Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploiting purity for atomicity

Multithreaded programs often exhibit erroneous behavior because of unintended interactions between concurrent threads. This paper focuses on the noninterference property of atomicity. A procedure is atomic if, for every execution, there is an equivalent serial execution in which the actions of the atomic procedure are not interleaved with actions of other threads. This key property makes atomic procedures amenable to sequential reasoning techniques, which significantly facilitates subsequent validation activities such as code inspection and testing. Several existing tools verify atomicity by using commutativity of actions to show that every execution reduces to a corresponding serial execution. However, experiments with these tools have highlighted a number of interesting procedures that, while intuitively atomic, are not reducible. In this paper, we exploit the notion of pure code blocks to verify the atomicity of such irreducible procedures. If a pure block terminates normally, then its evaluation does not change the program state and, hence, these evaluation steps can be removed from the program trace before reduction. We develop a static typed-based analysis for atomicity based on this insight, and we illustrate this analysis on a number of interesting examples that could not be verified using earlier tools based purely on reduction.
Holographic Reduced Representations: Convolution Algebra for Compositional Distributed Representations

A solution to the problem of representing compo-sitional structure using distributed representations is described. The method uses circular convolution to associate items, which are represented by v ec-tors. Arbitrary variable bindings, short sequences of various lengths, frames, and reduced representations can be compressed into a xed width vector. These representations are items in their own right, and can be used in constructing compositional structures. The noisy reconstructions given by convolution memories can be cleaned up by using a separate associative memory that has good recon-structive properties.
In Vivo Targeting of Underglycosylated MUC-1 Tumor Antigen Using a Multimodal Imaging Probe

One of the most difficult challenges of oncology is to improve methods for early tumor detection, which is crucial for the success of cancer therapy and greatly improves the survival rate. Underglycosylated mucin-1 antigen (uMUC-1) is one of the early hallmarks of tumorigenesis and is overexpressed and underglycosylated on almost all human epithelial cell adenocarcinomas as well as in nonepithelial cancer cell lines, as well as in hematological malignancies such as multiple myeloma, and some B-cell non-Hodgkin lymphomas. In this study, we designed, synthesized, and tested a novel multimodal imaging probe specifically recognizing in vivo uMUC-1 antigen in an animal model of human cancer. Furthermore, in vivo magnetic resonance- and near-infrared-imaging experiments on tumor-bearing animals showed specific accumulation of the probe in uMUC-1-positive tumors and virtually no signal in control tumors. We expect that this probe has a potential to greatly aid in screening prospective patients for early cancer detection and in monitoring the efficacy of drug therapy.
The Mitochondrial Protein Translocation Motor: Structural Conservation between the Human and Yeast Tim14/Pam18-Tim16/Pam16 co-Chaperones

Most of our knowledge regarding the process of protein import into mitochondria has come from research employing Saccharomyces cerevisiae as a model system. Recently, several mammalian homologues of the mitochondrial motor proteins were identified. Of particular interest for us is the human Tim14/Pam18-Tim16/Pam16 complex. We chose a structural approach in order to examine the evolutionary conservation between yeast Tim14/Pam18-Tim16/Pam16 proteins and their human homologues. For this purpose, we examined the structural properties of the purified human proteins and their interaction with their yeast homologues, in vitro. Our results show that the soluble domains of the human Tim14/Pam18 and Tim16/Pam16 proteins interact with their yeast counterparts, forming heterodimeric complexes and that these complexes interact with yeast mtHsp70.
Perceiving Possibilities for Action: On the Necessity of Calibration and Perceptual Learning for the Visual Guidance of Action

Tasks such as steering, braking, and intercepting moving objects constitute a class of behaviors, known as visually guided actions, which are typically carried out under continuous control on the basis of visual information. Several decades of research on visually guided action have resulted in an inventory of control laws that describe for each task how information about the sufficiency of one's current state is used to make ongoing adjustments. Although a considerable amount of important research has been generated within this framework, several aspects of these tasks that are essential for successful performance cannot be captured. The purpose of this paper is to provide an overview of the existing framework, discuss its limitations, and introduce a new framework that emphasizes the necessity of calibration and perceptual learning. Within the proposed framework, successful human performance on these tasks is a matter of learning to detect and calibrate optical information about the boundaries that separate possible from impossible actions. This resolves a long-lasting incompatibility between theories of visually guided action and the concept of an affordance. The implications of adopting this framework for the design of experiments and models of visually guided action are discussed.
Simulating secondary organic aerosol in a regional air quality model using the statistical oxidation model - Part 2: Assessing the influence of vapor wall losses

