Miracle-dz/UniFAR-FTUs huggingface dataset:
Object co-location and memory reuse for Java programs

We introduce a new memory management system, STEMA, which can improve the execution time of Java programs. STEMA detects prolific types on-the-fly and co-locates their objects in a special memory space which supports reuse of memory. We argue and show that memory reuse and co-location of prolific objects can result in improved cache locality, reduced memory fragmentation, reduced GC time, and faster object allocation. We evaluate STEMA using 16 benchmarks. Experimental results show that STEMA performs 2.7%, 4.0%, and 8.2% on average better than MarkSweep, CopyMS, and SemiSpace.
Overproduction of tyrosyl-tRNA synthetase is toxic to Escherichia coli: a genetic analysis

The tyrS genes from Escherichia coli and Bacillus stearothermophilus were toxic to E. coli when they were carried by plasmids with very high copy numbers (pEMBL8 and pEMBL9). We quantified this effect by comparing the efficiencies of plating of E. coli derivatives harboring recombinant plasmids in various experimental conditions. The toxicity was apparent at both 30 and 37 degrees C. It increased with the growth temperature, the strength of the tyrS promoter, and the copy number of the plasmidic vector. Two- to threefold enhancement of tyrS expression raised the toxicity 300-fold. Point mutations in tyrS that prevent interaction between its product, tyrosyl-tRNA synthetase, and tRNA(Tyr) but do not alter the rate of formation of tyrosyl-adenylate abolished the toxicity. Thus, the toxic effect was due to high cellular levels of synthetase activity. At 30 degrees C, the cellular concentration of tyrosyl-tRNA synthetase reached 55% of that of soluble proteins and led to decreased beta-galactosidase stability. We discuss possible causes of this toxic effect and describe its applications to the study of the recognition and interaction between the synthetase and tRNA(Tyr).
An Ultra-wideband Monopole Antenna of Small Size

Ultra-wideband antennas with omni-directional coverage have an increasing demand for the applications of e.g. wireless communication services. Most of these applications require an antenna of compact size and low profile. Compared with spheroidal, biconical, spiral or discone types of antennas which have been used for ultra wideband (UWB) systems, planar monopole antennas [1-3] have many advantages such as wide impedance bandwidth, omni-directional radiation pattern, compact and simple structure, low cost and ease of fabrication. However, a traditional monopole antenna usually has the dimension of about quarter wavelength at the low frequency band in order to radiate efficiently [1].
Comparison of logistic regression and neural network models in predicting the outcome of biopsy in breast cancer from MRI findings

Background: We designed an algorithmic model based on the logistic regression analysis and a non-algorithmic model based on the Artificial Neural Network (ANN). Materials and methods: The ability of these models was compared together in clinical application to differentiate malignant from benign breast tumors in a study group of 161 patients' records. Each patient’s record consisted of 6 subjective features extracted from MRI appearance. These findings were encoded as features for an ANN as well as a logistic regression model (LRM) to predict biopsy outcome. After both models had been trained perfectly on samples (n=100), the validation samples (n=61) were presented to the trained network as well as the established LRMs. Finally, the diagnostic performance of models were compared to that of the radiologist in terms of sensitivity, specificity and accuracy, using receiver operating characteristic curve (ROC) analysis. Results: The average output of the ANN yielded a perfect sensitivity (98%) and high accuracy (90%) similar to that one of an expert radiologist (96% and 92%) while specificity was smaller than that (67% verses 80%). The output of the LRM using significant features showed improvement in specificity from 60% for the LRM using all features to 93% for the reduced logistic regression model, keeping the accuracy around 90%. Conclusion: Results show that ANN and LRM prove the relationship between extracted morphological features and biopsy results. Using statistically significant variables reduced LRM outperformed of ANN with remarkable specificity while keeping high sensitivity is achieved. Iran. J. Radiat. Res., 2004; 1(4): 217-228
Enhanced write performance of a 64 Mb phase-change random access memory

A 1.8 V 64 Mb phase-change RAM with improved write performance is fabricated in a 0.12 /spl mu/m CMOS technology. The improvement of RESET and SET distributions is based on cell current regulation and multiple step-down pulse generators. The read access time and SET-write time are 68 ns and 180 ns respectively.
MiR-181b: new perspective to evaluate disease progression in chronic lymphocytic leukemia

Over the past decades numerous markers of the tumor burden have been discovered in chronic lymphocytic leukemia (CLL). Among these, the microRNAs seem to have a promising role. The development and validation of miRNAs as biomarkers should have significant impact in improving early cancer detection and diagnosis, enhancing therapeutic success, and increasing the life expectancy of patients. We identified miR-181b as a biomarker for the progression of this disease from indolent to aggressive. For this study we used sequential samples from patients with either progressive or stable course of the illness. Here, we discuss more extensively this issue by adding novel findings and introducing a novel approach for monitoring CLL patients.
Role of Low Energy Expenditure and Sitting in Obesity, Metabolic Syndrome, Type 2 Diabetes, and Cardiovascular Disease

