Miracle-dz/UniFAR-FTUs huggingface dataset:
Aspect-Aware Points-to Analysis

Points-to analysis is a fundamental analysis technique whose results are useful in compiler optimization and software engineering tools. Although many points-to analysis algorithms have been proposed for procedural and object-oriented languages like C and Java, there is no points-to analysis for aspect-oriented languages so far. Based on Andersen-style points-to analysis for Java, we propose flow- and context-insensitive points-to analysis for AspectJ. The main idea is to perform the analysis crossing the boundary between aspects and classes. Therefore, our technique is able to handle the uniqueaspectual features. To investigate the effectiveness of our technique, we implement our analysis approach on top of the ajc AspectJ compiler and evaluate it on nine AspectJ benchmarks. The experimental result indicates that, compared to existing Java approaches, the proposed technique can achieve a significant higher precision and run in practical time and space.
A role for the mismatch repair system during incipient speciation in Saccharomyces

The cause of reproductive isolation between biological species is a major issue in the field of biology. Most explanations of hybrid sterility require either genetic incompatibilities between nascent species or gross physical imbalances between their chromosomes, such as rearrangements or ploidy changes. An alternative possibility is that genomes become incompatible at a molecular level, dependent on interactions between primary DNA sequences. The mismatch repair system has previously been shown to contribute to sterility in a hybrid between established yeast species by preventing successful meiotic crossing‐over leading to aneuploidy. This system could also promote or reinforce the formation of new species in a similar manner, by making diverging genomes incompatible in meiosis. To test this possibility we crossed yeast strains of the same species but from diverse historical or geographic sources. We show that these crosses are partially sterile and present evidence that the mismatch repair system is largely responsible for this sterility.
Are neuroradiological or neurophysiological characteristics associated with upper-extremity hypertonia in severe ischaemia in supratentorial stroke?

OBJECTIVE The primary goal was to identify the neuroradiological and neurophysiological risk factors for upper-extremity hypertonia in patients with severe ischaemic supratentorial stroke. DESIGN Inception cohort. PATIENTS Forty-three consecutive patients with an acute ischaemic supratentorial stroke and an initial upper-extremity paralysis admitted to an academic hospital recruited over a 1.5-year period. MAIN OUTCOME MEASURES Upper-extremity hypertonia was assessed by the Ashworth scale and clinically relevant hypertonia was defined as Ashworth scale >or=2. Any association of (clinically relevant) hypertonia with neuroradiological (lesion side, extent of lesion, and stroke history), and neurophysiological (motor-evoked potential and silent period) characteristics was investigated. RESULTS Associations between hypertonia and the selected neuroradiological and neurophysiological risk factors were generally low. Univariate analyses yielded none of the selected neuroradiological or neurophysiological characteristics as significantly associated with hypertonia. CONCLUSION Despite the high incidence of hypertonia in these patients, we could not identify any of the selected neuroradiological or neurophysiological characteristics as a risk factor for hypertonia.
Poisoning the Mind: Arsenic Contamination and Cognitive Achievement of Children

Bangladesh has experienced the largest mass poisoning of a population in history owing to contamination of groundwater with naturally occurring inorganic arsenic. Continuous drinking of such metal-contaminated water is highly cancerous; prolonged drinking of such water risks developing diseases in a span of just 5-10 years. Arsenicosis-intake of arsenic-contaminated drinking water-has implications for children's cognitive and psychological development. This study examines the effect of arsenicosis at school and at home on cognitive achievement of children in rural Bangladesh using recent nationally representative school survey data on students. Information on arsenic poisoning of the primary source of drinking water-tube wells-is used to ascertain arsenic exposure. The findings show an unambiguously negative and statistically significant correlation between mathematics score and arsenicosis at home, net of exposure at school. Split-sample analysis reveals that the effect is only specific to boys; for girls, the effect is negative but insignificant. Similar correlations are found for cognitive and non-cognitive outcomes such as subjective well-being, that is, a self-reported measure of life satisfaction (also a direct proxy for health status) of students and their performance in primary-standard mathematics. These correlations remain robust to controlling for school-level exposure.
A developmentally regulated Na-H exchanger in Dictyostelium discoideum is necessary for cell polarity during chemotaxis

