Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracting and representing cross-language dependencies in diverse software systems

This paper presents an approach for dealing with multi-language software systems. Much of the focus of reverse engineering tools is in analyzing software systems written in one programming language. Nowadays, the abundance of new technologies and languages used to ease application development raises new challenges for reverse engineers. Therefore, this paper focuses on finding cross-language dependencies in such diverse, heterogeneous software systems. Our approach uses source navigator extractors to produce the facts inside each language. Then, we show an example for finding Java Native Interface (JNI) dependencies between facts from Java and C/C++ code. The integrated facts are produced in GXL form, and conform to a unified schema introduced in the paper. This approach is useful from several perspectives. It illustrates how to retrieve the dependencies from software systems written in more than one programming language. Also, the generated facts conform to the GXL format, which is accepted by many reverse engineering tools. The usefulness and scalability of the approach are tested in a case study.
Scanning the structure of ill‐known spaces: Part 1. Founding principles about mathematical constitution of space

Some necessary and sufficient conditions allowing a previously unknown space to be explored through scanning operators are reexamined with respect to measure theory. Some generalized concepts of distances and dimensionality evaluation are proposed, together with their conditions of validity and range of application to topological spaces. The existence of a Boolean lattice with fractal properties originating from non‐wellfounded properties of the empty set is demonstrated. This lattice provides a substratum with both discrete and continuous properties from which existence of physical universes can be proved, up to the function of conscious perception. Space‐time emerges as an ordered sequence of mappings of closed 3D Poincare sections of a topological four‐space provided by the lattice, and the function of conscious perception is founded on the same properties. Self‐evaluation of a system is possible against indecidability barriers through anticipatory mental imaging occurring in biological brain systems; then our embedding universe should be in principle accessible to knowledge. The possibility of existence of spaces with fuzzy dimension or with adjoined parts with decreasing dimensions is raised, together with possible tools for their study. The work presented here provides the introductory foundations supporting a new theory of space whose physical predictions (suppressing the opposition of quantum and relativistic approaches) and experimental proofs are presented in detail in Parts 2 and 3 of the study.
Extending the VoDKA architecture to improve resource modelling

VoDKA is a Video-on-Demand server developed using Erlang/OTP. In this paper, the evolution of the core architecture of the system, designed for improving resource modelling, is described. After explaining the main goals of the project, the steps taken towards an optimal architecture are explained. Finally, a new architecture is proposed, solving all the problems and limitations in the previous ones. Special attention is paid to the use of design patterns, implementation behaviours, and reusable software components.
A Source Analysis of the Conficker Outbreak from a Network Telescope

This paper discusses a dataset of some 16 million packets targeting port 445/tcp collected by a network telescope utilising a /24 netblock in South African IP address space. An initial overview of the collected data is provided. This is followed by a detailed analysis of the packet characteristics observed, including size and TTL. The peculiarities of the observed target selection and the results of the flaw in the Conficker worm's propagation algorithm are presented. An analysis of the 4 million observed source hosts is reported, grouped by both packet counts and the number of distinct hosts per network address block. Address blocks of size /8, 16 and 24 are used for groupings. The localisation, by geographic region and numerical proximity, of high ranking aggregate netblocks is highlighted. The observed shift in geopolitical origins observed during the evolution of the Conficker worm is also discussed. The paper concludes with some overall analyses, and consideration of the application of network telescopes to the monitoring of such outbreaks in the future.
Two myths about contextual effects on Middle Eastern women's employment: A multilevel analysis of trends in Egypt and Jordan

