Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithmic rate-distortion theory

Kolmogorov complexity is the accepted absolute measure of the information content of an individual finite object. It gives the ultimate limit on the number of bits resulting from lossless compression of the object--more precisely, the number of bits from which effective lossless decompression of the object is possible. A similar absolute approach is needed for lossy compression, that is, a rate-distortion theory giving the ultimate effective limits for individual finite data objects. We give natural definitions of the rate-distortion functions of individual data (independent of a random source producing those data). We analyze the possible shapes of the rate-distortion graphs for all data and all computable distortions. We formulate a new problem related to the practice of lossy compression. Is it the case that a lossily compressed representation that realizes least distortion of the source object at a given rate also captures an appropriate part of the ``essence'' or ``meaning'' of that object? We are deliberately vague here until we introduce the appropriate formalism. Clearly, this question cannot be well posed in the Shannon setting, where we deal with expected distortion in communication, but explicitly not with ``meaning. '' We show that in our setting this question is answered in the affirmative for every distortion measure that satisfies a certain parsimony-of-covering property.
An Integrated Approach to the Generation of Environments from Formal Specifications

This paper describes an experiment in the use of a persistent object store to support the construction and execution of a software development environment. This development environment presents the user with language specific editors which provide access to incremental parsers. The editors and parsers are automatically generated from a formal language specification based on attribute grammars. This is facilitated through the persistent management of types and values and a dynamically callable compiler. We demonstrate that the provision of a persistent object store gives the system designer more freedom and that this leads to the construction of novel software architectures.
NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP)

Models of biochemical systems with few copies of molecules should be stochastic and should account for the random interplay among networks. Despite mathematical tools to account for low-level intrinsic fluctuations are well-known, less is known about the modeling of interplay, especially in biology. Classical abstractions use extrinsic unbounded gaussian noises to model these interplays. However, recent literature showed that bounded noises are a more realistic abstraction. NoisySim is a Java library to simulate chemically reacting systems where both intrinsic stochasticity and extrinsic bounded noises are present. Intrinsic low-numbers fluctuations are accounted by a Gillespie-like approach, extrinsic noises are modeled as Langevin stochastic equations affecting the model jump rates. NoisySim allows to approximate the solution of the Chapman-Kolgomorov equation characterizing the system, thus allowing to asses whether biochemical noise plays a functional role for a target network.
Energy-Efficient Building HVAC Control Using Hybrid System LBMPC

Improving the energy-efficiency of heating, ventilation, and air-conditioning (HVAC) systems has the potential to realize large economic and societal benefits. This paper concerns the system identification of a hybrid system model of a building-wide HVAC system and its subsequent control using a hybrid system formulation of learning-based model predictive control (LBMPC). Here, the learning refers to model updates to the hybrid system model that incorporate the heating effects due to occupancy, solar effects, outside air temperature (OAT), and equipment, in addition to integrator dynamics inherently present in low-level control. Though we make significant modeling simplifications, our corresponding controller that uses this model is able to experimentally achieve a large reduction in energy usage without any degradations in occupant comfort. It is in this way that we justify the modeling simplifications that we have made. We conclude by presenting results from experiments on our building HVAC testbed, which show an average of 1.5MWh of energy savings per day (p = 0.002) with a 95% confidence interval of 1.0MWh to 2.1MWh of energy savings.
Finite Element Modeling of Chip Formation in the Domain of Negative Rake Angle Cutting

A thermo-elastic-plastic finite element modeling of orthogonal cutting with a large negative rake angle has been developed to understand the mechanism and thermal aspects of grinding. A stagnant chip material ahead of the tool tip, which is always observed with large negative rake angles, is assumed to act like a stable built-up edge. Serrated chips, one of typical shapes of chips observed in single grain grinding experiment, form when analyzing the machining of 0.93%C carbon steel SK-5 with a rake angle of minus forty five or minus sixty degrees. There appear high and low temperature zones alternately according to severe and mild shear in the primary shear zone respectively. The shapes of chips depend strongly on the cutting speed and undeformed chip thickness; as the cutting speed or the undeformed chip thickness decreases, chip shape changes from a serrated type to a bulging one to a wavy or flow type. Therefore, there exists the critical cutting speed over which a chip can form and flow along a rake face for a given large negative rake angle and undeformed chip thickness.
Inflammatory Blood Monocytes Contribute to Tumor Development and Represent a Privileged Target To Improve Host Immunosurveillance