Increased intracellular H+ efflux is speculated to be an evolutionarily conserved mechanism necessary for rapid assembly of cytoskeletal filaments and for morphological polarity during cell motility. In Dictyostelium discoideum, increased intracellular pH through undefined transport mechanisms plays a key role in directed cell movement. We report that a developmentally regulated Na-H exchanger in Dictyostelium discoideum (DdNHE1) localizes to the leading edge of polarized cells and is necessary for intracellular pH homeostasis and for efficient chemotaxis. Starved DdNHE1-null cells (Ddnhe1 −) differentiate, and in response to the chemoattractant cAMP they retain directional sensing; however, they cannot attain a polarized morphology, but instead extend mislocalized pseudopodia around the cell and exhibit decreased velocity. Consistent with impaired polarity, in response to chemoattractant, Ddnhe1 − cells lack a leading edge localization of F-actin and have significantly attenuated de novo F-actin polymerization but increased abundance of membrane-associated phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). These findings indicate that during chemotaxis DdNHE1 is necessary for establishing the kinetics of actin polymerization and PI(3,4,5)P3 production and for attaining a polarized phenotype.
The Lazy Flipper: MAP Inference in Higher-Order Graphical Models by Depth-limited Exhaustive Search

This article presents a new search algorithm for the NP-hard problem of optimizing functions of binary variables that decompose according to a graphical model. It can be applied to models of any order and structure. The main novelty is a technique to constrain the search space based on the topology of the model. When pursued to the full search depth, the algorithm is guaranteed to converge to a global optimum, passing through a series of monotonously improving local optima that are guaranteed to be optimal within a given and increasing Hamming distance. For a search depth of 1, it specializes to Iterated Conditional Modes. Between these extremes, a useful tradeoff between approximation quality and runtime is established. Experiments on models derived from both illustrative and real problems show that approximations found with limited search depth match or improve those obtained by state-of-the-art methods based on message passing and linear programming.
Phylogenetic Signal Dissection Identifies the Root of Starfishes

Relationships within the class Asteroidea have remained controversial for almost 100 years and, despite many attempts to resolve this problem using molecular data, no consensus has yet emerged. Using two nuclear genes and a taxon sampling covering the major asteroid clades we show that non-phylogenetic signal created by three factors - Long Branch Attraction, compositional heterogeneity and the use of poorly fitting models of evolution – have confounded accurate estimation of phylogenetic relationships. To overcome the effect of this non-phylogenetic signal we analyse the data using non-homogeneous models, site stripping and the creation of subpartitions aimed to reduce or amplify the systematic error, and calculate Bayes Factor support for a selection of previously suggested topological arrangements of asteroid orders. We show that most of the previous alternative hypotheses are not supported in the most reliable data partitions, including the previously suggested placement of either Forcipulatida or Paxillosida as sister group to the other major branches. The best-supported solution places Velatida as the sister group to other asteroids, and the implications of this finding for the morphological evolution of asteroids are presented.
Point Mutation in Essential Genes with Loss or Mutation of the Second Allele

Antigens that are tumor specific yet retained by tumor cells despite tumor progression offer stable and specific targets for immunologic and possibly other therapeutic interventions. Therefore, we have studied two CD4+ T cell–recognized tumor-specific antigens that were retained during evolution of two ultraviolet-light–induced murine cancers to more aggressive growth. The antigens are ribosomal proteins altered by somatic tumor-specific point mutations, and the progressor (PRO) variants lack the corresponding normal alleles. In the first tumor, 6132A-PRO, the antigen is encoded by a point-mutated L9 ribosomal protein gene. The tumor lacks the normal L9 allele because of an interstitial deletion from chromosome 5. In the second tumor, 6139B-PRO, both alleles of the L26 gene have point mutations, and each encodes a different tumor-specific CD4+ T cell–recognized antigen. Thus, for both L9 and L26 genes, we observe “two hit” kinetics commonly observed in genes suppressing tumor growth. Indeed, reintroduction of the lost wild-type L9 allele into the 6132A-PRO variant suppressed the growth of the tumor cells in vivo. Since both L9 and L26 encode proteins essential for ribosomal biogenesis, complete loss of the tumor-specific target antigens in the absence of a normal allele would abrogate tumor growth.
High-order epistasis shapes evolutionary trajectories

High-order epistasis—where the effect of a mutation is determined by interactions with two or more other mutations—makes small, but detectable, contributions to genotype-fitness maps. While epistasis between pairs of mutations is known to be an important determinant of evolutionary trajectories, the evolutionary consequences of high-order epistasis remain poorly understood. To determine the effect of high-order epistasis on evolutionary trajectories, we computationally removed high-order epistasis from experimental genotype-fitness maps containing all binary combinations of five mutations. We then compared trajectories through maps both with and without high-order epistasis. We found that high-order epistasis strongly shapes the accessibility and probability of evolutionary trajectories. A closer analysis revealed that the magnitude of epistasis, not its order, predicts is effects on evolutionary trajectories. We further find that high-order epistasis makes it impossible to predict evolutionary trajectories from the individual and paired effects of mutations. We therefore conclude that high-order epistasis profoundly shapes evolutionary trajectories through genotype-fitness maps.
Querying Inconsistent Description Logic Knowledge Bases under Preferred Repair Semantics

