Miracle-dz/UniFAR-FTUs huggingface dataset:
Software architecture transformations

In order to understand and improve software, we commonly examine and manipulate its architecture. For example, we may want to examine the architecture at different levels of abstraction or zoom-in on one portion of the system. We may discover that the extracted architecture has deviated from our mental model of the software and hence we may want to repair it. The paper identifies the commonality between these architectural transformation actions, i.e., by manipulating the architecture in order to understand analyze, and modify the software structure, we are in fact performing graph transformations. We categorize useful architectural transformations and describe them within the framework of graph transformations. By describing them in a unified way, we gain a better understanding of the transformations and thus, can work towards modeling, specifying and automating them.
ON THE DEVELOPMENT OF AN INTELLIGENT CODE VALIDATION SYSTEM FOR THE RAPID TRANSFER OF TURBULENCE MODEL TECHNOLOGY

Issues related to the development of a Code Validation System (CVS) are presented for the rapid transfer of turbulence models in Computational Fluid Dynamics (CFD) to industry and research. While CFD has become a successful and critical tool in many industries in both application and R&D, it has not kept pace with the progress made by turbulence models. This is due primarily to the inefficient and crude method of transfer of newly developed turbulence models to the CFD community. Timely transfer of this critical knowledge would help ensure that industry and government research scientists keep pace with current trends and progress made by turbulence modelers. Design considerations related to the development of a turbulence modeling information data base, or CVS, are presented that will bring together turbulence models, numerical algorithms, and experimental data and transfer this information via the Internet and World Wide Web to developers and end-users of CFD codes allowing proper use of the latest models and inherent their limitations.
Extracting Higher Order Relations From Biomedical Text

Argumentation in a scientific article is composed of unexpressed and explicit statements of old and new knowledge combined into a logically coherent textual argument. Discourse relations, linguistic coherence relations that connect discourse segments, help to communicate an argument’s logical steps. A biomedical relation exhibits a relationship between biomedical entities. In this paper, we are primarily concerned with the extraction of connections between biomedical relations, a connection that we call a higher order relation. We combine two methods, namely biomedical relation extraction and discourse relation parsing, to extract such higher order relations from biomedical research articles. Finding and extracting these relations can assist in automatically understanding the scientific arguments expressed by the author in the text.
Long-term treatment effects of imagery rehearsal therapy for nightmares in a population with diverse mental disorders

Nightmares are a common problem with debilitating consequences. Meta-analyses have revealed that imagery rehearsal therapy (IRT), in which the storyline of the recurring nightmare is changed, is the treatment of choice for nightmares. In a randomized clinical trial, we recently demonstrated that IRT was also effective in a population of patients with diverse mental disorders. In this trial, IRT showed moderate additional benefits over treatment as usual on nightmare distress, general psychopathology, and posttraumatic stress symptoms. In the current paper we report on the six- and nine month follow-up measurements of the IRT group of this trial. In the six- and nine-month follow-up the moderate improvements observed at post-treatment were sustained for all measures. This means that IRT has long-lasting effects, also in a sample with severe co-morbid psychopathology. IRT could be considered at an early stage in addition to the usual mental health treatment.
Key technologies for intelligent and safer cars - From motion estimation to predictive collision avoidance

One of the research areas that has received more and more interest during the last years is the development of driver assistant systems and semi-autonomous cars. However, densely populated environments like city centers are still a challenge for the operation of such systems. In this paper, we present approaches to two of the major tasks for autonomous driving in urban environments: self-localization and egomotion estimation and detection of dynamic objects such as cars and pedestrians. For each of these tasks we present a summary of the techniques we employ and results on real data. All modules have been implemented and tested on our autonomous car platform SmartTer.
SIRT1 inhibition impairs non-homologous end joining DNA damage repair by increasing Ku70 acetylation in chronic myeloid leukemia cells

Most chemotherapeutic agents for leukemia are DNA damaging agents. However, DNA lesions can be repaired by activities of DNA repair systems. Increasing evidence have shown that enhanced DNA damage repair capacity contributes to chemotherapy resistance in leukemia cells. Thus, targeting DNA repair mechanisms is a promising strategy for novel leukemia treatment. SIRT1 expressions were downregulated by lentivirus-delivered SIRT1 shRNA in myeloid leukemia cells. SIRT1 mRNA and protein levels were analyzed by real-time PCR and Western blot, respectively. Flow cytometry was carried out to analyze cell cycle progression, apoptosis and DNA damage repair efficiency. DNA damage levels were assessed by alkaline comet assay, and H2AX phosphorylation was analyzed by immunoblotting and immunofluorescence. A mouse leukemia model was established by transplanting lentivirus-infected K562 cells containing SIRT1 shRNA into sublethally irradiated NOD/SCID mice, and tumorigenesis was evaluated by detecting tumor weights and mice survival. SIRT1 expressions were upregulated in myeloid leukemic patients. Downregulation of SIRT1 by RNAi promoted etoposide-induced DNA damage in myeloid leukemia cells accompanied by reduced NHEJ activity, and increased Ku70 acetylation. Furthermore, SIRT1 knockdown resulted in cell cycle arrest, induction of apoptosis and reduction of K562 cell proliferation accompanied by enhanced p53 and FOXO1 acetylation in K562 cells after etoposide treatment. Importantly, SIRT1 downregulation reduced the tumorigenesis ability of K562 cells in mouse xenografts following chemotherapy treatment. These results revealed that SIRT1 promotes the NHEJ repair pathway by deacetylating Ku70 in K562 cells, suggesting that SIRT1 is a novel therapeutic target for treating myeloid leukemia.
Architectural requirements for energy efficient execution of graph analytics applications