Abstract. The influence of losses of organic vapors to chamber walls during secondary organic aerosol (SOA) formation experiments has recently been established. Here, the influence of such losses on simulated ambient SOA concentrations and properties is assessed in the University of California at Davis / California Institute of Technology (UCD/CIT) regional air quality model using the statistical oxidation model (SOM) for SOA. The SOM was fit to laboratory chamber data both with and without accounting for vapor wall losses following the approach of Zhang et al. (2014). Two vapor wall-loss scenarios are considered when fitting of SOM to chamber data to determine best-fit SOM parameters, one with “low” and one with “high” vapor wall-loss rates to approximately account for the current range of uncertainty in this process. Simulations were run using these different parameterizations (scenarios) for both the southern California/South Coast Air Basin (SoCAB) and the eastern United States (US). Accounting for vapor wall losses leads to substantial increases in the simulated SOA concentrations from volatile organic compounds (VOCs) in both domains, by factors of ∼ 2–5 for the low and ∼ 5–10 for the high scenarios. The magnitude of the increase scales approximately inversely with the absolute SOA concentration of the no loss scenario. In SoCAB, the predicted SOA fraction of total organic aerosol (OA) increases from ∼ 0.2 (no) to ∼ 0.5 (low) and to ∼ 0.7 (high), with the high vapor wall-loss simulations providing best general agreement with observations. In the eastern US, the SOA fraction is large in all cases but increases further when vapor wall losses are accounted for. The total OA ∕ ΔCO ratio captures the influence of dilution on SOA concentrations. The simulated OA ∕ ΔCO in SoCAB (specifically, at Riverside, CA) is found to increase substantially during the day only for the high vapor wall-loss scenario, which is consistent with observations and indicative of photochemical production of SOA. Simulated O : C atomic ratios for both SOA and for total OA increase when vapor wall losses are accounted for, while simulated H : C atomic ratios decrease. The agreement between simulations and observations of both the absolute values and the diurnal profile of the O : C and H : C atomic ratios for total OA was greatly improved when vapor wall-losses were accounted for. These results overall demonstrate that vapor wall losses in chambers have the potential to exert a large influence on simulated ambient SOA concentrations, and further suggest that accounting for such effects in models can explain a number of different observations and model–measurement discrepancies.
Cosmic microwave background constraints on the strong equivalence principle

We study the effect of a violation of the strong equivalence principle (SEP) on the cosmic microwave background (CMB). Such a violation would modify the weight of baryons in the primordial gravitational potentials and hence their impact in the establishment of the photon-baryon plasma acoustic oscillations before recombination. This cosmological Nordtvedt effect alters the odd peaks height of the CMB temperature anisotropy power spectrum. A gravitational baryonic mass density of the universe may already be inferred at the first peak scale from the analysis of WMAP data. Experimental constraints on a primordial SEP violation are derived from a comparison with the universe's inertial baryonic mass density measured either in a full analysis of the CMB, or in the framework of the standard big bang nucleosynthesis (BBN). Comment: Version accepted for publication in Phys. Rev. D, 8 pages, Revtex 4; discussion of "Experimental constraints" extended, references added, typos corrected
T-box3 is a ciliary protein and regulates stability of the Gli3 transcription factor to control digit number

Crucial roles for T-box3 in development are evident by severe limb malformations and other birth defects caused by T-box3 mutations in humans. Mechanisms whereby T-box3 regulates limb development are poorly understood. We discovered requirements for T-box at multiple stages of mouse limb development and distinct molecular functions in different tissue compartments. Early loss of T-box3 disrupts limb initiation, causing limb defects that phenocopy Sonic Hedgehog (Shh) mutants. Later ablation of T-box3 in posterior limb mesenchyme causes digit loss. In contrast, loss of anterior T-box3 results in preaxial polydactyly, as seen with dysfunction of primary cilia or Gli3-repressor. Remarkably, T-box3 is present in primary cilia where it colocalizes with Gli3. T-box3 interacts with Kif7 and is required for normal stoichiometry and function of a Kif7/Sufu complex that regulates Gli3 stability and processing. Thus, T-box3 controls digit number upstream of Shh-dependent (posterior mesenchyme) and Shh-independent, cilium-based (anterior mesenchyme) Hedgehog pathway function. DOI: http://dx.doi. org/10.7554/eLife.07897. 001
Identifying tumor promoting genomic alterations in tumor-associated fibroblasts via retrovirus-insertional mutagenesis

Tumor-associated fibroblasts (TAFs) are often essential for solid tumor growth. However, few genetic or epigenetic alterations have been found in TAFs during the progression of solid tumors. Employing a tumor-stromal cell co-injection model, we adapted here retroviral-insertional mutagenesis to stromal cells to identify novel tumor-associated genes in TAFs. We successfully identified 20 gene candidates that might modulate tumor growth if altered in TAFs at genomic level. To validate our finding, the function of one of the candidate genes, tubulin tyrosine ligase (Ttl), was further studied in TAFs from fibrosarcoma, colon, breast and hepatocarcinoma. We demonstrated that down-regulated TTL expression in TAFs indeed promoted tumor growth in mice. Interestingly, decreased expression of TTL in tumor stromal cells also correlated with poor outcome in human colon carcinoma. Thus, the co-injection model of tumor cells with retrovirus-modified fibroblasts proved a valid method to identify tumor-modulating genes in TAFs, allowing for a deeper insight into the role of the stroma for tumor development.
Tuberculosis: 2. History of the disease in Canada.