In studies on the influence of contextual factors on women’s employment in the Middle East, two myths figure regularly, which both seems to be related to the disentanglement of micro and macro levels. By applying a more comprehensive view and using multilevel models, we provide a more nuanced view of the relationship between the contextual and individual level regarding women’s non-agricultural employment in Egypt and Jordan. First, we show that large uniform contextual processes such as globalization and modernization are not satisfying in explaining women’s employment. The processes are more complex. Egypt and Jordan seem to modernize rather linearly, but if we look more closely at the processes and also take individual-level data in to account, women’s employment does not show the same pattern. Globalization and modernization are no panacea to gender equality. Second, we focus on the myth of ‘micro-level stability’ and have shown that the effect of individual and household factors has changed over time. The influence of education, the most important explanatory factor of women’s nonagricultural employment, has a declining effect. Furthermore, having (young) children seems to become a less restricting influence on women’s employment. Draft versions of this paper are presented at the 7th Middle East Economics Association, 29th-31st May 2008, Famagusta, North Cyprus and the Arab Thought Forum/Centre for International Business and Innovation conference on Globalization in the Arab World, 3rd-4th February 2008, Amman, Jordan. We thank the participations of these conferences for the useful comments. We are grateful to Ellen Webbink and Janine Huisman (Dep. of Economics, Radboud University Nijmegen) for their part in building the database used.
Regulation of Triacylglucose Fatty Acid Composition (Uridine Diphosphate Glucose:Fatty Acid Glucosyltransferases with Overlapping Chain-Length Specificity)

UDP-glucose (UDP-Glc):fatty acid glucosyltransferases catalyze the UDP-Glc-dependent activation of fatty acids as 1-O-acyl-[beta]-glucoses. 1-O-Acyl-[beta]-glucoses act as acyl donors in the biosynthesis of 2,3,4-tri-O-acylglucoses secreted by wild tomato (Lycopersicon pennellii) glandular trichomes. The acyl composition of L. pennellii 2,3,4-tri-O-acylglucoses is dominated by branched short-chain acids (4:0 and 5:0; approximately 65%) and straight and branched medium-chain-length fatty acids (10:0 and 12:0; approximately 35%). Two operationally soluble UDP-Glc:fatty acid glucosyltransferases (I and II) were separated and partially purified from L. pennellii (LA1376) leaves by polyethylene glycol precipitation followed by DEAE-Sepharose and Cibacron Blue 3GA-agarose chromatography. Whereas both transferases possessed similar affinity for UDP-Glc, glucosyltransferase I showed higher specificity toward short-chain fatty acids (4:0) and glucosyltransferase II showed higher specificity toward medium-chain fatty acids (8:0 and 12:0). The overlapping specificity of UDP-Glc:fatty acid glucosyltransferases for 4:0 to 12:0 fatty acid chain lengths suggests that the mechanism of 6:0 to 9:0 exclusion from acyl substituents of 2,3,4-tri-O-acylglucoses is unlikely to be controlled at the level of fatty acid activation. UDP-Glc:fatty acid glucosyltransferases are also present in cultivated tomato (Lycopersicon esculentum), and activities toward 4:0, 8:0, and 12:0 fatty acids do not appear to be primarily epidermal when assayed in interspecific periclinal chimeras.
Ectopic Insertion of the Pectoralis Minor Tendon: Inter-Reader Agreement and Findings in the Rotator Interval on MRI

Objective To evaluate magnetic resonance imaging (MRI) observer variability to detect ectopic insertion of the pectoralis minor tendon (EIPMT) and to investigate changes in the rotator interval in patients with EIPMT using MRI. Materials and Methods A total of 507 shoulder MRIs (male:female = 259:248; mean age, 55.4 years) were classified into 1) normal type insertion of the pectoralis minor tendon, 2) complete type EIPMT, and 3) partial type EIPMT independently by two radiologists. Inter-observer agreement was calculated using the kappa coefficient. Thickness of the fibrotic scar tissue in the subcoracoid triangle and humeral side axillary recess was measured. MRIs were reviewed by consensus with regard to the grade of fibrotic scar tissue proliferation in the rotator interval. Comparisons were made between normal and EIPMT and between partial and complete type EIPMT. Results The incidence of EIPMT was 13.4% (complete type, 7.7%; partial type, 5.7%). Inter-observer agreement was substantial (κ = 0.775). Fibrotic scar tissue in the subcoracoid triangle was thicker, and the grade of fibrotic scar tissue proliferation in the rotator interval was higher in the EIPMT group than those in the control group. No significant difference was observed in the thickness of humeral side axillary recess. The thicknesses of fibrotic scar tissue in the subcoracoid triangle and humeral side axillary recess as well as the grade of fibrotic scar tissue in the rotator interval were not significantly different between complete and partial type EIPMT. Conclusion MRI enabled detection of EIPMT with substantial observer agreement. Patients with EIPMT show a high tendency for fibrotic scar tissue proliferation in the rotator interval.
Processing and Retrieving Data Concurrently in Distributed Computing : A Service Based on Middleware

