Miracle-dz/UniFAR-FTUs huggingface dataset:
Phase Noise Simulation and Estimation Methods: a Comparative Study

—A comparison of various simulation and estimation methods available to predict the phase noise in oscillators is presented in this paper. The phase noise of two ring oscillators and one radio frequency CMOS oscillator was determined using the Hajimiri and Lee phase noise analysis method, and the commercial simulators SpectreRF and EldoRF. Good agreement was obtained between the estimated and simulated phase noise performances. These oscillators were fabricated in a 0.35-m CMOS process. The measured data also shows reasonable agreement with the analysis and simulations.
New Developments in Blastomycosis

Abstract Blastomyces dermatitidis, the etiologic agent of blastomycosis, is a thermally dimorphic fungus that grows as a filamentous mold in the environment and as budding yeast in human tissue. This pathogen is endemic to North America, particularly in the states bordering the Mississippi and Ohio rivers, the Great Lakes, and the St. Lawrence Seaway. Infection with B. dermatitidis causes a broad array of clinical manifestations ranging from asymptomatic infection to fulminant sepsis with acute respiratory distress syndrome and death. B. dermatitidis can infect almost any organ in the body, but has a predilection for lungs and skin. There have been recent advances in the understanding of the pathogenesis, diagnosis, and treatment of this fungus. The Infectious Diseases Society of America published updated guidelines in 2008 to guide clinicians in the treatment of this important pathogen.
Temporal horn index and volume of medial temporal lobe atrophy using a new semiautomated method for rapid and precise assessment.

BACKGROUND AND PURPOSE Quantitative markers of Alzheimer disease (AD), particularly in the early stages, are needed for clinical assessment and monitoring. We have evaluated a novel method to segment and visualize the ventricular system and obtain volumetric measures thereof. The temporal horn volume (THV) and index in patients with mild cognitive impairment (MCI) and in those with AD were evaluated. METHODS High-resolution T1-weighted volume imaging was performed in 52 subjects (21 patients with MCI, 10 with AD, and 21 healthy control subjects). An interactive watershed transformation and semiautomated histogram analysis were implemented to produce segmented THV and temporal horn indices (THI) (ratio of THV to lateral ventricular volume). RESULTS Cerebral ventricular and temporal horn size could be semiautomatically quantified from all 52 datasets. The method was fast and rater-independent. Qualitative ventricular inspections using surface rendering shading could uncover atrophic process with enlargement of the whole and especially temporal horn volume. Both THV and THI of patients with AD were significantly larger than those of patients with MCI or control subjects (P < .005). There was no significant difference in THV and THI between patients with MCI or control subjects (P > .05). There was a significant correlation between the neuropsychologic performance and both THI and THV across groups (P < .01). CONCLUSION THV and THI could be used as markers of AD in the clinical environment and are expected to be helpful in monitoring therapeutic intervention.
Common Seed Analysis to Identify Off-Target Effects in siRNA Screens

Genome-scale small interfering RNA (siRNA) screens have become an increasingly popular approach to new target identification and pathway elucidation. However, the large data sets generated from siRNA screens have demonstrated high false-positive rates and the requirement for extensive experimental triage to distinguish true hits. A number of groups have independently reported the presence of siRNAs with identical seed sequences among their top screening hits. Based on these observations, we have developed a comprehensive technique for detecting and visualizing seed-based off-target effects in siRNA screening data. This is accomplished by analyzing the behavior of siRNAs that share identical seed sequences, which we refer to as common seed analysis (CSA). By applying these techniques to primary screening data of the Wnt pathway, we identify 158 distinct seed sequences that have a statistically significant effect on the assay. The promiscuous seed sequences identified in this manner can then be discounted in the analysis of follow-up experiments using single siRNAs. The ability to detect off-target effects when sufficient numbers of siRNAs share a common seed has significant implications for the design of siRNA screening experiments, data analysis, hit selection, and library design.
Web searcher interaction with the Dogpile.com metasearch engine

Metasearch engines are an intuitive method for improving the performance of Web search by increasing coverage, returning large numbers of results with a focus on relevance, and presenting alternative views of information needs. However, the use of metasearch engines in an operational environment is not well understood. In this study, we investigate the usage of Dogpile.com, a major Web metasearch engine, with the aim of discovering how Web searchers interact with metasearch engines. We report results examining 2,465,145 interactions from 534,507 users of Dogpile.com on May 6, 2005 and compare these results with findings from other Web searching studies. We collect data on geographical location of searchers, use of system feedback, content selection, sessions, queries, and term usage. Findings show that Dogpile.com searchers are mainly from the USA (84% of searchers), use about 3 terms per query (mean = 2.85), implement system feedback moderately (8.4% of users), and generally (56% of users) spend less than one minute interacting with the Web search engine. Overall, metasearchers seem to have higher degrees of interaction than searchers on non-metasearch engines, but their sessions are for a shorter period of time. These aspects of metasearching may be what define the differences from other forms of Web searching. We discuss the implications of our findings in relation to metasearch for Web searchers, search engines, and content providers.
Artemether–lumefantrine in the treatment of uncomplicated Plasmodium falciparum malaria