In the pre-chemotherapy era, tuberculosis (TB) was almost universal, affected young and old, presented a wide array of morbid effects and carried a high mortality rate. In the post-chemotherapy era, the epidemiology has changed, and the strategies for controlling TB have had to be refocused. The abrupt switch from sanatorium to outpatient care taught important lessons about compliance with drug treatment. This short history of TB will describe how the disease came to Canada, its effect on various population groups and what measures have been taken to control, prevent and treat it. For those who want to explore this subject more fully, several valuable publications are available.
A TSK-type recurrent fuzzy network for dynamic systems processing by neural network and genetic algorithms

In this paper, a TSK-type recurrent fuzzy network (TRFN) structure is proposed. The proposal calls for the design of TRFN by either neural network or genetic algorithms depending on the learning environment. A recurrent fuzzy network is described which develops from a series of recurrent fuzzy if-then rules with TSK-type consequent parts. The recurrent property comes from feeding the internal variables, derived from fuzzy firing strengths, back to both the network input and output layers. In this configuration, each internal variable is responsible for memorizing the temporal history of its corresponding fuzzy rule. The internal variable is also combined with external input variables in each rule's consequence, which shows an increase in network learning ability. TRFN design under different learning environments is next advanced. For problems where supervised training data is directly available, TRFN with supervised learning (TRFN-S) is proposed, and a neural network (NN) learning approach is adopted for TRFN-S design. An online learning algorithm with concurrent structure and parameter learning is proposed. With flexibility of partition in the precondition part, and outcome of TSK-type, the TRFN-S displays both small network size and high learning accuracy. For problems where gradient information for NN learning is costly to obtain or unavailable, like reinforcement learning, TRFN with Genetic learning (TRFN-G) is put forward. The precondition parts of TRFN-G are also partitioned in a flexible way, and all free parameters are designed concurrently by genetic algorithm. Owing to the well-designed network structure of TRFN, TRFN-G, like TRFN-S, is characterized by high learning accuracy. To demonstrate the superior properties of TRFN, TRFN-S is applied to dynamic system identification and TRFN-G to dynamic system control. By comparing the results to other types of recurrent networks and design configurations, the efficiency of TRFN is verified.
A COMPARISON OF THE RESULTS OF REGULATORY COMPLIANCE INSPECTIONS IN 1999 BY THE STATES OF TEXAS, MAINE, AND WASHINGTON

Abstract— Inspection outcome data provided by the state of Washington Department of Health, Division of Radiation Protection, for licensees of radioactive materials was encoded according to a system established by the Texas Department of Health, Bureau of Radiation Control. The data, representing calendar year 1999 inspection activities, were then analyzed and the results compared to previously published studies for the same year in the states of Texas and Maine. Despite significant differences in regulatory program size, age, and geographic proximity, the most frequently cited violation for radioactive materials licensees were shown to be similar for all three states. Of particular note were the violations that were identified to be consistently issued in all three states. These included physical inventories and utilization logs not performed, not available, or incomplete; leak testing not performed or not performed on schedule; inadequate or unapproved operating and safety procedures; radiation survey and disposal records not available or incomplete; detection or measurement instrument calibration not performed or records not available; and radiation surveys or sampling not performed or performed with a noncalibrated instrument. Comparisons were made in an attempt to generate a summary of the most commonly issued violations that could be generalized to users of radioactive materials across the United States. A generalized list of common violations would be an invaluable tool for radiation protection programs, serving to aid in the reduction of the overall instance of program non-compliance. Any reduction in instances of non-compliance would result in the conservation of finite public health resources that might then be directed to other pressing public health matters.
An approach to automated conceptual database design based on the IML activity diagram

This paper presents an approach to the automated design of the initial conceptual database model. The UML activity diagram, as a frequently used business process modeling notation, is used as the starting point for the automated generation of the UML class diagram representing the conceptual database model. Formal rules for automated generation cover the automatic extraction of business objects and business process participants, as well as the automatic generation of corresponding classes and their associations. Based on these rules we have implemented an automatic generator and evaluated it on a real business model.
Proposition of New Genetic Operator for Solving Joint Production and Maintenance Scheduling: Application to the Flow Shop Problem