Recently several inconsistency-tolerant semantics have been introduced for querying inconsistent description logic knowledge bases. Most of these semantics rely on the notion of a repair, defined as an inclusion-maximal subset of the facts (ABox) which is consistent with the ontology (TBox). In this paper, we study variants of two popular inconsistency-tolerant semantics obtained by replacing classical repairs by various types of preferred repair. We analyze the complexity of query answering under the resulting semantics, focusing on the lightweight logic DL-Lite_R. Unsurprisingly, query answering is intractable in all cases, but we nonetheless identify one notion of preferred repair, based upon priority levels, whose data complexity is "only" coNP-complete. This leads us to propose an approach combining incomplete tractable methods with calls to a SAT solver. An experimental evaluation of the approach shows good scalability on realistic cases.
Geldanamycin Induces Cell Cycle Arrest in K562 Erythroleukemic Cells

Geldanamycin (GA), a benzoquinone ansamycin, is one of the specific inhibitors of 90‐kDa heat shock protein and induces growth inhibition and apoptosis in certain cancer cell lines. We have investigated the mechanism of GA‐induced growth inhibition in K562 erythroleukemic cells. DNA flow‐cytometric analysis indicated that GA‐induced growth arrest was associated with G2/M phase arrest of the cell cycle. GA treatment down‐regulated the expression of cyclin B1 and inhibited phosphorylation of Cdc2 protein, both key regulatory proteins at the G2/M boundary. GA also markedly inhibited the Cdc2 kinase activity, which may be in part a result of up‐regulation of p27KIP1 by GA. The present results suggest a novel mechanism that p27KIP1 could be involved in the regulation of G2 to M phase transition.
B0712+472: a new radio four-image gravitational lens

A new four-image gravitational lens system, B0712+472, has been discovered during the Cosmic Lens All-Sky Survey. This system consists of four flat-spectrum radio images that are also seen on a Hubble Space Telescope (HST) image, together with the lensing galaxy. We present MERLIN, VLA and VLBA maps and WHT spectra of the system as well as the HST images. The light distribution of the tensing galaxy is highly elongated and so too is the mass distribution deduced from modelling. We suggest a redshift of similar to 1.33 for the lensed object the lens redshift will require further investigation. The discovery of this new system further increases the ratio of four-image to two-image lens systems currently known, exacerbating problems of required ellipticity of matter distributions in lensing galaxies.
Metabolic Syndrome and Risks of Colon and Rectal Cancer : the European Prospective Investigation into Cancer and Nutrition Study Running title : Metabolic Syndrome and Risks of Colon and Rectal Cancer

n=250) Metabolic syndrome (MetS) is purportedly related to risk of colorectal cancer, however the association of MetS, as defined according to recent international criteria, and colorectal cancer has not been yet evaluated. In particular, it remains unclear to what extent the MetS components individually account for such an association. We addressed these issues in a nested case-control study that included 1,093 incident cases matched (1:1) to controls using incidence-density sampling. Conditional logistic regression was used to estimate relative risks (RRs) and 95% confidence intervals (CIs). MetS was defined according to the criteria of the National Cholesterol Education Program/Adult Treatment Panel III (NCEP/ATPIII), the International Diabetes Federation and the 2009 harmonized definition. Among individual components, abdominal obesity (RR=1.51;95%CI:1.16-1.96) was associated with colon cancer; whereas abnormal glucose metabolism was associated with both colon (RR=2.05; 95%CI:1.57-2.68) and rectal cancer (RR=2.07;95%CI:1.45-2.96). MetS as defined by each of the definitions was similarly associated with colon cancer (e.g.RR=1.91;95%CI:1.47-2.42 for MetS by NCEP/ATPIII); whereas MetS by NCEP/ATPIII, but not IDF or harmonised definition was associated with rectal cancer (RR=1.45;95%CI:1.02-2.06). Overall, these associations were stronger in women compared with men. However, the association between MetS and colorectal cancer was accounted for by abdominal obesity and abnormal glucose metabolism, such that MetS did not provide risk information beyond these components (likelihood ratio test P=0.10 for MetS by NCEP/ATPIII). These data suggest that simple assessment of abnormal glucose metabolism and/or abdominal obesity to identify individuals at colorectal cancer risk may have higher clinical utility compared to applying more complex MetS definitions. Cancer Research. on October 18, 2017. © 2011 American Association for cancerpreventionresearch.aacrjournals. org Downloaded from Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Author Manuscript Published OnlineFirst on June 22, 2011; DOI: 10.1158/1940-6207.CAPR-11-0218
' s personal copy Transfer of object category knowledge across visual and haptic modalities : Experimental and computational studies