The World Health Organization strongly recommends artemisinin-based combination therapy (ACT) regimens for the treatment of uncomplicated Plasmodium falciparum malaria cases in endemic areas. Among the combinations of compounds that are available at present, excellent results have been obtained for the artemisinin derivative artemether, in a combination galenic preparation with lumefantrine (artemether–lumefantrine, AL). Here, the pharmacological properties and the therapeutic options of both substances are briefly reviewed and a cursory overview is given on recent trials that have compared the therapeutic effects of AL in the standard 6-dose regimen with other antimalarials and combinations. In order to ensure the most achievable and reliable adherence and compliance of children in the treatment of malaria, a dispersible formulation of AL is now attainable. Recent reports on the emergence of resistance to ACT regimens in Asia, however, are alarming.
Observer-based H control for a class of nonlinear networked systems

This paper is concerned with the problem of robust Hinfin control for a class of uncertain networked control systems with nonlinear perturbations. The uncertainties are assumed to be time-varying and norm-bounded. The perturbations are assumed to be time-varying and satisfy global Lipschitz conditions and appear in both the state and measurement output equations. An observer-based controller is designed, which guarantees the exponential stability and a prescribed Hinfin performance level of the closed-loop system subject to the network-induced delay and data dropout. Sufficient conditions on the existences of the stabilizing controller are established. The controller gains can be obtained by solving these conditions. An illustrative example is given to demonstrate the effectiveness of the proposed methods.
Effect of low voltage pulsed magnetic field on microstructure and wear behaviour of eutectic Al–Si alloys

Abstract Effect of discharging frequency of low voltage pulsed magnetic field (LVPMF) on the morphology and size of eutectic Si in eutectic Al–Si (Al–12Si) alloys has been investigated, and some characteristic parameters the characterised the microstructure of the eutectic Si phase were obtained. Dry sliding wear behaviour of eutectic Al–Si alloys without and with LVPMF treatment were also tested using a pin-on-disc wear testing machine, and scanning electron microscopy and energy dispersive spectroscopy X-ray of worn surfaces were carried out to determine the governing mechanisms in the eutectic Al–Si alloys without and with LVPMF treatment. The results show that the eutectic Si became smaller with the increase in discharging frequency. Fine short rod-like or rounded particle-like eutectic silicon with 2·3 μm in length, 0·6 μm in the width, and 3·8 in aspect ratio was formed in eutectic Al–Si alloy treated by 6 Hz LVPMF. The wear resistance of eutectic Al–Si alloys increased with the increase in discharging frequency. The adhesive wear was observed in eutectic Al–Si alloy without LVPMF treatment under normal load of 80 N. However, mainly abrasive was observed in eutectic Al–Si alloy with 6 Hz LVPMF treatment.
Quantitative magnetic resonance spectroscopic imaging in Parkinson’s disease, progressive supranuclear palsy and multiple system atrophy

Background and purpose: Magnetic resonance spectroscopy (MRS) allows the measurement of a number of brain tissue metabolites in vivo, including N‐acetylaspartate (NAA), a putative marker of neuronal integrity. Unlike single voxel MRS, magnetic resonance spectroscopic imaging (MRSI) enables quantification of these metabolites simultaneously from multiple anatomically localized voxels. Both single voxel MRS and MRSI allow the absolute quantification of these metabolites and, when combined with tissue segmentation, can give accurate metabolite concentrations even in the presence of partial volume effects from nearby cerebrospinal fluid.
PTM: A Pervasive Trust Management Model for Dynamic Open Environments ⁄

Trust is considered as a fundamental aspect for interdomain relationships. We have reviewed existing trust models and their drawbacks when they are applied to pervasive environments. We present PTM, a new decentralised trust management model for pervasive computing environments. PTM overcomes the challenges posed by dynamic open environments, making use of the autonomy and cooperable behaviour of the entities. Our model facilitates ad-hoc trust relationships, captures entities dynamic behaviour along time, and allows trust information exchange through a recommendation protocol.
Frequent amplification of 8q24, 11q, 17q, and 20q‐specific genes in pancreatic cancer

