Miracle-dz/UniFAR-FTUs huggingface dataset:
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

SUMMARY Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. AVAILABILITY Single-click, self-updating web installation is available at http://proteome.gs. washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
Learning from examples in unstructured, outdoor environments

In this paper, we present a multi‐pronged approach to the “Learning from Example” problem. In particular, we present a framework for integrating learning into a standard, hybrid navigation strategy, composed of both plan‐based and reactive controllers. Based on the classification of colors and textures as either good or bad, a global map is populated with estimates of preferability in conjunction with the standard obstacle information. Moreover, individual feedback mappings from learned features to learned control actions are introduced as additional behaviors in the behavioral suite. A number of real‐world experiments are discussed that illustrate the viability of the proposed method. © 2007 Wiley Periodicals, Inc.
A Delay Probability Metric for Input Pattern Ranking Under Process Variation and Supply Noise

Ongoing technology scaling has increased delay defects in integrated circuits. Some of the delay defects are due to crosstalk, supply noise, process variations, etc. They degrade the performance and field reliability of circuits. However, testing the circuits with path delay patterns under worst-case conditions helps to detect such defects. Estimation of patterns with worst-case path delay becomes difficult using the conventional techniques due to their unpredictable behavior. In this paper, we first describe the problem and then propose our approach in identifying a worst-case path delay pattern under the impact of process variations and supply noise. A delay probability metric ispresented in this work, for an efficient identification of worst-case path delay pattern, which is the basis of our ranking method. The simulation results of ITC'99 benchmark circuits show the feasibility of our delay probability metric.
Effects of Ocean Acidification on the Ballast of Surface Aggregates Sinking through the Twilight Zone

The dissolution of CaCO3 is one of the ways ocean acidification can, potentially, greatly affect the ballast of aggregates. A diminution of the ballast could reduce the settling speed of aggregates, resulting in a change in the carbon flux to the deep sea. This would mean lower amounts of more refractory organic matter reaching the ocean floor. This work aimed to determine the effect of ocean acidification on the ballast of sinking surface aggregates. Our hypothesis was that the decrease of pH will increase the dissolution of particulate inorganic carbon ballasting the aggregates, consequently reducing their settling velocity and increasing their residence time in the upper twilight zone. Using a new methodology for simulation of aggregate settling, our results suggest that future pCO2 conditions can significantly change the ballast composition of sinking aggregates. The change in aggregate composition had an effect on the size distribution of the aggregates, with a shift to smaller aggregates. A change also occurred in the settling velocity of the particles, which would lead to a higher residence time in the water column, where they could be continuously degraded. In the environment, such an effect would result in a reduction of the carbon flux to the deep-sea. This reduction would impact those benthic communities, which rely on the vertical flow of carbon as primary source of energy.
In vitro activity of para-guanidinoethylcalix[4]arene against susceptible and antibiotic-resistant Gram-negative and Gram-positive bacteria.

OBJECTIVES Emergence of multidrug-resistant bacteria has encouraged vigorous efforts to develop antimicrobial agents with new mechanisms of action. In this study, the in vitro antibacterial activity of para-guanidinoethylcalix[4]arene was evaluated and compared with that of its constitutive monomer, para-guanidinoethylphenol. Hexamidine, a widely used antiseptic, and synthalin A, an old antidiabetic and anti-trypanosomal compound, were chosen as references. METHODS MIC and MBC were determined for five reference strains (Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923 and ATCC 29213, Enterococcus faecalis ATCC 29212 and Pseudomonas aeruginosa ATCC 27853), as well as five antibiotic-resistant clinical isolates. Toxicity on MRC-5 and HaCaT eukaryotic cell lines was also evaluated by MTT and Neutral Red assays. RESULTS No antibacterial activity was observed for para-guanidinoethylphenol (MIC >or= 512 mg/L) and synthalin A (MIC >or= 64 mg/L). Conversely, para-guanidinoethylcalix[4]arene and hexamidine: (i) showed a broad antibacterial spectrum, both on Gram-positive and on Gram-negative bacteria (MIC = 4 mg/L against E. coli and 8 mg/L against S. aureus for para-guanidinoethylcalix[4]arene), to a lesser degree against E. faecalis and P. aeruginosa (MIC = 32 mg/L); (ii) were bacteriostatic (MBC >or= 256 mg/L); and (iii) MICs and MBCs obtained for clinical isolates were similar to those obtained with reference strains. Both compounds, the monomer and the calixarene, showed no apparent cytotoxicity, whereas hexamidine and synthalin A had significant toxic effects that increased with time and concentration and in a range of 100-1000 times that for calixarene. CONCLUSIONS In conclusion, results confirm para-guanidinoethylcalix[4]arene as a broad-spectrum new agent or an auxiliary in antimicrobial chemotherapy.
Thermal-Aware Scheduling in Multicore Systems Using Chaotic Attractor Predictors