Intelligent data analysis has become more important in the last decade especially because of the significant increase in the size and availability of data. In this paper, we focus on the common execution models and characteristics of iterative graph analytics applications. We show that the features that improve work efficiency can lead to significant overheads on existing systems. We identify the opportunities for custom hardware implementation, and outline the desired architectural features for energy efficient computation of graph analytics applications.
A Fast, Reliable, and Sensitive Method for Detection and Quantification of Listeria monocytogenes and Escherichia coli O157:H7 in Ready-to-Eat Fresh-Cut Products by MPN-qPCR

In the present work we developed a MPN quantitative real-time PCR (MPN-qPCR) method for a fast and reliable detection and quantification of Listeria monocytogenes and Escherichia coli O157:H7 in minimally processed vegetables. In order to validate the proposed technique, the results were compared with conventional MPN followed by phenotypic and biochemical assays methods. When L. monocytogenes and E. coli O157:H7 were artificially inoculated in fresh-cut vegetables, a concentration as low as 1 CFU g−1 could be detected in 48 hours for both pathogens. qPCR alone allowed a limit of detection of 101 CFU g−1 after 2 hours of enrichment for L. monocytogenes and E. coli O157:H7. Since minimally processed ready-to-eat vegetables are characterized by very short shelf life, our method can potentially address the consistent reduction of time for microbial analysis, allowing a better management of quality control. Moreover, the occurrences of both pathogenic bacteria in mixed salad samples and fresh-cut melons were monitored in two production plants from the receipt of the raw materials to the early stages of shelf life. No sample was found to be contaminated by L. monocytogenes. One sample of raw mixed salad was found positive to an H7 enterohemorrhagic serotype.
Voice Conversion Using Dynamic Frequency Warping With Amplitude Scaling, for Parallel or Nonparallel Corpora

In Voice Conversion (VC), the speech of a source speaker is modified to resemble that of a particular target speaker. Currently, standard VC approaches use Gaussian mixture model (GMM)-based transformations that do not generate high-quality converted speech due to “over-smoothing” resulting from weak links between individual source and target frame parameters. Dynamic Frequency Warping (DFW) offers an appealing alternative to GMM-based methods, as more spectral details are maintained in transformation; however, the speaker timbre is less successfully converted because spectral power is not adjusted explicitly. Previous work combines separate GMM- and DFW-transformed spectral envelopes for each frame. This paper proposes a more effective DFW-based approach that (1) does not rely on the baseline GMM methods, and (2) functions on the acoustic class level. To adjust spectral power, an amplitude scaling function is used that compares the average target and warped source log spectra for each acoustic class. The proposed DFW with Amplitude scaling (DFWA) outperforms standard GMM and hybrid GMM-DFW methods for VC in terms of both speech quality and timbre conversion, as is confirmed in extensive objective and subjective testing. Furthermore, by not requiring time-alignment of source and target speech, DFWA is able to perform equally well using parallel or nonparallel corpora, as is demonstrated explicitly.
Synthesis, Characterization, Antimicrobial and Antioxidant Activities of The Homocyclotrimer Of 4-Oxo-4h-Thieno[3,4-C]Chromene-3-Diazonium Sulfate

The in situ formed 4-oxo-4H-thieno[3,4-c]chromene-3-diazonium sulfate (5) in the coupling reactions involving the parent 2-aminothiophene (4) and various phenolic and arylamines’ couplers, readily undergoes homocyclotrimerization at low temperature to afford in fairly good yield the first ever reported eighteen member ring heteroaromatic holigomer 6. Compound 6 was fully characterized by its elemental analysis, IR, UV-Vis, 1H-NMR, 13C-NMR and HRMS spectral data. The HMBC and HSQC techniques were used to ascertain the structural assignments. A comparative study on the antimicrobial and antioxidant activities of compounds 3, 4 and 6 was carried out to assess the SAR due to the transformations (from 3 to 6 via 4) on the tested compounds. It was found that compounds 6 and 4 were respectively the most active compounds against bacteria (MIC = 32-64 μg/ml) and yeasts (MIC = 16–64 μg/ml). Compound 6 also showed high radical-scavenging activities and ferric reducing power when compared with vitamin C and BHT used as reference antioxidants.
Darmstadt Discussion Papers in Economics Jefficiency vs. Efficiency in Social Network Models