Genetic changes involved in the development and progression of pancreatic cancer are still partly unknown, despite the progress in recent years. In this study, comparative genomic hybridization analysis in 31 pancreatic cancer cell lines showed that chromosome arms 8q, 11q, 17q, and 20q are frequently gained in this tumor type. Copy number analysis of selected genes from these chromosome arms by fluorescence in situ hybridization showed amplification of the MYC oncogene in 54% of the cell lines, whereas CCND1 was amplified in 28%. In the 17q arm, the ERBB2 oncogene was amplified in 20% of the cell lines, TBX2 in 50%, and BIRC5 in 58%, indicating increased involvement toward the q telomere of chromosome 17. In the 20q arm, the amplification frequencies varied from 32% to 83%, with the CTSZ gene at 20q13 being most frequently affected. These results illustrate that amplification of genes from the 8q, 11q, 17q, and 20q chromosome arms is common in pancreatic cancer. © 2002 Wiley‐Liss, Inc.
Illuminating the underground: the reality of unauthorised file sharing

This paper presents a new conceptualisation of online communities by exploring how an online community forms and is maintained. Many stakeholders in the music industry rightly point out that unauthorised file sharing is illegal, so why do so many people feel it is acceptable to download music without paying? Our study found highly cohesive, well‐organised groups that were motivated by scarcity and the lack of high quality music files. Our ethnographic research provides insight into the values and beliefs of music file sharers: their demands are not currently being met. Using Actor‐network theory, we are able to propose that the file sharers represent a growing potential market in the music industry and that music distribution systems should be developed accordingly to meet the demands of this user group. Therefore, this study can serve as a springboard for understanding unauthorised file sharing and perhaps other deviant behaviours using technology.
Evidence for the Involvement of the Unique C-Tail of S100A9 in the Binding of Arachidonic Acid to the Heterocomplex S100A8/A9

Abstract Protein complexes formed by S100A8 and S100A9 represent the only AAbinding capacity in the human neutrophilic cytosol and are involved in the intracellular arachidonic acid metabolism. The formation of S100A8/A9 protein complexes and the binding of calcium to the complexes are prerequisites for the specific binding of polyunsaturated fatty acids. The present study was undertaken to characterize the fatty acid binding site within the protein complex. Deletions at both termini and point mutations of different basic amino acids especially within the extended Cterminal tail of human S100A9 were introduced. The S100A9 mutant proteins were then analyzed with respect to proteinprotein interaction (GST pull downassay and yeast twohybrid system) and functional properties (arachidonic acid and calcium binding). The data give strong evidence that the unique Ctail of S100A9 containing the three consecutive histidine residues (His103-His105) represents the region to which the fatty acid carboxygroup is bound to the protein complex. The localization of the AAbinding site within the unique Ctail of S100A9 correlates with the fact that fatty acid binding has not yet been reported for other S100 proteins.
Origin and Consequences of the Relationship between Protein Mean and Variance

Cell-to-cell variance in protein levels (noise) is a ubiquitous phenomenon that can increase fitness by generating phenotypic differences within clonal populations of cells. An important challenge is to identify the specific molecular events that control noise. This task is complicated by the strong dependence of a protein's cell-to-cell variance on its mean expression level through a power-law like relationship (σ2∝μ1.69). Here, we dissect the nature of this relationship using a stochastic model parameterized with experimentally measured values. This framework naturally recapitulates the power-law like relationship (σ2∝μ1.6) and accurately predicts protein variance across the yeast proteome (r2 = 0.935). Using this model we identified two distinct mechanisms by which protein variance can be increased. Variables that affect promoter activation, such as nucleosome positioning, increase protein variance by changing the exponent of the power-law relationship. In contrast, variables that affect processes downstream of promoter activation, such as mRNA and protein synthesis, increase protein variance in a mean-dependent manner following the power-law. We verified our findings experimentally using an inducible gene expression system in yeast. We conclude that the power-law-like relationship between noise and protein mean is due to the kinetics of promoter activation. Our results provide a framework for understanding how molecular processes shape stochastic variation across the genome.
Design by Contract with JML

This document gives a tutorial introduction to the Java Modeling Language (JML), and explains how JML can be used as a powerful design by contract (DBC) tool for Java. JML is a formal behavioral interface specification language for Java that contains the essential notations used in DBC as a subset. The basic concepts of DBC are explained with a particular emphasis on how to use JML notations to specify Java classes and interfaces. JML tools such as JML compiler (jmlc) are also introduced, with examples of their use.
The effect of unreliable wireless channel on the call performance in mobile network

In this paper, we propose a model to study the call performance in mobile network taking into account the inherent time varying wireless channel. The performance metrics call complete probability and call complete ratio are introduced and further derived with the general call holding time. The impacts of the wireless channel error characteristics and the system parameters on the call performance are illustrated and discussed. The sensitivity problem with respect to the call holding time distribution is investigated. The result indicates that both call complete probability and call complete ratio exhibit a significantly different variation under different call holding time. The analytical model is verified by simulation result.
Single-symbol decodable distributed STBC for two-path successive relay networks