Modern processors crudely manage thermal emergencies through Dynamic Thermal Management (DTM), where the processor monitors the die temperature and dynamically adjusts the processor voltage and frequency (DVFS) to throttle down the processor when necessary. However, DVFS tends to yield marked degradation in both application performance and system reliability. Thus, pro-active scheduling techniques that avoid thermal emergencies are preferable over reactive hardware techniques like DTM. Based on our previously introduced thermal Chaotic Attractor Predictors (CAPs), which take into account key thermal indicators and system performance metrics for overall energy consumption estimation, we have developed and evaluated an effective thread scheduler for multicore systems. Besides CAPs, our scheduler makes use of two basic principles to minimize server energy consumption: (1) selecting the thread with the least probability of causing a DTM during the subsequent time quantum, for execution in each core, and (2) migrating execution threads on thermally overextended cores to other cool cores via load balancing so as to observe the thermal envelope. Our developed scheduler is evaluated in practice to assess its potential advantage resulting from thermal-awareness by incorporating thermal CAPs (for temperature prediction) and basic principles (for energy reduction) into the existing scheduler in the FreeBSD operating system. Our implemented scheduler is run on a server with the Intel Xeon processor for gathering measures of interest (including die temperature readings and run times) when benchmark codes from the PARSEC suite are executed. The gathered results reveal that our proposed scheduler exhibits reduction in mean core on-die temperatures by up to 12.8◦C while mostly experiencing only 1% to 4% performance degradation.
Disturbance decoupling by measurement feedback

Abstract The paper addresses the disturbance decoupling problem for MIMO discrete-time nonlinear systems. A sufficient conditions are derived to solve the problem by dynamic measurement feedback, i.e. the feedback that depends on measurable outputs only. The solution to the disturbance decoupling problem, described in this paper, is based on the input-output linearization, which is used to linearize certain functions. Two examples are added to illustrate the results.
A simplified decoding algorithm for nonbinary LDPC codes

A simplified decoding algorithm for low-density parity-check (LDPC) codes over high order Galois field is proposed to reduce the complexity of traditional sum-product algorithm (SPA). There are only addition operation and comparison operation in this algorithm, without complex multiplication operation. The computation complexity of proposed algorithm is much smaller than the SPA. The signal-to-noise power ratio (SNR) isn't needed in this algorithm, so the process of SNR estimation can also be removed. The simulation results show that the bit error rate (BER) performance of proposed algorithm degrades only about 0.5dB than the SPA, so the proposed algorithm is an efficient simplified algorithm in engineering.
Project and Cost Engineers' Handbook

Cost Engineering Basics. Cost Accounting. Cost Estimating. Economic Equivalence and Profitability. Cost Control and Reporting. Project Management and Schedule Control. Cost Indexes, Escalation, and Location Factors. Operations Research Techniques. Risk Analysis: How to Do it and How Not to Do it. Cost Engineering in a Worldwide Economy. Computer Applications for Project Control. Cost Engineering Ethics
Programming Research Group Network Performance Assessment under the Bsp Model Network Performance Assessment under the Bsp Model

The BSP model by L.G. Valiant has been proposed as a unifying and bridging model for the design, analysis and programming of general purpose parallel computing systems. A number of libraries have been implemented that allow programming following the BSP paradigm with one of them being the Oxford BSP Toolset. Algorithm designers and software engineers are able to study the performance of their implementations under the BSP model on a particular hardware platform and predict its behavior in others if the parameters of the BSP model are available for these machines. The assessment of the communication and synchronization requirements poses a serious challenge. As most machines were not designed and built as BSP computers , the study of their behavior as BSP computers is an interesting exercise and the experimental measurement of the BSP parameters p, L and g raises challenging questions. In this work we study the network performance of three parallel hardware platforms (a Cray T3D, an IBM SP2 and an SGI Power Challenge) under the BSP model when BSPlib is used to realize the BSP programming paradigm. This study is, to the best of our knowledge, the rst exhaustive experimental work that tries to model realistic parallel machines as BSP computers. We show that simpliications in the original BSP cost model may lead to inconsistencies and errors in performance estimation. We provide evidence that more exhaustive tests are needed than the ones currently used, to obtain reliable and consistent estimates of L and g.
Achievable Degrees of Freedom on K-user Y Channels