Genetic algorithms are used in scheduling leading to efficient heuristic methods for large sized problems. The efficiency of a GA based heuristic is closely related to the quality of the used GA scheme and the GA operators: mutation, selection and crossover. In this paper, we propose a joint genetic algorithm (JGA), for joint production and maintenance scheduling problem in permutation flowshop, in which different genetic joint operators are used. We also proposed a joint structure to represent an individual in with two fields: the first one for production data and the second one for maintenance data. We used different Taillard benchmarks to compare the performances of JGA with each proposed operator
Physiologically Relevant Measurements of Nitric Oxide in Cardiovascular Research Using Electrochemical Microsensors

Nitric oxide (NO) plays an important role in the regulation of blood flow. Pharmacological tools and a series of other techniques have been developed for studying the NO/L-arginine pathway, but it has proved difficult to make a quantitative link between effect and tissue NO concentration. NO microsensors have been applied with success for the measurement of NO in suspensions of mitochondria and cells, such as platelets and leukocytes, and in cell cultures, which together with other interventions or measurements are particularly useful for the examination of cell signalling related to the NO/L-arginine pathway. In isolated vascular segments, studies using the NO microsensor have defined the relationship between NO concentration and relaxation and revealed residual NO release in the presence of NO synthase inhibitors. Moreover, simultaneous measurements of NO concentration and vasorelaxation in isometric preparations have shown that agonist-induced relaxation is L-arginine dependent and NO release is reduced in hypertension. By placing NO microsensors in catheters, it is possible to measure NO in the living animal and man. This approach has been applied for the measurements of NO concentration in relation to increases in flow, erection, in conditions of hypoxia, and in endotoxemia. However, further methodological development of NO microsensors is necessary to avoid the influence of changes in temperature, pH and oxygen on the measurements.
A translational neuroscience framework for the development of socioemotional functioning in health and psychopathology

Abstract The development of socioemotional functioning is a complex process that occurs over a protracted time period and requires coordinating affective, cognitive, and social faculties. At many points in development, the trajectory of socioemotional development can be deleteriously altered due to a combination of environmental insults and individual vulnerabilities. The result can be psychopathology. However, researchers are just beginning to understand the neural and genetic mechanisms involved in the development of healthy and disordered socioemotional functioning. We propose a translational developmental neuroscience framework to understand the transactional process that results in socioemotional functioning in both healthy and disordered populations. We then apply this framework to healthy socioemotional development, pediatric anxiety, pediatric depression, and autism spectrum disorder, selectively reviewing current literature in light of the framework. Finally, we examine ways that the framework can help to frame future directions of research on socioemotional development and translational implications for intervention.
Improved achievable secrecy rate of visible light communication with cooperative jamming

In this paper we study the problem of securing a visible light communication (VLC) link against passive eavesdropping, with the help of a (friendly) jammer. Differently from radio frequency (RF) communications, VLC imposes a peak amplitude constraint on the input distribution which renders Gaussian inputs not admissible. We provide an achievable secrecy rate that improves upon a recently established one in a concurrent work by Mostafa and Lampe. Our scheme follows from both the secrecy capacity result by Wyner and the artificial noise scheme by Goel and Negi, but using truncated Gaussian input distributions instead of uniform ones. Via numerical results, we show that our secrecy rate outperforms the concurrent rate in different settings.
Defining abstract entities: development in pre-adolescents, adolescents, and young adults.

Students ages 12, 15, 18, and 23 (n = 60 per group) wrote definitions for 16 abstract nouns (e.g., pride, courage, realization). Responses were analyzed for the Aristotelian style, a type of definition that mentions both the superordinate category term and one or more characteristics of the word (e.g., "Pride is a sense of delight about a possession or accomplishment"). This response type was of interest because it is a sophisticated and literate defining style that is modeled in classrooms, textbooks, and dictionaries-a style that is informative, concise, and efficient. The results indicated that a number of important changes occur in the ability to provide Aristotelian definitions for abstract nouns during the developmental period from late childhood to early adulthood. Specifically, there was an increasing tendency for students to mention the appropriate category to which a word belongs, core features of the word, and subtle aspects of meaning. The study contributes to the knowledge base concerning the nature of language development in pre-adolescents, adolescents, and young adults.
Gadgets, approximation, and linear programming

The authors present a linear-programming based method for finding "gadgets", i.e., combinatorial structures reducing constraints of one optimization problem to constraints of another. A key step in this method is a simple observation which limits the search space to a finite one. Using this new method they present a number of new, computer-constructed gadgets for several different reductions. This method also answers the question of how to prove the optimality of gadgets-they show how LP duality gives such proofs. The new gadgets improve hardness results for MAX CUT and MAX DICUT, showing that approximating these problems to within factors of 60/61 and 44/45 respectively is NP-hard (improving upon the previous hardness of 71/72 for both problems). They also use the gadgets to obtain an improved approximation algorithm for MAX 3SAT which guarantees an approximation ratio of 0.801, This improves upon the previous best bound of 0.7704.