We study people’s abilities to transfer object category knowledge across visual and haptic domains. If a person learns to categorize objects based on inputs from one sensory modality, can the person categorize these same objects when the objects are perceived through another modality? Can the person categorize novel objects from the same categories when these objects are, again, perceived through another modality? Our work makes three contributions. First, by fabricating Fribbles (3-D, multi-part objects with a categorical structure), we developed visual-haptic stimuli that are highly complex and realistic, and thus more ecologically valid than objects that are typically used in haptic or visual-haptic experiments. Based on these stimuli, we developed the See and Grasp data set, a data set containing both visual and haptic features of the Fribbles, and are making this data set freely available on the world wide web. Second, complementary to previous research such as studies asking if people transfer knowledge of object identity across visual and haptic domains, we conducted an experiment evaluating whether people transfer object category knowledge across these domains. Our data clearly indicate that we do. Third, we developed a computational model that learns multisensory representations of prototypical 3-D shape. Similar to previous work, the model uses shape primitives to represent parts, and spatial relations among primitives to represent multi-part objects. However, it is distinct in its use of a Bayesian inference algorithm allowing it to acquire multisensory representations, and sensory-specific forward models allowing it to predict visual or haptic features from multisensory representations. The model provides an excellent qualitative account of our experimental data, thereby illustrating the potential importance of multisensory representations and sensory-specific forward models to multisensory perception. 2012 Elsevier B.V. All rights reserved.
Income Comparisons and Non-Cognitive Skills

People gain utility from occupying a higher ranked position in the income distribution of the reference group. This paper investigates whether these gains depend on an individual’s set of non-cognitive skills. Using the 2000-2008 waves of the German Socioeconomic Panel dataset (SOEP), a subjective question on Life Satisfaction, and three different sets of non-cognitive skills indicators, we find significant and robust differences across skills groups. People who are more neurotic, extravert and have low external locus of control and low negative reciprocity are more sensitive to their individual position in the economic ladder. By contrast, the Life Satisfaction reaction to changes in economic status is significantly lower among individuals who score high (low) in negative (positive) reciprocity, and are at the bottom of the distribution of neuroticism, extraversion. The heterogeneity on the importance of income comparisons needs to be taken into account when, for example, introducing them into economic models, predicting individuals’ behaviour, or making welfare judgments.
Toward System-Optimal Routing in Traffic Networks: A Reverse Stackelberg Game Approach

In the literature, several road pricing methods based on hierarchical Stackelberg games have been proposed to reduce congestion in traffic networks. We propose three novel schemes to apply the extended reverse Stackelberg game, through which traffic authorities can induce drivers to follow routes that are computed to reach a system-optimal distribution of traffic on the available routes of a freeway, e.g., to minimize the total time spent of traffic in the network and to reduce traffic emissions in urban traffic networks. In this game-theoretical approach, the leader player representing the traffic authority communicates with the followers (drivers) via an onboard computer, in which the main instrument of the leader is the so-called leader function. This function maps the follower's decision space into the leader's decision space, resulting in a leader decision that is directly dependent on the follower's decision variables. Compared with the original game, we can rely on solution methods developed for the general reverse Stackelberg game and show that a system-optimal behavior can be reached, while taking heterogeneous driver classes into account.
Identifying Strategic Factors of the Implantation CSR in the Airline Industry: The Case of Asia-Pacific Airlines

Sustainable development has always been the objective of many fields, including the tourism and transportation sector. However, a major part of this sector, the airline industry, deals with many negative impacts, such as air pollution, noise, CO 2 emission, and labor practice. Corporate social responsibility (CSR) is a strategic business activity that can enhance the sustainability of the airline industry. The results of the Dow Jones Sustainability Indices (DJSI) reveal that airlines of Western countries exhibit a more remarkable CSR performance than Asia-Pacific airlines, suggesting that the CSR programs of Asia-Pacific airlines need improvement. By constructing an evaluation hierarchy and applying the decision-making trial and evaluation laboratory (DEMATEL) method, this study found that the key strategic factors in the airline industry’s implementation of CSR include corporate governance, risk and crisis management, brand management, and product responsibility (safety).