In this paper, we consider K-user Y channels where K users simultaneously exchange messages with each other via an intermediate relay. Degrees of freedom (DOF) of Y channels with multiple antennas is not known in general. Investigation of the feasibility conditions of signal space alignment for network coding is an initial step for addressing this open problem. We verify that when user i with M_i antennas sends K-1 independent messages to the other users through a relay with N antennas and each message achieves the DOF of d, the total DOF of dK (K-1) is attained if Mi ≥ d(K-1), N ≥ {dK(K-1)/2} and N<; min {Mi+Mj -d|∀ i ≠ j}. It is accomplished by adopting the signal space alignment for the network coding during both the multiple access phase and the broadcast phase. It is shown that the proposed scheme obtains not only a network coding gain but also an alignment gain in terms of the normalized DOF, as K → ∞. Also for Y channels where all nodes have a single antenna, we show that the DOF of 2 is achieved regardless of the number of users by using the rational dimension framework.
Sample Selection Bias in the Estimation of Recreation Demand Functions: An Application to Sportfishing

Estimating the value of public actions through behavior implied by the demand for recreation has proved valuable in many settings. Early applications were based on grouped data. However the sharpening of tools of welfare analysis has led economists to exploit individual, rather than grouped, data. The appropriate use of individual observations in estimating recreational demand models is not obvious and depends on the economic theory and its behavioral implications and the statistical characteristics of models. The difficulty in exploiting individual observations in estimating recreational demand functions is that a large portion of a randomly sampled population in a given geographical region is likely to be non-participants in the recreational activity of interest. That is, they are observed to demand zero trips. The qualitative implications of such samples seem to be recognized (Bockstael, Hanemann, and Strand 1986; Mullahy 1987), but there are few (Smith 1988; Shaw 1988) published comparisons of the implications of alternative models.
The Genes of Watermelon

Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is a major vegetable crop in the world, accounting for 6.8% of the world area devoted to vegetable crops. Wa- termelon is a useful vegetable crop for genetic research because of its small genome size, and the many available gene mutants. The watermelon genes were originally organized and summarized in 1944, and have been expanded and updated periodically. However, the action of some watermelon genes has not been described clearly in some cases. Also, the interaction of multiple gene loci that control similar traits needs to be described more clearly. Finally, it is necessary to identify the inbred lines having each published gene mutant, for use as type lines in studies of gene action, allelism, and linkage. The objective of this work was to update the gene list, identify the cultivar or line having each gene mutant, and collect seeds of the lines for use by interested researchers. In addition, the gene descriptions were expanded and clarifi ed, information on gene interactions was added, and errors in naming or citing previously described genes were corrected. New genes that have not previously been described (cr, Ctr, dw-3, ms-2, Ti, ts and zym-FL) were added to the list, for a total of 163 watermelon gene mutants. Watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai) is a major cucurbit crop that accounts for 6.8% of the world area devoted to vegetable crops (FAO, 2002). Watermelon is grown for its fl eshy, juicy, and sweet fruit. Mostly eaten fresh, they provide a delicious and refreshing dessert especially in hot weather. The watermelon has high lycopene content in the red-fl eshed cultivars: 60% more than tomato. Lycopene has been classifi ed as use- ful in the human diet for prevention of heart attacks and certain types of cancer. Watermelon is native to central Africa where it was domesticated as a source of water, a staple food crop, and an animal feed. It was cultivated in Africa and the Middle East for >4000 years, then introduced to China around 900 AD, and fi nally brought to the New World in the 1500s. There are 1.3 million ha of watermelon grown in the world, with China and the Middle Eastern countries the major consumers. China is the largest watermelon producer, with 68.9% of the total production. The other major watermelon producing countries are Turkey, Iran, Egypt, United States, Mexico, and Korea (FAO, 2002). In the United States, watermelon is used fresh as a dessert, or in salads. U.S. production is concentrated in Florida, California, Texas, and Georgia (USDA, 2002), increasing from 1.2 Mt in 1980 to 3.9 Mt in 2002, with a farm value of $329 million (USDA, 2002). Watermelon is a useful crop species for genetic research because of its small genome size, and the many available gene mutants. Genome size of watermelon is 424 million base pairs. DNA sequence analysis revealed high conservation useful for comparative genomic analysis with other plant species, as well as within the Cucurbitaceae. Like some of the other cultivated cucurbits, watermelon
RELEVANCE OF THE X . 500 DIRECTORY TO CSCW APPLICATIONS