A fast-decodable distributed space-time block code (STBC) is proposed for a two-path successive relay network that can achieve both full diversity and full transmission rate. The proposed STBC employs a precoder to rotate the constellation of transmitted symbols at source. After decode-and-forward by relays, the rotated information symbols are decoded at destination. It is shown that single complex symbol decoding can be obtained at the destination. Simulation results demonstrate that the full diversity is offered by the newly proposed distributed STBC for the two-path successive relay network.
DCCP video streaming over multiple connections in the wireless internet

Multiplexing a single video stream over several datagram congestion control (DCCP) connections is a way of coping with wireless channel losses and traffic congestion in the wireless internet, without the need for complex cross-layer intervention. Multi-connections introduce the need for data re-ordering at the receiver. This paper considers the potential delay at an uplink destination on the internet and extends this to a scheme for user-to-user mobile device communication via the wired internet. It also considers the impact on video quality of packet drops due both to channel loss and router buffer overflow, when the DCCP congestion controller is applied. Results for IEEE 802.16e (mobile WiMAX) broadband wireless stages show a worthwhile gain in video quality from using three or more connections over a single connection but with start-up delay due to the need to avoid possible buffer underflow. More connections will be necessary to preserve sufficient wireless link utilisation if the path is lengthened to reach an end device that is also mobile.
Genetic Characterization of a Core Set of a Tropical Maize Race Tuxpeño for Further Use in Maize Improvement

The tropical maize race Tuxpeño is a well-known race of Mexican dent germplasm which has greatly contributed to the development of tropical and subtropical maize gene pools. In order to investigate how it could be exploited in future maize improvement, a panel of maize germplasm accessions was assembled and characterized using genome-wide Single Nucleotide Polymorphism (SNP) markers. This panel included 321 core accessions of Tuxpeño race from the International Maize and Wheat Improvement Center (CIMMYT) germplasm bank collection, 94 CIMMYT maize lines (CMLs) and 54 U.S. Germplasm Enhancement of Maize (GEM) lines. The panel also included other diverse sources of reference germplasm: 14 U.S. maize landrace accessions, 4 temperate inbred lines from the U.S. and China, and 11 CIMMYT populations (a total of 498 entries with 795 plants). Clustering analyses (CA) based on Modified Rogers Distance (MRD) clearly partitioned all 498 entries into their corresponding groups. No sub clusters were observed within the Tuxpeño core set. Various breeding strategies for using the Tuxpeño core set, based on grouping of the studied germplasm and genetic distance among them, were discussed. In order to facilitate sampling diversity within the Tuxpeño core, a minicore subset of 64 Tuxpeño accessions (20% of its usual size) representing the diversity of the core set was developed, using an approach combining phenotypic and molecular data. Untapped diversity represents further use of the Tuxpeño landrace for maize improvement through the core and/or minicore subset available to the maize community.
Adaptive surface decomposition for the distance computation of arbitrarily shaped objects

We propose an adaptive decomposition algorithm to compute separation distances between arbitrarily shaped objects. Using the Gilbert-JohnsonKeerthi algorithm (GJK), we search for sub-mesh pairs whose convex hulls do not intersect. We show how to employ characteristics of GJK to guide a recursive decomposition of the objects in the case of intersections. We further show how to employ GJK to derive lower and upper distance bounds in nonintersecting cases. The bounds are used in a spatial subdivision scheme to enforce a twofold culling of the domain. Experiments show the applicability of the algorithm in dynamic scenarios with dynamically moving rigid and deformable objects.
Toward a Deterministic Model of Planetary Formation. III. Mass Distribution of Short-Period Planets around Stars of Various Masses

The origin of a recently discovered close-in Neptune-mass planet around GJ 436 poses a challenge to the current theories of planet formation. On the basis of the sequential accretion hypothesis and the standard theory of gap formation and orbital migration, we show that around M dwarf stars, close-in Neptune-mass ice giant planets may be relatively common, while close-in Jupiter-mass gas giant planets are relatively rare. The mass distribution of close-in planets generally has two peaks at about Neptune mass and Jupiter mass. The lower mass peak takes the maximum frequency for M dwarfs. Around more massive solar-type stars (G dwarfs), the higher mass peak is much more pronounced. Planets around G dwarfs undergo orbital migration after fully accreting gas, while those around M dwarfs tend to migrate before starting rapid gas accretion. Close-in Neptune-mass planets may also exist around G dwarfs, although they tend to be mostly composed of silicates and iron cores and their frequency is expected to be much smaller than that of Neptune-mass planets around M dwarfs and that of gas giants around G dwarfs. We also show that the conditions for planets' migration due to their tidal interaction with the disk and the stellar mass dependence in the disk mass distribution can be calibrated by the mass distribution of short-period planets around host stars with various masses.