Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays

Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional profiling. To aid in such studies, we have developed a protocol for making reverse-phase protein lysate microarrays with larger numbers of spots than previously feasible. Our first application of these arrays was to profiling of the 60 human cancer cell lines (NCI-60) used by the National Cancer Institute to screen compounds for anticancer activity. Each glass slide microarray included 648 lysate spots representing the NCI-60 cell lines plus controls, each at 10 two-fold serial dilutions to provide a wide dynamic range. Mouse monoclonal antibodies and the catalyzed signal amplification system were used for immunoquantitation. The signal levels from the >30,000 data points for our first 52 antibodies were analyzed by using p-scan and a quantitative dose interpolation method. Clustered image maps revealed biologically interpretable patterns of protein expression. Among the principal early findings from these arrays were two promising pathological markers for distinguishing colon from ovarian adenocarcinomas. When we compared the patterns of protein expression with those we had obtained for the same genes at the mRNA level by using both cDNA and oligonucleotide arrays, a striking regularity appeared: cell-structure-related proteins almost invariably showed a high correlation between mRNA and protein levels across the NCI-60 cell lines, whereas non-cell-structure-related proteins showed poor correlation.
Thread Optimizations in Concurrent Object Oriented Languages Thread Optimizations in Concurrent Object Oriented Languages

Thread Optimizations in Concurrent Object Oriented Languages by Jing Wang With the current growth of the networks, distributed systems are becoming more and more popular. It is desirable to integrate heterogeneous machines into a coherent distributed system and to share resources among them. Scalable network computing also requires reliability, portability, and suitable programming abstractions. The Kan system was developed to meet these requirements. It supports ne-grained concurrency for the programmers, but hides the object distribution and concurrency control. This thesis introduces the concepts and implementations of asynchronous methods, nested atomic actions, guards, and some related concurrency issues. Concurrency involves extra time and space overheads of creating and scheduling threads. We want to achieve eecient multi-threaded without sacriicing good sequential performance. Some cost-eeective implementations, thread in-lining and an adaptive thread pool, are applied in our research project. The rst approach handles thread creation as a standard method invocation and creates a real thread only when necessary. An adaptive thread pool provides a way to reuse threads at runtime. We chose Java as the base language for the Kan project, due to its portabil-ity and support for heterogeneous systems. We enhance the Java programming model to support our new functionality by modifying an existing Java compiler. v Acknowledgements
Large Motion Control of an Experimental Mobile Manipulator with Limited Sensing

ABSTRACT Two recently developed motion control algorithms for mobile manipulators are applied to an experimental system. The manipulator motions induce significant dynamic interactions with its vehicle and suspension. A conventional fixed-base controller, which typically neglects these dynamic interactions, is shown to lead to poor performance. Both mobile manipulator control algorithms, however, which account for dynamic vehicle motions caused by manipulator motions, are shown to perform well, despite practical limitations imposed on the sensory data available for control in field environments.
The perception of time, risk and return during periods of speculation

Abstract What return should you expect when you take on a given amount of risk? How should that return depend upon other people's behaviour? What principles can you use to answer these questions? In this paper, I approach these topics by exploring the consequences of two simple hypotheses about risk. The first is a common-sense invariance principle: assets with the same perceived risk must have the same expected return. It leads directly to the well known Sharpe ratio and the classic risk-return relationships of arbitrage pricing theory and the capital asset pricing model. The second hypothesis concerns the perception of time. I conjecture that in times of speculative excitement, short-term investors may instinctively imagine stock prices to be evolving in a time measure different from that of calendar time. They may perceive and experience the risk and return of a stock in intrinsic time, a dimensionless time scale that counts the number of trading opportunities that occur, but pays no attention to the calendar time that passes between them. Applying the first hypothesis in the intrinsic time measure suggested by the second, I derive an alternative set of relationships between risk and return. Its most noteworthy feature is that, in the short-term, a stock's trading frequency affects its expected return. I show that short-term stock speculators will expect returns proportional to the temperature of a stock, where temperature is defined as the product of the stock's traditional volatility and the square root of its trading frequency. Furthermore, I derive a modified version of the capital asset pricing model in which a stock's excess return relative to the market is proportional to its traditional beta multiplied by the square root of its trading frequency. I also present a model for the joint interaction of long-term calendar-time investors and short-term intrinsic-time speculators that leads to market bubbles characterized by stock prices that grow super-exponentially with time. Finally, I show that the same short-term approach to options speculation can lead to an implied volatility skew. I hope that this model will have some relevance to the behaviour of investors expecting inordinate returns in highly speculative markets.
Efficiently List-Decodable Punctured Reed-Muller Codes

