Miracle-dz/UniFAR-FTUs huggingface dataset:
A type and effect system for atomicity

Ensuring the correctness of multithreaded programs is difficult, due to the potential for unexpected and nondeterministic interactions between threads. Previous work addressed this problem by devising tools for detecting race conditions, a situation where two threads simultaneously access the same data variable, and at least one of the accesses is a write. However, verifying the absence of such simultaneous-access race conditions is neither necessary nor sufficient to ensure the absence of errors due to unexpected thread interactions.We propose that a stronger non-interference property is required, namely atomicity. Atomic methods can be assumed to execute serially, without interleaved steps of other threads. Thus, atomic methods are amenable to sequential reasoning techniques, which significantly simplifies both formal and informal reasoning about program correctness.This paper presents a type system for specifying and verifying the atomicity of methods in multithreaded Java programs. The atomic type system is a synthesis of Lipton's theory of reduction and type systems for race detection.We have implemented this atomic type system for Java and used it to check a variety of standard Java library classes. The type checker uncovered subtle atomicity violations in classes such as <tt>java.lang. String</tt> and <tt>java.lang. String-Buffer</tt> that cause crashes under certain thread interleavings.This paper proposes that a stronger non-interference property is required, namely atomicity, and presents a type system for verifying the atomicity of methods in multithreaded Java programs. Methods in a class can be annotated with the keyword <tt>atomic</tt>. Clients of a well-typed class can then assume that each atomic method is executed in one step, thus significantly simplifying both formal and informal reasoning about the client's correctness.
Deriving Production Rules for Incremental View Maintenance

It is widely recognized that production rules in database systems can be used to automatically maintain derived data such as views. However, writing a correct set of rules for effciently maintaining a given view can be a diffcult and ad-hoc process. We provide a facility whereby a user defines a view as an SQL select expression, from which the system automatically derives set-oriented production rules that maintain a materialization of that view. The maintenance rules are triggered by operations on the view's base tables. Generally, the rules perform incremental maintenance: the materialized view is modified according to the sets of changes made to the base tables, which are accessible through logical tables provided by the rule language. However, for some operations substantial recomputation may be required. We give algorithms that, based on key information, perform syntactic analysis on a view definition to determine when effcient maintenance is possible.
Using cluster analysis methods for multivariate mapping of traffic accidents

Abstract Many factors affect the occurrence of traffic accidents. The classification and mapping of the different attributes of the resulting accident are important for the prevention of accidents. Multivariate mapping is the visual exploration of multiple attributes using a map or data reduction technique. More than one attribute can be visually explored and symbolized using numerous statistical classification systems or data reduction techniques. In this sense, clustering analysis methods can be used for multivariate mapping. This study aims to compare the multivariate maps produced by the K-means method, K-medoids method, and Agglomerative and Divisive Hierarchical Clustering (AGNES) method, which among clustering analysis methods, with real data. The results from the study will suggest which clustering methods should be preferred in terms of multivariate mapping. The results show that the K-medoids method is more appropriate in terms of clustering success. Moreover, the aim is to reveal spatial similarities in traffic accidents according to the results of traffic accidents that occur in different years. For this aim, multivariate maps created from traffic accident data of two different years in Turkey are used. The methods are compared, and the use of the maps produced with these methods for risk management and planning is discussed. Analysis of the maps reveals significant similarities for both years.
Intracellular Survival of Staphylococcus aureus in Endothelial Cells: A Matter of Growth or Persistence