Progressing tumors in humans and mice are frequently infiltrated by a highly heterogeneous population of inflammatory myeloid cells that contribute to tumor growth. Among these cells, inflammatory Gr-1+ monocytes display a high developmental plasticity in response to specific microenvironmental signals, leading to diverse immune functions. These observations raise the question of the immune mechanisms by which inflammatory monocytes may contribute to tumor development. In this study, we found that adoptive transfer of normal inflammatory Gr-1+ monocytes in tumor-bearing mice promotes tumor growth. In this tumoral environment, these monocytes can differentiate into tolerogenic dendritic cells (DCs) that produce IL-10 and potently induce regulatory T cell responses in vivo. Moreover, diverting the differentiation of Gr-1+ monocytes into tolerogenic DCs by forced expression of IL-10 soluble receptor and IL-3 in tumor cells improves host immunosurveillance by reducing the regulatory T cell frequency and by inducing immunogenic DCs in the tumor. As a consequence, tumor growth is strongly reduced. Our findings indicate that Gr-1+ monocytes represent a valuable target for innovative immunotherapeutic strategies against cancer.
Factored Markov decision processes with Imprecise Transition Probabilities

This paper presents a short survey of the research we have carried out on planning under uncertainty where we consider different forms of imprecision on the probability transition functions. Our main results are on efficient solutions for Markov Decision Process with Imprecise Transition Probabilities (MDP-IPs), a generalization of a Markov Decision Process where the imprecise probabilities are given in terms of credal sets. Noting that the key computational bottleneck in the solution of MDP-IPs is the need to repeatedly solve an optimization problem. Our results show how to target approximation techniques to drastically reduce the computational overhead of the optimization solver while producing bounded, approximately optimal solutions.
Application‐specific thread schedulers for internet server applications

This paper describes CATAPULTS (Creating And Testing APplication‐specific User Level Thread Schedulers), a domain‐specific language for creating and testing application‐specific user‐level thread schedulers. Using a domain‐specific language to write user‐level thread schedulers provides three advantages. First, doing so modularizes the thread scheduler, making it easy to plug in and experiment with different thread scheduling strategies. Second, using a domain‐specific language for scheduling code helps prevent several of the common programming mistakes that are easy to make when developing thread schedulers. Finally, the CATAPULTS translator has multiple backends that generate code for different languages and libraries. This makes it easy to prototype an application in a high‐level language and then later port it to a low‐level language; the CATAPULTS translator will take care of generating the appropriate code for both the prototype and the final version of the program from a single scheduler specification. This paper describes how we have used CATAPULTS to improve the performance of two important and representative Internet server applications. Copyright © 2011 John Wiley & Sons, Ltd.
RNA, but not protein partners, is directly responsible for translational silencing by a bacterial Hfq-binding small RNA

SgrS is an Hfq-binding small RNA that is induced under glucose phosphate stress in Escherichia coli. It forms a specific ribo nucleo protein complex with Hfq and RNase E resulting in translational repression and rapid degradation of ptsG mRNA, encoding the glucose transporter. Here, we report translational silencing of ptsG mRNA in a defined in vitro system. We demonstrate that SgrS and Hfq are the minimum components for translational silencing to faithfully reproduce the reaction in cells. We show that ptsG-SgrS base pairing is sufficient to cause translational repression when the ptsG mRNA is forced to base pair with SgrS without the help of Hfq. The extent of translational repression correlates with the extent of duplex formation. We conclude that base pairing itself but not Hfq is directly responsible for translational silencing and the major role of Hfq in gene silencing is to stimulate the base pairing between SgrS and ptsG mRNA. This simple mechanism is in striking contrast to miRNA action in eukaryote in which the RNA is believed to act only as a guide of protein partners.
Aligned Single‐Crystalline β‐Si3N4 Whiskers Prepared with SHS Process

Aligned single‐crystalline β‐Si3N4 whiskers with high aspect ratio were first prepared via a Self‐propagating high temperature‐synthesis (SHS) process, by using tungsten powders as catalysts. The as‐synthesized Si3N4 whiskers typically have uniform diameters of 400 nm, length about 200 µm, and exhibit smooth and straight surfaces. Above all, the products possesses a perfect aligned structure, which is quite different from the reported β‐Si3N4 whiskers. Elastic bending modulus of individual whiskers was measured by in‐situ TEM process, the average value of elastic bending modulus of individual as‐synthesized whiskers was 488 GPa. Results revealed that tungsten powders plays an significant effects on the morphology of Si3N4 whiskers.
The expanding syndrome of amyotrophic lateral sclerosis: a clinical and molecular odyssey

Recent advances in understanding amyotrophic lateral sclerosis (ALS) have delivered new questions. Disappointingly, the initial enthusiasm for transgenic mouse models of the disease has not been followed by rapid advances in therapy or prevention. Monogenic models may have inadvertently masked the true complexity of the human disease. ALS has evolved into a multisystem disorder, involving a final common pathway accessible via multiple upstream aetiological tributaries. Nonetheless, there is a common clinical core to ALS, as clear today as it was to Charcot and others. We stress the continuing relevance of clinical observations amid the increasing molecular complexity of ALS.
Motion planning in environments with danger zones