The Reed–Muller (RM) code, encoding <inline-formula> <tex-math notation="LaTeX">$n$ </tex-math></inline-formula>-variate degree-<inline-formula> <tex-math notation="LaTeX">$d$ </tex-math></inline-formula> polynomials over <inline-formula> <tex-math notation="LaTeX">$ \mathbb {F}_{q}$ </tex-math></inline-formula> for <inline-formula> <tex-math notation="LaTeX">$d < q$ </tex-math></inline-formula>, with its evaluation on <inline-formula> <tex-math notation="LaTeX">$ \mathbb {F}_{q}^{n}$ </tex-math></inline-formula>, has a relative distance <inline-formula> <tex-math notation="LaTeX">$1-d/q$ </tex-math></inline-formula> and can be list decoded from a <inline-formula> <tex-math notation="LaTeX">$1-O(\sqrt {d/q})$ </tex-math></inline-formula> fraction of errors. In this paper, for <inline-formula> <tex-math notation="LaTeX">$d \ll q$ </tex-math></inline-formula>, we give a length-efficient puncturing of such codes, which (almost) retains the distance and list decodability properties of the RM code, but has a much better rate. Specifically, when <inline-formula> <tex-math notation="LaTeX">$q =\Omega ( d^{2}/ \varepsilon ^{2})$ </tex-math></inline-formula>, we give an explicit rate <inline-formula> <tex-math notation="LaTeX">$\Omega \left ({\frac { \varepsilon }{d! }}\right )$ </tex-math></inline-formula> puncturing of RM codes, which have a relative distance at least <inline-formula> <tex-math notation="LaTeX">$(1- \varepsilon )$ </tex-math></inline-formula> and efficient list decoding up to <inline-formula> <tex-math notation="LaTeX">$(1-\sqrt { \varepsilon })$ </tex-math></inline-formula> error fraction. This almost matches the performance of random puncturings, which work with the weaker field size requirement <inline-formula> <tex-math notation="LaTeX">$q= \Omega ( d/ \varepsilon ^{2})$ </tex-math></inline-formula>. We can also improve the field size requirement to the optimal (up to constant factors) <inline-formula> <tex-math notation="LaTeX">$q =\Omega ( d/ \varepsilon )$ </tex-math></inline-formula>, at the expense of a worse list decoding radius of <inline-formula> <tex-math notation="LaTeX">$1- \varepsilon ^{1/3}$ </tex-math></inline-formula> and rate <inline-formula> <tex-math notation="LaTeX">$\Omega \left ({\frac { \varepsilon ^{2}}{d! }}\right )$ </tex-math></inline-formula>. The first of the above tradeoffs is obtained by substituting for the variables functions with carefully chosen pole orders from an algebraic function field; this leads to a puncturing for which the RM code is a subcode of a certain algebraic-geometric code (which is known to be efficiently list decodable). The second tradeoff is obtained by concatenating this construction with a Reed–Solomon-based multiplication friendly pair, and using the list recovery property of algebraic-geometric codes.
Effect of Varying Epistasis on the Evolution of Recombination