The Gram-positive human pathogen Staphylococcus aureus is a leading cause of severe bacterial infections. Recent studies have shown that various cell types could readily internalize S. aureus and infected cells have been proposed to serve as vehicle for the systemic dissemination of the pathogen. Here we focused on the intracellular behavior of the Community-Associated Methicillin-Resistant S. aureus strain USA300. Supporting earlier observations, we found that wild-type S. aureus strain USA300 persisted for longer period within endothelial cells than within macrophages and that a mutant displaying the small colony variant phenotype (ΔhemDBL) had increased intracellular persistence. Time-lapse microscopy revealed that initial persistence of wild-type bacteria in endothelial cells corresponded to distinct single cell events, ranging from active intracellular bacterial proliferation, leading to cell lysis, to non-replicating bacterial persistence even 1 week after infection. In sharp contrast, ΔhemDBL mutant bacteria were essentially non-replicating up to 10 days after infection. These findings suggest that internalization of S. aureus in endothelial cells triggers its persistence and support the notion that endothelial cells might constitute an intracellular persistence niche responsible for reported relapse of infection after antibiotic therapy.
Revisiting the formal foundation of Probabilistic Databases

One of the core problems in soft computing is dealing with uncertainty in data. In this paper, we revisit the formal foundation of a class of probabilistic databases with the purpose to (1) obtain data model independence, (2) separate metadata on uncertainty and probabilities from the raw data, (3) better understand aggregation, and (4) create more opportunities for optimization. The paper presents the formal framework and validates data model independence by showing how to a obtain probabilistic Datalog as well as a probabilistic relational algebra by applying the framework to their non-probabilistic counterparts. We conclude with a discussion on the latter three goals.
Riparian plant biodiversity reduces stream channel migration rates in three rivers in Michigan, U.S.A.

Recent work has shown that the biodiversity of organisms can influence geophysical processes such as the transport of streambed sediments and the erosion of soils. Yet most of this work has been conducted in small‐scale fluvial system mimics, demonstrating a clear need to investigate the relationship between biodiversity and erosion in natural systems. We conducted an observational field study across 3 rivers in forested watersheds in northern Michigan, U.S.A. , quantifying streambank retreat rates using aerial photos and measuring riparian plant community biodiversity and abundance. We hypothesized that more diverse riparian plant communities would produce greater woody plant stem density and basal area, which in turn would reduce erosion rates of streambanks due to increased root production. We used structural equation modelling to compare causal networks using plant biodiversity metrics to predict streambank migration rate indirectly through effects on plant abundance, as well as models that used migration rate to predict plant abundance indirectly through effects on plant biodiversity. Although structural equation models explained both causal pathways successfully, models using biodiversity to predict migration rate were a better fit to data than models that used migration rate to predict plant biodiversity and abundance. The best performing models suggested plant biodiversity was indirectly negatively correlated with erosion rate (average standardized path coefficient = −0.22), after accounting for environmental differences between sites. This work adds to a growing body of evidence indicating that biodiversity can modify geophysical processes, demonstrating the need to explicitly account for biological variation when considering ecogeomorphic feedbacks.
Efficient DAG construction and heuristic calculation for instruction scheduling

A number of heuristic algorithms for DAG-based instruction scheduling have been proposed over the past few years. In this paper, we explore the efficiency of three DAG construction algorithms and survey 26 proposed heuristics and their methods of calculation. Six scheduling algorithms are analyzed in terms of DAG construction and heuristic use. DAG suuctural statistics and scheduling times for the three construction algorithms are given for several popular benchmarks. The table-building algorithms are shown to extremely efficient for programs with large basic blocks and yet appropriately handle the problem of retaining important transitive arcs. The node revisitation overhead of intermediate heuristic calculation steps is also investigated and shown to be negligible.
Evaluation of Technology Term Recognition with Random Indexing

In this paper, we propose a method that combines the principles of automatic term recognition and the distributional hypothesis to identify technology terms from a corpus of scientific publications. We employ the random indexing technique to model terms’ surrounding words, which we call the context window, in a vector space at reduced dimension. The constructed vector space and a set of reference vectors, which represents manually annotated technology terms, in a k-nearest-neighbour voting classification scheme are used for term classification. In this paper, we examine a number of parameters that influence the obtained results. First, we inspect several context configurations, i.e. the effect of the context window size, the direction in which co-occurrence counts are collected, and information about the order of words within the context windows. Second, in the k-nearest-neighbour voting scheme, we study the role that neighbourhood size selection plays, i.e. the value of k. The obtained results are similar to word space models. The performed experiments suggest the best performing context are small (i.e. not wider than 3 words), are extended in both directions and encode the word order information. Moreover, the accomplished experiments suggest that the obtained results, to a great extent, are independent of the value of k.
Domain-independent entity extraction from web search query logs