In the context of distributed computing and Grid computing, an application needs to retrieve the required data across networks. The data retrieval can involve not only low-speed disk activities but also a narrow-link or a crowded transmission channel. Therefore, an application requesting data from remote hosts must wait a significant amount of time for the arrival of data than from a host in a local area network, especially when the size of the data is large. In such a situation, the use of concurrent data access is one way to optimize resource utilization in a distributed environment and improve the application’s throughput. To make concurrent data access possible, one common method is to use asynchronous I/O functions as supported by the operating system after the remote file content is cached in the local disk; another method is to asynchronously retrieve data from a remote host. This paper describes our work on a middlewarebased remote data access service (ARDAS) that allows the data to be retrieved asynchronously from remote hosts, not through the cached data. Preliminary tests using a specific application show that the asynchronous access can reduce the application’s execution time by about 17% on average compared to the synchronous method.
Macrophage oxygen-dependent antimicrobial activity. IV. Role of endogenous scavengers of oxygen intermediates

The activities of the endogenous O2- and H2O2 scavenging enzymes, superoxide dismutase (SOD), glutathionine peroxidase (GP), and catalase, were measured in lysates of the intracellular parasite, Toxoplasma gondii, and in various macrophage populations. During 72 h of cultivation in standard medium alone, the catalase activity of in vivo-activated toxoplasma-immune macrophages (IM) and immune-boosted macrophages (IB) progressively increased by eight- to ninefold, and correlated with the previously observed parallel decline in these cells' antitoxoplasma activity and capacity to release H2O2. SOD and GP activities either remained constant or decreased during this 3-d period. Lymphokine exposure, which preserved the antitoxoplasma activity and oxidative capacity of 48- and 72-h cultures of IB and IM cells, blunted the rise in catalase levels and had no effect on SOD or GP. Inhibition of IB and IM macrophage catalase by aminotriazole maintained toxoplasmastatic activity otherwise lost after 48 h of cultivation. In addition, IB and IM cells from acatalasemic mice contained 20- to 30-fold less catalase, and showed comparatively little decline in either H2O2 release or antitoxoplasma activity during 72 h in culture. In vitro-(lymphokine) activated resident macrophages from normal mice had the highest levels of SOD, GP, and catalase, and these cells failed to kill or inhibit T. gondii despite enhanced extracellular release of O2- and H2O2. Toxoplasmas were also found to contain all three enzymatic scavengers. Aminotriazole inhibition of lymphokine-activated cells' catalase or of toxoplasma catalase was effective in inducing these macrophages to display antitoxoplasma activity. Moreover, and in contrast to normocatalasemic resident cells, those from acatalesemic mice were readily induced by lymphokine to inhibit the replication of untreated virulent toxoplasmas. These results suggest that endogenous O2- and H2O2 scavenging enzymes, which function within both T. gondii and activated macrophages as host cell antioxidant protective mechanisms, may reduce the effectiveness of phagocyte antimicrobial activity. Thus, the presence of SOD, GP, and especially catalase within both target and effector cell may be important determinants of macrophage oxygen-dependent processes.
Psychophysical Evaluation of a Sanshool Derivative (Alkylamide) and the Elucidation of Mechanisms Subserving Tingle