Whether recombination decelerates or accelerates a population's response to selection depends, at least in part, on how fitness-determining loci interact. Realistically, all genomes likely contain fitness interactions both with positive and with negative epistasis. Therefore, it is crucial to determine the conditions under which the potential beneficial effects of recombination with negative epistasis prevail over the detrimental effects of recombination with positive epistasis. Here, we examine the simultaneous effects of diverse epistatic interactions with different strengths and signs in a simplified model system with independent pairs of interacting loci and selection acting only on the haploid phase. We find that the average form of epistasis does not predict the average amount of linkage disequilibrium generated or the impact on a recombination modifier when compared to results using the entire distribution of epistatic effects and associated single-mutant effects. Moreover, we show that epistatic interactions of a given strength can produce very different effects, having the greatest impact when selection is weak. In summary, we observe that the evolution of recombination at mutation–selection balance might be driven by a small number of interactions with weak selection rather than by the average epistasis of all interactions. We illustrate this effect with an analysis of published data of Saccharomyces cerevisiae. Thus to draw conclusions on the evolution of recombination from experimental data, it is necessary to consider the distribution of epistatic interactions together with the associated selection coefficients.
Image Classification and Quantification Form for Stroke Lesions and Background Brain Appearance on CT and MR Imaging Including CT/MR Angiography and CT/MR Perfusion Imaging

Acute Stroke Lesions The following templates were initially devised as a rapid method of classifying and quantifying acute ischaemic and hemorrhagic stroke lesions on CT or MR imaging during JMW’s MD project. The method of dividing the brain into typical arterial territories involved in acute ischaemic stroke covered in Question 5, including the assessment of lesion swelling, was validated in an observer reliability study, and subsequently used in stroke registers and observational studies.
High Performance and the Transformation of Work? The Implications of Alternative Work Practices for the Experience and Outcomes of Work

Using data from a 1997 telephone survey of 508 employed Canadians, the author explores the implications for workers of alternative work practices (AWPs) associated with the high-performance model. There are three main findings. First, moderate levels of AWP adoption were associated with increased “belongingness,” empowerment, task involvement, and ultimately job satisfaction, esteem, commitment, and citizenship behavior. At higher levels of adoption, however, these associations declined in magnitude and even became negative. AWP adoption was also associated with more stressful work. Second, whereas traditional (that is, supervised) group or team systems represented a substantial improvement over individualized work arrangements, “lean” and “team” forms of work organization associated with the high-performance model did not. Third, although team-based work and information sharing had positive effects, team autonomy and responsibility for a good or service—both associated with the high-performance model—had negative effects, as did “Just-in-Time” (JIT) systems and re-engineering programs.
Using Spectral Clustering for Finding Students' Patterns of Behavior in Social Networks

The high dimensionality of the data generated by social net- works has been a big challenge for researchers. In order to solve the problems associated with this phenomenon, a number of methods and techniques were developed. Spectral clustering is a data mining method used in many applications; in this paper we used this method to find students' behavioral patterns performed in an elearning system. In ad- dition, a software was introduced to allow the user (tutor or researcher) to define the data dimensions and input values to obtain appropriate graphs with behavioral pattens that meet his/her needs. Behavioral pat- terns were compared with students' study performance and evaluation with relation to their possible usage in collaborative learning.
The scaling of experiments on volcanic systems

In this article, the basic principles of the scaling procedure are first reviewed by a presentation of scale factors. Then, taking an idealized example of a brittle volcanic cone intruded by a viscous magma, the way to choose appropriate analogue materials for both the brittle and ductile parts of the cone is explained by the use of model ratios. Lines of similarity are described to show that an experiment simulates a range of physical processes instead of a unique natural case. The pi theorem is presented as an alternative scaling procedure and discussed through the same idealized example to make the comparison with the model ratio procedure. The appropriateness of the use of gelatin as analogue material for simulating dyke formation is investigated. Finally, the scaling of some particular experiments such as pyroclastic flows or volcanic explosions is briefly presented to show the diversity of scaling procedures in volcanology.
Integrable PolyVector fields