It is not uncommon for people to spend one-half of their waking day sitting, with relatively idle muscles. The other half of the day includes the often large volume of nonexercise physical activity. Given the increasing pace of technological change in domestic, community, and workplace environments, modern humans may still not have reached the historical pinnacle of physical inactivity, even in cohorts where people already do not perform exercise. Our purpose here is to examine the role of sedentary behaviors, especially sitting, on mortality, cardiovascular disease, type 2 diabetes, metabolic syndrome risk factors, and obesity. Recent observational epidemiological studies strongly suggest that daily sitting time or low nonexercise activity levels may have a significant direct relationship with each of these medical concerns. There is now a need for studies to differentiate between the potentially unique molecular, physiologic, and clinical effects of too much sitting (inactivity physiology) separate from the responses caused by structured exercise (exercise physiology). In theory, this may be in part because nonexercise activity thermogenesis is generally a much greater component of total energy expenditure than exercise or because any type of brief, yet frequent, muscular contraction throughout the day may be necessary to short-circuit unhealthy molecular signals causing metabolic diseases. One of the first series of controlled laboratory studies providing translational evidence for a molecular reason to maintain high levels of daily low-intensity and intermittent activity came from examinations of the cellular regulation of skeletal muscle lipoprotein lipase (LPL) (a protein important for controlling plasma triglyceride catabolism, HDL cholesterol, and other metabolic risk factors). Experimentally reducing normal spontaneous standing and ambulatory time had a much greater effect on LPL regulation than adding vigorous exercise training on top of the normal level of nonexercise activity. Those studies also found that inactivity initiated unique cellular processes that were qualitatively different from the exercise responses. In summary, there is an emergence of inactivity physiology studies. These are beginning to raise a new concern with potentially major clinical and public health significance: the average nonexercising person may become even more metabolically unfit in the coming years if they sit too much, thereby limiting the normally high volume of intermittent nonexercise physical activity in everyday life. Thus, if the inactivity physiology paradigm is proven to be true, the dire concern for the future may rest with growing numbers of people unaware of the potential insidious dangers of sitting too much and who are not taking advantage of the benefits of maintaining nonexercise activity throughout much of the day.
Regulation of Adenosine Receptor Subtypes during Cultivation of Human Monocytes: Role of Receptors in Preventing Lipopolysaccharide-Triggered Respiratory Burst

ABSTRACT Adenosine is a potent anti-inflammatory agent that modulates the function of cells involved in the inflammatory response. Here we show that it inhibits lipopolysaccharide (LPS)-induced formation of reactive oxygen intermediates (ROI) in both freshly isolated and cultured human monocytes. Blocking of adenosine uptake and inactivation of the adenosine-degrading enzyme adenosine deaminase enhanced the inhibitory action of adenosine, indicating that both pathways regulate the extracellular adenosine concentration. Adenosine-mediated inhibition could be reversed by XAC (xanthine amine congener), an antagonist of the adenosine receptor A2A, and MRS 1220 {N-9-chloro-2-(2-furanyl)[1, 2, 4]-triazolo[1,5-c]quinazolin-5-benzeneacetamide}, an A3 receptor antagonist, in both cell populations, while DPCPX (1,3-dipropyl-8-cyclopentylxanthine), an A1 receptor antagonist, had no effect. Similar to what was seen with adenosine, CGS 21680, an A2A and A3 receptor agonist, and IB-MECA, a nonselective A1 and A3 receptor agonist, dose dependently prevented ROI formation, indicating the involvement of A3 and probably also A2A in the suppressive effect of adenosine. Pretreatment of monocytes with adenosine did not lead to changes in the LPS-induced increase in intracellular calcium levels ([Ca2+]i). Thus, participation of [Ca2+]i in the action of adenosine seems unlikely. The adenosine-mediated suppression of ROI production was found to be more pronounced when monocytes were cultured for 18 h, a time point at which changes in the mRNA expression of adenosine receptors were observed. Most prominent was the increase in the A2A receptor mRNA. These data demonstrate that cultivation of monocytes is accompanied by changes in the inhibitory action of adenosine mediated by A3 and probably also the A2A receptor and that regulation of adenosine receptors is an integral part of the monocyte differentiation program.
Initial Myocardial Adjustments to Brief Periods of Ischemia and Reperfusion in the Conscious Dog

