycoprotein Hyposialylation Gives Rise to a Nephrotic-Like Syndrome That Is Prevented by Sialic Acid Administration in GNE V572L Point-Mutant Mice

Mutations in the key enzyme of sialic acid biosynthesis, UDP-N-acetylglucosamine 2-epimerase/N-acetyl-mannosamine kinase, result in distal myopathy with rimmed vacuoles (DMRV)/hereditary inclusion body myopathy (HIBM) in humans. Sialic acid is an acidic monosaccharide that modifies non-reducing terminal carbohydrate chains on glycoproteins and glycolipids, and it plays an important role in cellular adhesions and interactions. In this study, we generated mice with a V572L point mutation in the GNE kinase domain. Unexpectedly, these mutant mice had no apparent myopathies or motor dysfunctions. However, they had a short lifespan and exhibited renal impairment with massive albuminuria. Histological analysis showed enlarged glomeruli with mesangial matrix deposition, leading to glomerulosclerosis and abnormal podocyte foot process morphologies in the kidneys. Glycan analysis using several lectins revealed glomerular epithelial cell hyposialylation, particularly the hyposialylation of podocalyxin, which is one of important molecules for the glomerular filtration barrier. Administering Neu5Ac to the mutant mice from embryonic stages significantly suppressed the albuminuria and renal pathology, and partially recovered the glomerular glycoprotein sialylation. These findings suggest that the nephrotic-like syndrome observed in these mutant mice resulted from impaired glomerular filtration due to the hyposialylation of podocyte glycoproteins, including podocalyxin. Furthermore, it was possible to prevent the nephrotic-like disease in these mice by beginning Neu5Ac treatment during gestation.
Symbiosis in the Intranet: How Document Retrieval Benefits from Database Information

The enterprise information space is split in two hemispheres. Documents contain unstructured or semistructured information; structured information is stored in databases. As regards the content, both kinds of information are complementary parts. However, enterprise information systems usually focus on one part, only. Our approach improves document retrieval in the intranet by exploiting the enterprise’s databases. In particular, we exploit database information to describe the context of documents and exploit this context to enhance common full text search. In this paper, we show how to model and compute document context and present results on runtime performance.
Identifying differentially expressed genes using false discovery rate controlling procedures

MOTIVATION DNA microarrays have recently been used for the purpose of monitoring expression levels of thousands of genes simultaneously and identifying those genes that are differentially expressed. The probability that a false identification (type I error) is committed can increase sharply when the number of tested genes gets large. Correlation between the test statistics attributed to gene co-regulation and dependency in the measurement errors of the gene expression levels further complicates the problem. In this paper we address this very large multiplicity problem by adopting the false discovery rate (FDR) controlling approach. In order to address the dependency problem, we present three resampling-based FDR controlling procedures, that account for the test statistics distribution, and compare their performance to that of the naïve application of the linear step-up procedure in Benjamini and Hochberg (1995). The procedures are studied using simulated microarray data, and their performance is examined relative to their ease of implementation. RESULTS Comparative simulation analysis shows that all four FDR controlling procedures control the FDR at the desired level, and retain substantially more power then the family-wise error rate controlling procedures. In terms of power, using resampling of the marginal distribution of each test statistics substantially improves the performance over the naïve one. The highest power is achieved, at the expense of a more sophisticated algorithm, by the resampling-based procedures that resample the joint distribution of the test statistics and estimate the level of FDR control. AVAILABILITY An R program that adjusts p-values using FDR controlling procedures is freely available over the Internet at www.math.tau.ac. il/~ybenja.