We present a framework for designing curl-free tangent vector fields on discrete surfaces. Such vector fields are gradients of locally-defined scalar functions, and this property is beneficial for creating surface parameterizations, since the gradients of the parameterization coordinate functions are then exactly aligned with the designed fields. We introduce a novel definition for discrete curl between unordered sets of vectors (PolyVectors), and devise a curl-eliminating continuous optimization that is independent of the matchings between them. Our algorithm naturally places the singularities required to satisfy the user-provided alignment constraints, and our fields are the gradients of an inversion-free parameterization by design.
Building Carbon Bridges on and between Fullerenes in Helium Nanodroplets

We report the observation of sequential encounters of fullerenes with C atoms in an extremely cold environment. Experiments were performed with helium droplets at 0.37 K doped with C60 molecules and C atoms derived from a novel, pure source of C atoms. Very high-resolution mass spectra revealed the formation of carbenes of the type C60(C:)n with n up to 6. Bridge-type bonding of the C adatoms to form the known dumbbell C60=C=C60 also was observed. Density functional theory calculations were performed that elucidated the carbene character of the C60(C:)n species and their structures. Mass spectra taken in the presence of water impurities and in separate experiments with added H2 also revealed the formation of the adducts C60Cn(H2O)n and C60Cn(H2)n probably by H–OH and H–H bond insertion, respectively, and nonreactivity for the dumbell. So C adatoms that form carbenes C60(C:)n can endow pristine C60 with a higher chemical reactivity.
T Cell LFA-1 Engagement Induces HuR-Dependent Cytokine mRNA Stabilization through a Vav-1, Rac1/2, p38MAPK and MKK3 Signaling Cascade

Background Engagement of the β2 integrin, lymphocyte function-associated antigen-1 (LFA-1), results in stabilization of T cell mRNA transcripts containing AU-rich elements (AREs) by inducing rapid nuclear-to-cytosolic translocation of the RNA-stabilizing protein, HuR. However, little is known regarding integrin-induced signaling cascades that affect mRNA catabolism. This study examines the role of the GTPases, Rac 1 and Rac 2, and their downstream effectors, in the LFA-1-induced effects on mRNA. Methodology/Principal Findings Engagement of LFA-1 to its ligand, ICAM-1, in human peripheral T cells resulted in rapid activation of Rac1 and Rac2. siRNA-mediated knockdown of either Rac1 or Rac2 prevented LFA-1-stimulated stabilization of the labile transcripts encoding IFN-γ and TNF-α, and integrin mediated IFN-γ mRNA stabilization was absent in T cells obtained from Rac2 gene-deleted mice. LFA-1 engagement-induced translocation of HuR and stabilization of TNF- α mRNA was lost in Jurkat cells deficient in the Rac guanine nucleotide exchange factor Vav-1 (J.Vav1). The transfection of J.Vav1 cells with constitutively active Rac1 or Rac2 stabilized a labile β-globin reporter mRNA, in a HuR-dependent manner. Furthermore, LFA-1-mediated mRNA stabilization and HuR translocation in mouse splenic T cells was dependent on the phosphorylation of the mitogen-activated protein kinase kinase, MKK3, and its target MAP kinase p38MAPK, and lost in T cells obtained from MKK3 gene-deleted mice. Conclusions/Significance Collectively, these results demonstrate that LFA-1-induced stabilization of ARE-containing mRNAs in T cells is dependent on HuR, and occurs through the Vav-1, Rac1/2, MKK3 and p38MAPK signaling cascade. This pathway constitutes a molecular switch that enhances immune and pro-inflammatory gene expression in T cells undergoing adhesion at sites of activation and effector function.
Annotation and features of non-native Mandarin tone quality