Query logs of a Web search engine have been increasingly used as a vital source for data mining. This paper presents a study on large-scale domain-independent entity extraction from search query logs. We present a completely unsupervised method to extract entities by applying pattern-based heuristics and statistical measures. We compare against existing techniques that use Web documents as well as search logs, and show that we improve over the state of the art. We also provide an in-depth qualitative analysis outlining differences and commonalities between these methods.
Genome‐wide screen identifies a novel p97/CDC‐48‐dependent pathway regulating ER‐stress‐induced gene transcription

The accumulation of misfolded proteins in the endoplasmic reticulum (ER) activates the Unfolded Protein Response (UPRER) to restore ER homeostasis. The AAA+ ATPase p97/CDC‐48 plays key roles in ER stress by promoting both ER protein degradation and transcription of UPRER genes. Although the mechanisms associated with protein degradation are now well established, the molecular events involved in the regulation of gene transcription by p97/CDC‐48 remain unclear. Using a reporter‐based genome‐wide RNAi screen in combination with quantitative proteomic analysis in Caenorhabditis elegans, we have identified RUVB‐2, a AAA+ ATPase, as a novel repressor of a subset of UPRER genes. We show that degradation of RUVB‐2 by CDC‐48 enhances expression of ER stress response genes through an XBP1‐dependent mechanism. The functional interplay between CDC‐48 and RUVB‐2 in controlling transcription of select UPRER genes appears conserved in human cells. Together, these results describe a novel role for p97/CDC‐48, whereby its role in protein degradation is integrated with its role in regulating expression of ER stress response genes.
Animal behaviour Developmental stress predicts social network position

The quantity and quality of social relationships, as captured by social network analysis, can have major fitness consequences. Various studies have shown that individual differences in social behaviour can be due to variation in exposure to developmental stress. However, whether these developmental differences translate to consistent differences in social network position is not known. We experimentally increased levels of the avian stress hormone corticosterone (CORT) in nestling zebra finches in a fully balanced design. Upon reaching nutritional independence, we released chicks and their families into two free-flying rooms, where we measured daily social networks over five weeks using passive integrated transponder tags. Developmental stress had a significant effect on social behaviour: despite having similar foraging patterns, CORT chicks had weaker associations to their parents than control chicks. Instead, CORT chicks foraged with a greater number of flock mates and were less choosy with whom they foraged, resulting in more central network positions. These findings highlight the importance of taking developmental history into account to understand the drivers of social organization in gregarious species.
Metric Nearness : Problem Formulation and Algorithms

Many problems in machine learning, data mining, databases and statistics involve the pairwise dissimilarities among a set of objects. It is often desirable for these dissimilarities to satisfy the properties of a metric— especially the triangle inequality. Applications where metric data are crucial include clustering, classification, metric-based indexing, query processing, and approximation algorithms. This paper presents the Metric Nearness Problem: Given a dissimilarity matrix, find the “nearest” matrix of distances that satisfy the triangle inequalities. For `p nearness measures, the paper develops efficient algorithms that compute globally optimal solutions by exploiting the deep structure of the problem. Empirically, the algorithms have time and storage costs that are linear in the number of triangle constraints. The methods can easily be parallelized for additional speed.
A New CULLIN 1 Mutant Has Altered Responses to Hormones and Light in Arabidopsis1[C][OA]