Previous studies investigated the neural and molecular underpinnings of the tingle sensation evoked by sanshool and other natural or synthetic alkylamides. Currently, we sought to characterize the psychophysical properties associated with administration of these compounds. Like other chemesthetic stimuli, the synthetic tingle analog isobutylalkylamide (IBA) evoked a sensation that was temporally dynamic. Repeated IBA application at short (30 sec) interstimulus intervals (ISI) resulted in a tingle sensation that increased across trials. Application at longer ISIs (∼30 min) resulted in a sensation of decreased intensity consistent with self-desensitization. Prior treatment with the TRPV1 or TRPA1 agonists, capsaicin and mustard oil did not cross-desensitize the tingle sensation evoked by IBA suggesting that neither TRPV1 nor TRPA1 participate in the transduction mechanism sub-serving tingle. When evaluated over 30-min time period, lingual IBA evoked a sensation that was described initially as tingling and pungent but after approximately 15 min, as a cooling sensation. Further, we found that the sensation evoked by lingual IBA was potentiated by simultaneous application of cold (0°C) and cool (21°C) thermal stimuli but was unaffected by warm (33°C) and hot (41°C) temperatures. Finally, to test the hypothesis that the tingling sensation is subserved by the activation of mechanosensitve fibers, we evaluated lingual tactile thresholds in the presence and absence of lingual IBA. The presence of IBA significantly raised lingual tactile thresholds, whereas capsaicin did not, identifying a role for mechanosensitive fibers in conveying the tingle sensation evoked by sanshool-like compounds. Collectively, these results show that lingual alkylamide evokes a complex sensation that is temporally dynamic and consistent with in vitro and in vivo experiments suggesting these compounds activate mechanosensitve neurons via blockade of KCNK two-pore potassium channels to induce the novel tingling sensation.
Analysis of a Simplified Hopping Robot

This article offers some analytical results concerning sim plified models of Raibert's hopper. We represent the task of achieving a recurring hopping height for an actuated "ball" robot as a stability problem in a nonlinear discrete dynamical control system. We model the properties of Raibert's control scheme in a simplified fashion and argue that his strategy leads to closed-loop dynamics governed by a well-known class of functions, the unimodal maps. The rich mathematical literature on this subject greatly advances our ability to determine the presence of an essentially globally attracting fixed point-the formal ren dering of what we intuitively mean by a "correct" strat egy. The motivation for this work is the hope that it will facilitate the development of general design principles for "dynamically dexterous" robots.
PfGCN5-Mediated Histone H3 Acetylation Plays a Key Role in Gene Expression in Plasmodium falciparum

ABSTRACT Histone acetylation, regulated by the opposing actions of histone acetyltransferases (HATs) and deacetylases, is an important epigenetic mechanism in eukaryotic transcription. Although an acetyltransferase (PfGCN5) has been shown to preferentially acetylate histone H3 at K9 and K14 in Plasmodium falciparum, the scale of histone acetylation in the parasite genome and its role in transcriptional activation are essentially unknown. Using chromatin immunoprecipitation (ChIP) and DNA microarray, we mapped the global distribution of PfGCN5, histone H3K9 acetylation (H3K9ac) and trimethylation (H3K9m3) in the P. falciparum genome. While the chromosomal distributions of H3K9ac and PfGCN5 were similar, they are radically different from that of H3K9m3. In addition, there was a positive, though weak correlation between relative occupancy of H3K9ac on individual genes and the levels of gene expression, which was inversely proportional to the distance of array elements from the putative translational start codons. In contrast, H3K9m3 was negatively correlated with gene expression. Furthermore, detailed mapping of H3K9ac for selected genes using ChIP and real-time PCR in three erythrocytic stages detected stage-specific peak H3K9ac enrichment at the putative transcriptional initiation sites, corresponding to stage-specific expression of these genes. These data are consistent with H3K9ac and H3K9m3 as epigenetic markers of active and silent genes, respectively. We also showed that treatment with a PfGCN5 inhibitor led to reduced promoter H3K9ac and gene expression. Collectively, these results suggest that PfGCN5 is recruited to the promoter regions of genes to mediate histone acetylation and activate gene expression in P. falciparum.
Radar GIS for site acceptance testing