This paper addresses the problem of path planning for a free-flying object in a (three-dimensional) environment that contains both obstacles and so-called danger zones. The path should (obviously) avoid collisions with the obstacles. The path is allowed to intersect with the danger zones, but this should be avoided as much as possible. We show that under some mild conditions, a path always exists in which the moving object never completely penetrates the danger zones. Based on this result we present a probabilistically complete roadmap method that finds such paths. The methods has been implemented and some experimental results are given.
Host specialization in ticks and transmission of tick-borne diseases: a review

Determining patterns of host use, and the frequency at which these patterns change, are of key importance if we are to understand tick population dynamics, the evolution of tick biodiversity, and the circulation and evolution of associated pathogens. The question of whether ticks are typically host specialists or host generalists has been subject to much debate over the last half-century. Indeed, early research proposed that morphological diversity in ticks was linked to host specific adaptations and that most ticks were specialists. Later work disputed this idea and suggested that ticks are largely limited by biogeographic conditions and tend to use all locally available host species. The work presented in this review suggests that the actual answer likely lies somewhere between these two extremes. Although recent observational studies support the view that phylogenetically diverse host species share ticks when found on similar ecological ranges, theory on host range evolution predicts that host specialization should evolve in ticks given their life history characteristics. Contemporary work employing population genetic tools to examine host-associated population structure in several tick systems support this prediction and show that simple species records are not enough to determine whether a parasite is a true host generalist; host specialization does evolve in ticks at local scales, but may not always lead to speciation. Ticks therefore seem to follow a pattern of being global generalists, local specialists. Given this, the notion of host range needs to be modified from an evolutionary perspective, where one simply counts the number of hosts used across the geographic distribution, to a more ecological view, where one considers host use at a local scale, if we are to better understand the circulation of tick-borne pathogens and exposure risks for humans and livestock.
Comparative Activity and β-Lactamase Stability of Cefoperazone, a Piperazine Cephalosporin

The in vitro activity and β-lactamase stability of 7-[d(−)-α-(4-ethyl-2,3-dioxopiperazino-carbonylamino) -p-hydroxyphenylacetamido]-3-[(1-methyl)-5-tetrazolylthiomethyl] -Δ3-cephem-4-carboxylic acid (cefoperazone), a cephalosporin analog of piperacillin, were compared with the activities and stabilities of other cephalosporins and cephamycins. The compound was less active than cephalothin or cefamandole in inhibiting Staphylococcus aureus; it was as active as cefamandole and cefoxitin against most of the Enterobacteriaceae but less active than cefotaxime. It was more active than carbenicillin or piperacillin against Pseudomonas aeruginosa. In general, the compound was not active against Bacteroides. It was hydrolyzed by the β-lactamases of some Escherichia coli which hydrolyzed cefamandole, but was stable to most plasmid-mediated, chromosomally mediated, inducible β-lactamases in the Enterobacteriaceae and Pseudomonas.
Effects of ear-canal standing waves on measurements of distortion-product otoacoustic emissions.

At frequencies above 3 kHz, standing waves in the ear canal complicate calibration of stimulus sound-pressure levels (SPLs) for measurements of distortion-product otoacoustic emissions (DPOAEs). In the literature, two stimulus-presentation strategies have been used for DPOAE measurements. In the "in-the-ear adjustment" strategy, the voltage command to the speakers is adjusted to maintain a constant stimulus SPL across frequency at the DPOAE-measurement microphone. In the "iso-voltage" strategy, the voltage presented to the speakers is held constant across frequency, on the basis of the assumption that the frequency response of the speakers is approximately flat at the eardrum in the average human ear canal. Because of standing-wave effects, there are large, systematic but idiosyncratic differences of stimulus SPL between the two strategies. DPOAE-versus-frequency functions ("DPOAE audiograms") obtained using both stimulus-presentation strategies in the same ears are presented. The differences of stimulus SPL between the two strategies, and the associated differences of DPOAE amplitude, are described and quantified. Around frequencies of standing-wave minima at the DPOAE probe, the in-the-ear adjustment strategy resulted in smaller DPOAEs at high L1 = L2, but much larger DPOAEs at low L1 = L2, than did the iso-voltage strategy. For any L1, the DPOAE-amplitude differences between the two strategies varied systematically with L1-L2. At the stimulus levels used to construct previously published population norms for clinical applications (i.e., L1 > or = 65 dB SPL), there are only small differences of mean DPOAE amplitudes, and of the standard deviations of these means, between the two strategies.
Robust facial feature tracking using selected multi-resolution linear predictors