Paola Pennelli * Tecnopolis ~CSATA Novus Drtus . Str. Prov. Casamassima km 3 Valenzano (Bari),· Italy pennelli@ibacsata.bitnet • at present staying at GMD In 1Q88 the standardization bodies ISO and CCnT released the first international standard of a distributed Directory Service [8]. The purpose of the Directory as it is described by the standard is to supply a global nam.eserver and an application independent management and infonnation service. But these applications are not exhausting the possibilities of a Directory usage. It is the intention of this paper to present the possibilities and chances the Directory offers to applications in the CSCW area. Our investigation focuses on CSCW models and applications that support and coordinate communications in groups [15]. First the paper identifies ami analyses components which most of these applications have in common. For the analysis we introduce the classification of activity oriented models and conversation oriented models. Then, after a brief introduction into the X.50D Directory Service, it is shown in which way the identified components can be represented by the Directory Service. The paper concludes with a discussion of desirable improvements on the Directory Service.
Parallel Molecular Evolution in an Herbivore Community

Making the Change The Apocynaceae plant family produces toxic cardenolids. However, many insects have managed to escape the deleterious effects of these chemicals and even, in some cases, use them in their own defense. Zhen et al. (p. 1634) investigated a broad range of taxa and found several examples of parallel changes, as well as duplications, in members of the ATPα family that likely explain the shift to allow insects to avoid the toxic effects of these plants. Thus, natural selection can harness a combination of gene duplication, protein evolution, and regulatory evolution to allow distantly related species to adapt to specific niches. Parallel mutations in the alpha subunit of the sodium pump allow insects to specialize on host plants that produce ouabain. Numerous insects have independently evolved the ability to feed on plants that produce toxic secondary compounds called cardenolides and can sequester these compounds for use in their defense. We surveyed the protein target for cardenolides, the alpha subunit of the sodium pump, Na+,K+-ATPase (ATPα), in 14 species that feed on cardenolide-producing plants and 15 outgroups spanning three insect orders. Despite the large number of potential targets for modulating cardenolide sensitivity, amino acid substitutions associated with host-plant specialization are highly clustered, with many parallel substitutions. Additionally, we document four independent duplications of ATPα with convergent tissue-specific expression patterns. We find that unique substitutions are disproportionately associated with recent duplications relative to parallel substitutions. Together, these findings support the hypothesis that adaptation tends to take evolutionary paths that minimize negative pleiotropy.
Context in Human-Machine Problem Solving: A Survey

Context appears in AI as a challenge for the coming years as shown by the various scientific events focusing on context held since 1995. However, context is already considered in other domains, as Natural Language, although through few aspects of context. We present in this paper a survey of the literature dealing directly and explicitly with context whatever the domain is. This permits to have a clear view on the context in AI. One of the conclusions of this survey is to point out the existence of different types of context along knowledge representation, the mechanisms of reasoning on the knowledge, and the interaction of the computer system with a human.
Impact of Video Content on Video Quality for Video over Wireless Networks

Video streaming is a promising multimedia application and is gaining popularity over wireless/mobile communications. The quality of the video depends heavily on the type of content. The aim of the paper is threefold. First, video sequences are classified into groups representing different content types using cluster analysis based on the spatial (edges) and temporal (movement) feature extraction. Second, we conducted experiments to investigate the impact of packet loss on video contents and hence find the threshold in terms of upper, medium and lower quality boundary at which users’ perception of service quality is acceptable. Finally, to identify the minimum send bitrate to meet Quality of Serive (QoS) requirements (e.g. to reach communication quality with Mean Opinion Score (MOS) greater than 3.5) for the different content types over wireless networks. We tested 12 different video clips reflecting different content types. We chose Peak-Signal-to-Noise-Ratio (PSNR) and decodable frame rate (Q) as end-to-end video quality metrics and MPEG4 as the video codec. The work should help optimizing bandwidth allocation for specific content in content delivery networks.
An Intelligent Anti-Money Laundering Method for Detecting Risky Users in the Banking Systems

During the last decades, universal economy has experienced money laundering and its destructive impact on the economy of the countries. Money laundering is the process of converting or transferring an asset in order to conceal its illegal source or assist someone that is involved in such crimes. Criminals generally attempt to clean the sources of the funds obtained by crime, using the banking system. Due to the large amount of information in the banks, detecting such behaviors is not feasible without anti-money laundering systems. Money laundering detection is one of the areas, where data mining tools can be useful and effective. In this research, some of the features of the users are extracted from their profiles by studying them. These features may include large financial transactions in risky areas regarding money laundering, reactivation of dormant accounts with considerable amounts, etc. Network training is performed by designing a fuzzy system, developing an adaptive neuro-fuzzy inference system and adding feature vectors of the users to it. The network output can determine the riskiness of the user behavior. The evaluation results reveal that the proposed method increases the accuracy of detecting risky users.