The changes in left ventricular (LV) dynamics induced by brief periods of ischemia (100 seconds) and subsequent reperfusion were analyzed in conscious dogs. Global LV ischemia, induced by partially occluding the left main coronary artery, reduced LV flow homogeneously and impaired LV function as reflected by decreases in LV stroke “work” (89 ± 4% M ± SE), systolic shortening (72 ± 4%), velocity of shortening (56 ± 6%), LV systolic pressure (34 ± 5%), and dP/dt (59 ± 6%). Regional LV ischemia, induced by occluding either the left circumflex or anterior descending coronary artery completely, reduced flow to the ischemic segment (82 ± 3%) while decreasing segment work (96 ± 5%), shortening (82 ± 3%), and velocity of shortening (70 ± 5%), with minimal depression of overall LV function. In both groups the extent of shortening was reduced more rapidly and greater (P < 0.01) than shortening velocity. Moreover, with localized ischemia, segment work was reduced more (P < 0.01) than shortening. With reperfusion, a transient overshoot in function above preischemic control levels was observed in both groups (global work increased by 60 ± 12% and regional work by 28 ± 4% above control). This overshoot was not dependent on adrenergic mechanisms, but was prevented by inhibiting reactive hyperemia. Thus myocardial ischemia induces a dissociation between extent and rate of yocardial shortening. A further dissociation between shortening and work is apparent with regional ischemia. After reperfusion there is a transient overshoot in function which appears to be dependent upon the associated reactive hyperemia.
Analysis of Lsm1p and Lsm8p domains in the cellular localization of Lsm complexes in budding yeast

In eukaryotes, two heteroheptameric Sm‐like (Lsm) complexes that differ by a single subunit localize to different cellular compartments and have distinct functions in RNA metabolism. The cytoplasmic Lsm1–7p complex promotes mRNA decapping and localizes to processing bodies, whereas the Lsm2–8p complex takes part in a variety of nuclear RNA processing events. The structural features that determine their different functions and localizations are not known. Here, we analyse a range of mutant and hybrid Lsm1 and Lsm8 proteins, shedding light on the relative importance of their various domains in determining their localization and ability to support growth. Although no single domain is either essential or sufficient for cellular localization, the Lsm1p N‐terminus may act as part of a nuclear exclusion signal for Lsm1–7p, and the shorter Lsm8p N‐terminus contributes to nuclear accumulation of Lsm2–8p. The C‐terminal regions seem to play a secondary role in determining localization, with little or no contribution coming from the central Sm domains. The essential Lsm8 protein is remarkably resistant to mutation in terms of supporting viability, whereas Lsm1p appears more sensitive. These findings contribute to our understanding of how two very similar protein complexes can have different properties.
Microbial Fuel Cell Sensors for Water and Wastewater Monitoring

Microbial fuel cells (MFCs) use bacteria to convert chemical energy in organic substrate to electrical energy. MFC biosensoric capabilities are based on its ability to detect a change in current or voltage caused by introduction of an analyte. The operating principle is the linear relationship between analyte concentration and current or voltage output in the biosensor. The objective of this review is to provide an overview of the application of MFC biosensors for water and wastewater monitoring through biological/chemical oxygen demand (BOD/COD) or toxicity. While most reviews focus on operating principles and designs/configurations of MFC biosensors, this review also covers microbial consortium, current generation mechanisms and performance indicators. Factors affecting operation and challenges of the technology are also discussed. MFC biosensors have been widely investigated because of their simple architecture, cost effective construction, and potential selfsustaining power source. An efficient MFC biosensor must be capable of rapid and precise in-situ monitoring of a target compound, have long operational stability with low maintenance requirements and quick recovery after sudden disturbance. MFC biosensor performance is limited by several factors including electron transfer at the anode, substrate concentration, internal resistance of the system and environmental variables (i.e. temperature and pH). These limitations could be minimized by improving the reactor materials, design and operation. However, practical applications have proven that improving one factor does not necessarily result in an overall improvement
Providing fairness on shared-memory multiprocessors via process scheduling

Competition for shared memory resources on multiprocessors is the most dominant cause for slowing down applications and makes their performance varies unpredictably. It exacerbates the need for Quality of Service (QoS) on such systems. In this paper, we propose a fair-progress process scheduling (FPS) policy to improve system fairness. Its strategy is to force the equally-weighted applications to have the same amount of slowdown when they run concurrently. The basic approach is to monitor the progress of all applications at runtime. When we find an application suffered more slowdown and accumulated less effective work than others, we allocate more CPU time to give it a better parity. Our policy also allows different weights to different threads, and provides an effective and robust tuner that allows the OS to freely make tradeoffs between system fairness and higher throughput. Evaluation results show that FPS can significantly improve system fairness by an average of 53.5% and 65.0% on a 4-core processor with a private cache and a 4-core processor with a shared cache, respectively. The penalty is about 1.1% and 1.6% of the system throughput. For memory-intensive workloads, FPS also improves system fairness by an average of 45.2% and 21.1% on 4-core and 8-core system respectively at the expense of a throughput loss of about 2%.
The Emperor's New Clothes: Redressing Digital Business Ecosystem Design