Radar site acceptance testing is a demanding and costly task and requires good planning of the routes for probing aircraft and ships. In this work a preparation for radar site acceptance is presented with use of Advanced Refractive Effects Prediction System (AREPS) propagation model and ArcGIS charting of interesting points detected by the model. This approach enables prediction of radar coverage and significant cost reduction in actual aircraft and ship probing due to optimal route planning. This methodology was applied during recent modernization and optimization of the coastal radar network for the Croatian Navy and Croatian Ministry of the Interior.
Identifying RNA-binding residues based on evolutionary conserved structural and energetic features

Increasing numbers of protein structures are solved each year, but many of these structures belong to proteins whose sequences are homologous to sequences in the Protein Data Bank. Nevertheless, the structures of homologous proteins belonging to the same family contain useful information because functionally important residues are expected to preserve physico-chemical, structural and energetic features. This information forms the basis of our method, which detects RNA-binding residues of a given RNA-binding protein as those residues that preserve physico-chemical, structural and energetic features in its homologs. Tests on 81 RNA-bound and 35 RNA-free protein structures showed that our method yields a higher fraction of true RNA-binding residues (higher precision) than two structure-based and two sequence-based machine-learning methods. Because the method requires no training data set and has no parameters, its precision does not degrade when applied to ‘novel’ protein sequences unlike methods that are parameterized for a given training data set. It was used to predict the ‘unknown’ RNA-binding residues in the C-terminal RNA-binding domain of human CPEB3. The two predicted residues, F430 and F474, were experimentally verified to bind RNA, in particular F430, whose mutation to alanine or asparagine nearly abolished RNA binding. The method has been implemented in a webserver called DR_bind1, which is freely available with no login requirement at http://drbind.limlab. ibms.sinica. edu.tw.
A slope detection method based on 3D LiDAR suitable for quadruped robots

This paper introduces a slope detection method based on point cloud data from 3D LiDAR for quadruped robots in unknown environments. For quadruped robots, they need to adjust their gaits according to different slope angles to avoid some potential dangers. 3D LiDAR is used to gather point cloud data, which is superior to 2D LiDAR in speed and accuracy. In this paper, a slope detection method using bilateral filtering and RANSAC algorithms is discussed. The experiments of slope detection are fulfilled with the consideration of different angles of slopes and different orientations to the slopes, and the results demonstrate that errors of angle estimation is small.
USE OF CEMENT KILN DUST FOR SUBGRADE STABILIZATION

Poor subgrade soil conditions can result in inadequate pavement support and reduce pavement life. Soils may be improved through the addition of chemical or cementitious additives. These chemical additives range from waste products to manufactured materials and include lime, Class C fly ash, portland cement, cement kiln dust from pre-calciner and long kiln processes, and proprietary chemical stabilizers. These additives can be used with a variety of soils to help improve their native engineering properties. The effectiveness of these additives depends on the soil treated and the amount of additive used. This report contains a summary of the performance of a wide range of soils treated with pre-calciner cement kiln dust (CKD), and is intended to be viewed as a companion report to the previously published Kansas Department of Transportation report, "Performance of Soil Stabilization Agents. " CKD has been used as a soil additive to improve the texture, increase strength and reduce swell characteristics. CKD was combined with a total of eight different soils with classifications of CH, CL, ML, SM, and SP. Durability testing procedures included freeze-thaw, wet-dry, and leach testing. Atterberg limits and strength tests were also conducted before and after selected durability tests. Changes in pH were monitored during leaching. Relative values of soil stiffness were also tracked over a 28-day curing period using the soil stiffness gauge. Treatment with CKD was found to be an effective option for improvement of soil properties, based on the testing conducted as a part of this research. Strength and stiffness were improved and plasticity and swell potential were substantially reduced. Durability of CKD treated samples in wet-dry testing was comparable to that of soil samples treated with the other additives, while performance was not as good in freeze thaw testing. CKD treated samples performed very well in leaching tests and in many cases showed additional reductions in plasticity and some strength gains after leaching. It is recommended based on the results of this research that CKD be considered a viable option for the stabilization of subgrade soils. As with all additives, it is recommended that a mix design be conducted prior to selection to confirm the CKD selected and the amount specified will provide satisfactory performance.