Regulated protein degradation contributes to plant development by mediating signaling events in many hormone, light, and developmental pathways. Ubiquitin ligases recognize and ubiquitinate target proteins for subsequent degradation by the 26S proteasome. The multisubunit SCF is the best-studied class of ubiquitin ligases in Arabidopsis (Arabidopsis thaliana). However, the extent of SCF participation in signaling networks is unclear. SCFs are composed of four subunits: CULLIN 1 (CUL1), ASK, RBX1, and an F-box protein. Null mutations in CUL1 are embryo lethal, limiting insight into the role of CUL1 and SCFs in later stages of development. Here, we describe a viable and fertile weak allele of CUL1, called cul1-6. cul1-6 plants have defects in seedling and adult morphology. In addition to reduced auxin sensitivity, cul1-6 seedlings are hyposensitive to ethylene, red, and blue light conditions. An analysis of protein interactions with the cul1-6 gene product suggests that both RUB (related to ubiquitin) modification and interaction with the SCF regulatory protein CAND1 (cullin associated and neddylation dissociated) are disrupted. These findings suggest that the morphological defects observed in cul1-6 plants are caused by defective SCF complex formation. Characterization of weak cul1 mutants provides insight into the role of SCFs throughout plant growth and development.
Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf. mpi-inf.mpg. de/.
Building a Control-flow Graph from Scheduled Assembly Code

A variety of applications have arisen where it is worthwhile to apply code optimizations directly to the machine code (or assembly code) produced by a compiler. These include link-time whole-program analysis and optimization, code compression, binaryto-binary translation, and bit-transition reduction (for power). Many, if not most, optimizations assume the presence of a control-flow graph (cfg). Compiled, scheduled code has properties that can make cfg construction more complex than it is inside a typical compiler. In this paper, we examine the problems of scheduled code on architectures that have multiple delay slots. In particular, if branch delay slots contain other branches, the classic algorithms for building a cfg produce incorrect results. We explain the problem using two simple examples. We then present an algorithm for building correct cfgs from scheduled assembly code that includes branches in branch-delay slots. The algorithm works by building an approximate cfg and then refining it to reflect the actions of delayed branches. If all branches have explicit targets, the complexity of the refining step is linear with respect to the number of branches in the code. Analysis of the kind presented in this paper is a necessary first step for any system that analyzes or translates compiled, assembly-level code. We have implemented this algorithm in our power-consumption experiments based on the TMS320C6200 architecture from Texas Instruments. The development of our algorithm was motivated by the output of TI’s compiler. Authors’ address: Department of Computer Science; Rice University, MS 132; Houston, TX, USA 77005. Corresponding author: waterman@rice.edu
Combination of Classifiers for Indoor Room Recognition CGS participation at ImageCLEF2010 Robot Vision Task

This paper represents a description of our approach to the problem of topological localization of a mobile robot using visual information. Our method has been developed for ImageCLEF 2010 Robot Vision Task challenge. The challenge was focused on the problem of visual place classification, with a special focus on generalization. The goal was to recognize rooms by the images captured with a stereo camera mounted on a mobile robot within an office environment. Algorithms should be able to reply to question "Where are you? ", saying "I don't know" if the room analyzed was not presented during training phase. For the challenge three sequences were given: Training Set, Validation Set and Test Set acquired on three different floors of the same building. We chose to approach the challenge realizing a multi- Level machine learning architecture, made of a first "weak" classifiers Level based on visual features extracted from images and of a second Level performing fusion of first Level outputs. We developed four configurations to determine the best approach to problem solving: Committees of Experts, Stacked Regression with Support Vector Machines stage, Stacked Regression with Artificial Neural Network stage, Weighted Linear Combination of all the three previous methods. Finally the result of twenty RUNs, five RUNs for each of the four different system configurations, were submitted at ImageCLEF challenge.
From interaction to trajectories: designing coherent journeys through user experiences

The idea of interactional trajectories through interfaces has emerged as a sensitizing concept from recent studies of tangible interfaces and interaction in museums and galleries. We put this concept to work as a lens to reflect on published studies of complex user experiences that extend over space and time and involve multiple roles and interfaces. We develop a conceptual framework in which trajectories explain these user experiences as journeys through hybrid structures, punctuated by transitions, and in which interactivity and collaboration are orchestrated. Our framework is intended to sensitize future studies, help distill craft knowledge into design guidelines and patterns, identify technology requirements, and provide a boundary object to connect HCI with Performance Studies.