While digital business ecosystem is emerging as a paradigm in next generation of system development and business servicing models, the design goal has not changed. The aim is still about achieving interoperability - the convergence of ICT integration, business processes and human interaction into an optimised model for not just digitalising enterprises' business servicing but maximising competitive advantage. Business researchers, such as Hill, Prahalad, Hamel, Miller, Eisenstat and Foote, are recognising the importance of using enterprise architecture methodologies in bringing together people, process and ICT resources and their capabilities to create core competencies for strategic advantage. In light of this recognition, there is value in incorporating EA governance in DBE development. Another value add to DBE development is using emerging ontology methodologies in defining DBE knowledge structures. Ontology is the study and conceptualisation of domain knowledge based on agreements of formal methods and product frameworks. In DBE development, ontology methodologies can be used to foster social and technology semantic knowledge sharing in DBE project management and SDLC workflows, and DBE product designs through using open standards in DBE data modelling. One such ontology methodology that fulfils these two role requirements is the MSPM ontology methodology, a Curtin University research product nearing completion. The MSPM ontology methodology can be potentially extended and exploited for future DBE research and development.
Chloroplast evolution, structure and functions

In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism.
ARC-H: uniform CPU scheduling for heterogeneous services

Extending our work on adaptive rate-controlled scheduling, we present a novel CPU scheduler for heterogeneous applications running on general purpose computers. Our scheduler can effectively support diverse application requirements without resorting to scheduling algorithms of diverse types. Rather it employs uniform rate-based sharing, and application heterogeneity is satisfied by partitioning CPU capacity into service classes, each with a different criterion for admission control. As a result, we are able to provide at once guaranteed performance, flexible allocation of rates with excellent scalability, as well as intermediate service classes offering tradeoffs between reserved rate utilization and the strength of guarantees. Our scheduler has been implemented in Solaris 2.5. 1. It runs existing applications without modifications. We present extensive experimental results showing the scalability, efficiency guaranteed performance, and overload performance aspects of our scheduler. We also demonstrate the importance of priority inheritance implemented in our scheduler for stable system performance.
Targeting protein for Xenopus kinesin‐like protein 2 knockdown enhances radiation sensitivity of human lung squamous carcinoma cell

The targeting protein for Xenopus kinesin‐like protein 2 (TPX2) has been demonstrated to be associated with the tumourigenesis of many cancers. In the present study, we investigated the role and preliminary mechanism of TPX2 in the resistance of lung squamous carcinoma to radiation therapy. The results showed that SK‐MES‐1R and NCI‐H226R cells were more resistant to X‐ray irradiation than the parental cells (SK‐MES‐1 and NCI‐H226). Moreover, TPX2 was upregulated in the radioresistant cells compared with the parental cells. TPX2 knockdown significantly decreased TPX2 expression in SK‐MES‐1 cells, while TPX2 overexpression increased TPX2 expression in NCI‐H226 cells compared with the corresponding control cells. TPX2 knockdown enhanced the radiosensitivity of SK‐MES‐1 and promoted cell apoptosis following exposure to irradiation, whereas TPX2 overexpression decreased the radiosensitivity of NCI‐H226 and inhibited cell apoptosis. In in vivo studies, the combination of TPX2 knockdown and irradiation significantly inhibited tumour growth, decreased tumour weight, downregulated TPX2 expression in tumour tissue and induced cell apoptosis in nude mice, while TPX2 overexpression exerted an opposite effect. Our results indicated that TPX2 was correlated with cell radioresistance and it might be served as a therapeutic target to enhance cell radiosensitivity in the radiation therapy of lung squamous carcinoma.
A NEW APPROACH OF ITERATIVE LEARNING CONTROL STRATEGY TOWARDS TUNING OF PI CONTROLLER IN A SPHERICAL TANK LEVEL PROCESS

This paper provides the design and implementation of an Enhanced Iterative Learning control Strategy (EILCS) in a spherical tank level process. The dynamics of the process are described by differential equation and worst case model parameters are identified by influencing the step test technique. By means relay feedback technique, the periodic reference signal is generated and utilized as the input of EILCS loop. From the input and output chattering signals of the EILCS, optimized PI controller parameters are identified using Recursive Least Squares (RLS) fitting technique. The simulation results are furnished to illustrate the effectiveness of proposed method. Robustness is also analyzed.