Native speakers of non-tonal languages, such as American English, frequently have difficulty accurately producing the tones of Mandarin Chinese. This paper describes a corpus of Mandarin Chinese spoken by non-native speakers and annotated for tone quality using a simple good/bad system. We examine interrater correlation of the annotations and highlight the differences in feature distribution between native, good non-native, and bad non-native tone productions. We find that the features of tones judged by a simple majority to be bad are significantly different from features from tones judged to be good, and tones produced by native speakers.
Dynamic ECO-driving for arterial corridors

There are a variety of strategies that are now being considered to reduce fuel consumption and carbon dioxide (CO2) emissions from the transportation sector. One strategy that is gaining interest worldwide is known as “eco-driving”. Eco-driving typically consists of changing a person's driving behavior based on general (static) advice to the driver, such as accelerating slowly, driving smoothly, reducing high speeds, etc. Taking this one-step further, it is possible to provide realtime advice to drivers based on changing traffic and infrastructure conditions for even greater fuel and emission savings. This concept of dynamic eco-driving takes advantage of real-time traffic sensing and infrastructure information, which can then be communicated to a vehicle with a goal of reducing fuel consumption and emissions. In this paper, we consider dynamic eco-driving in an arterial corridor with traffic signals, where signal phase and timing information of a traffic light is provided to the vehicle. The vehicle can then adjust its velocity while traveling through a signalized corridor with the goal of minimizing fuel consumption and emissions. A dynamic eco-driving velocity planning algorithm has been developed and is described herein. This algorithm has then been tested in simulation, showing initial fuel economy and CO2 improvements of around 12%.
Community ecology in the age of multivariate multiscale spatial analysis

Species spatial distributions are the result of population demography, behavioral traits, and species interactions in spatially heterogeneous environmental conditions. Hence the composition of species assemblages is an integrative response variable, and its variability can be explained by the complex interplay among several structuring factors. The thorough analysis of spatial variation in species assemblages may help infer processes shaping ecological communities. We suggest that ecological studies would benefit from the combined use of the classical statistical models of community composition data, such as constrained or unconstrained multivariate analyses of site-by-species abundance tables, with rapidly emerging and diversifying methods of spatial pattern analysis. Doing so allows one to deal with spatially explicit ecological models of beta diversity in a biogeographic context through the multiscale analysis of spatial patterns in original species data tables, including spatial characterization of fitted or residual variation from environmental models. We summarize here the recent progress for specifying spatial features through spatial weighting matrices and spatial eigenfunctions in order to define spatially constrained or scale-explicit multivariate analyses. Through a worked example on tropical tree communities, we also show the potential of the overall approach to identify significant residual spatial patterns that could arise from the omission of important unmeasured explanatory variables or processes.
An equation for the latent heat of vaporization

An expression for the latent heat of vaporization of a fluid is formulated employing renormalization-group theory predictions for the thermodynamics of fluids in the vicinity of the critical point. A least-squares fit of the latent heat data of water is made using the general and relatively simple equation: L = a/sub 1/t/sup . beta. / + a/sub 2/t/sup . beta. /sup +/. delta. / + a/sub 4/t/sup 1-. cap alpha. +. beta. / + . sigma.M/sub n=1/b/sub n/t/sup n/, 3 less than or equal to M less than or equal to 5, yielding predicted values that are in excellent agreement with the data throughout a wide range of temperature. The optimum value of the critical temperature, 373.92/sup 0/C, is found to be somewhat lower than the tabulated value.
Teaching Robotics and Computer Science with Pinball Machines

Roboticists need to have a solid understanding of hardware and software. The standard computer science education in the United States, however, tends to teach students only about software. To remedy this situation, we explore new ways of teaching them about hardware in a playful way. Realizing that pinball machines are simple robots, we have developed a pinball machine interface between a PC and a recent Lord of the Rings pinball machine, which enables students to implement pinball games and gain knowledge of hardware and interface programming in the process. This paper describes both our pinball machine interface and our experience developing it. As far as we know, this is the first time that anyone has managed to control an existing pinball machine completely.