This paper proposes a learnt data-driven approach for accurate, real-time tracking of facial features using only intensity information. Constraints such as a-priori shape models or temporal models for dynamics are not required or used. Tracking facial features simply becomes the independent tracking of a set of points on the face. This allows us to cope with facial configurations not present in the training data. Tracking is achieved via linear predictors which provide a fast and effective method for mapping pixel-level information to tracked feature position displacements. To improve on this, a novel and robust biased linear predictor is proposed in this paper. Multiple linear predictors are grouped into a rigid flock to increase robustness. To further improve tracking accuracy, a novel probabilistic selection method is used to identify relevant visual areas for tracking a feature point. These selected flocks are then combined into a hierarchical multi-resolution LP model. Experimental results also show that this method performs more robustly and accurately than AAMs, without any a priori shape information and with minimal training examples.
Pair Approximations of Takeover Dynamics in Regular Population Structures

In complex adaptive systems, the topological properties of the interaction network are strong governing influences on the rate of flow of information throughout the system. For example, in epidemiological models, the structure of the underlying contact network has a pronounced impact on the rate of spread of infectious disease throughout a population. Similarly, in evolutionary systems, the topology of potential mating interactions (i.e., population structure) affects the rate of flow of genetic information and therefore affects selective pressure. One commonly employed method for quantifying selective pressure in evolutionary algorithms is through the analysis of the dynamics with which a single favorable mutation spreads throughout the population (a.k.a. takeover time analysis). While models of takeover dynamics have been previously derived for several specific regular population structures, these models lack generality. In contrast, so-called pair approximations have been touted as a general technique for rapidly approximating the flow of information in spatially structured populations with a constant (or nearly constant) degree of nodal connectivities, such as in epidemiological and ecological studies. In this work, we reformulate takeover time analysis in terms of the well-known Susceptible-Infectious-Susceptible model of disease spread and adapt the pair approximation for takeover dynamics. Our results show that the pair approximation, as originally formulated, is insufficient for approximating pre-equibilibrium dynamics, since it does not properly account for the interaction between the size and shape of the local neighborhood and the population size. After parameterizing the pair approximation to account for these influences, we demonstrate that the resulting pair approximation can serve as a general and rapid approximator for takeover dynamics on a variety of spatially-explicit regular interaction topologies with varying population sizes and varying uptake and reversion probabilities. Strengths, limitations, and potential applications of the pair approximation to evolutionary computation are discussed.
DataView: National Health Expenditure Projections, 1994–2005

Using 1993 as a baseline and assuming that current laws and practices continue, the authors project U.S. health expenditures through the year 2005. Annual spending growth has declined since 1990, and, in the scenario reported here, that trend continues in 1994. Growth of health spending increases thereafter, but remains below the average experience of the past decade. Even so, health expenditures grow faster than the gross domestic product (GDP), and by 2005, account for 17.9 percent of the GDP. Unless the system changes, Medicare and Medicaid are projected to pay for an increasing share of total spending during the next decade.
Multi-Objective Programming in SVMs

We propose a general framework for support vector machines (SVM) based on the principle of multi-objective optimization. The learning of SVMs is formulated as a multi-objective program by setting two competing goals to minimize the empirical risk and minimize the model capacity. Distinct approaches to solving the MOP introduce various SVM formulations. The proposed framework enables a more effective minimization of the VC bound on the generalization risk. We develop a feature selection approach based on the MOP framework and demonstrate its effectiveness on hand-written digit data.
Continuous Integration (CI) Needs and Wishes for Developers of Proprietary Code

Continuous integration (CI) systems automate the compilation, building, and testing of software. Despite CI being one of the most widely used processes in software engineering, we do not know what motivates developers to use CI, and what barriers and unmet needs they face. Without such knowledge developers make easily avoidable errors, managers reduce the productivity of developers by making misinformed decisions, tool builders invest in the wrong direction, and researchers miss many opportunities for improving the software engineering practice. Given the large fraction of proprietary code development, understanding how proprietary developers are using CI is vital to improving it. We present the first study of how CI is used in the proprietary development of software. We conduct 16 semi-structured interviews with developers from different industries and development scale. We generalize these findings by surveying 523 developers from all over the world. We find that 78% of developers feel more productive when using CI, and 85% think that using CI causes developers to give more value to automated testing. However, unlike open-source developers, many proprietary developers want to use CI but are not allowed to do so. 50% of developers have problems troubleshooting CI builds, and more than half of developers want easier configurations for CI tools and services.