The mainly used welfare criterion in the social network literature is Bentham ́s utilitarian concept. The shortcomings of this concept are well-known. We compare the outcomes of the utilitarian concept with the Nash social welfare function. By using a Taylor approximation we deduce a formula which allows the direct comparison of both concepts. The implications of welfare considerations of important network formation models are evaluated by using the multiplicative concept. We introduce a new symmetric connection model which is related to Nash ́s welfare function in the same way as the original model is related to the utilitarian function. Based on the observation that heavy tail distributions like the power law distribution and the Pareto distribution can be explained by multiplicative structures we propose to use multiplicative utility functions in social network models. Furthermore, multiplicative utility and welfare functions together exhibit favorable characteristics both in normative and positive terms. Many empirically observed social networks have structures which are better modelled by multiplicative functions. From the normative perspective, multiplicative functions might be attractive since the Nash product introduces some form of justice. JEL Classification: A13, D11, D23, D61, D63, L14, Z13
Studying the Effects of Affective Feedback in Embodied Tutors

We present a study designed to explore the effect of feedback on perception of an interactive embodied agent as well as the overall performance and experience of primary school children aged 12-13 carrying out a treasure hunt activity. We use an interactive dialogue agent to compare three experimental conditions: no feedback, neutral feedback, and affective feedback. We study if the agent in the affective condition helps in engagement of the task more than the two other conditions.
Inverted Pendulum Control: A Brief Overview

Inverted Pendulum is a classic example of an inherently unstable system. This paper studies the Control of Inverted Pendulum. It focuses on the Mobile Inverted Pendulum. A few papers have been referred to get a brief overview of the work going on in this field. A short survey of these papers has been done for the purpose. Along with it, the basic idea of the mobile inverted pendulum and 2 control strategies have been discussed.
Fast and reliable MCMC for cosmological parameter estimation

Markov Chain Monte Carlo (MCMC) techniques are now widely used for cosmological parameter estimation. Chains are generated to sample the posterior probability distribution obtained following the Bayesian approach. An important issue is how to optimize the efﬁciency of such sampling and how to diagnose whether a ﬁnite-length chain has adequately sampled the underlying posterior probability distribution. We show how the power spectrum of a single such ﬁnite chain may be used as a convergence diagnostic by means of a ﬁtting function, and discuss strategies for optimizing the distribution for the proposed steps. The methods devel-oped are applied to current CMB and LSS data interpreted using both a pure adiabatic cosmological model and a mixed adiabatic/isocurvature cosmological model including possible correlations between modes. For the latter application, because of the increased dimensionality and the presence of degeneracies, the need for tuning MCMC methods for maximum efﬁciency becomes particularly acute.
1 Multi-document Summarization Focusing on Extracting and Integrating Similarities and Differences among Documents

The study was to develop a method for automatic summarization of sets of related research abstracts. This summarization method focused on extracting and integrating similarities and differences among different abstracts. In the research studies which aim to look for relationships between research concepts, similarities and differences are mainly reflected through research concepts and relationships expressed in the text. Thus the summarization method extracts research concepts and relationships from each research abstract, integrates similar concepts and relationships across different abstracts, and incorporates them into new sentences to produce a summary. This paper reports the three main summarization steps – discourse parsing, concept extraction and integration, and relationship extraction and integration. Each step was evaluated by comparing the machine output against
CD81 Is Required for Hepatitis C Virus Glycoprotein-Mediated Viral Infection

ABSTRACT CD81 has been described as a putative receptor for hepatitis C virus (HCV); however, its role in HCV cell entry has not been characterized due to the lack of an efficient cell culture system. We have examined the role of CD81 in HCV glycoprotein-dependent entry by using a recently developed retroviral pseudotyping system. Human immunodeficiency virus (HIV) pseudotypes bearing HCV E1E2 glycoproteins show a restricted tropism for human liver cell lines. Although all of the permissive cell lines express CD81, CD81 expression alone is not sufficient to allow viral entry. CD81 is required for HIV-HCV pseudotype infection since (i) a monoclonal antibody specific for CD81 inhibited infection of susceptible target cells and (ii) silencing of CD81 expression in Huh-7.5 hepatoma cells by small interfering RNAs inhibited HIV-HCV pseudotype infection. Furthermore, expression of CD81 in human liver cells that were previously resistant to infection, HepG2 and HH29, conferred permissivity of HCV pseudotype infection. The characterization of chimeric CD9/CD81 molecules confirmed that the large extracellular loop of CD81 is a determinant for viral entry. These data suggest a functional role for CD81 as a coreceptor for HCV glycoprotein-dependent viral cell entry.
Cooperative device-to-device communications in the downlink of cellular networks

We propose a cooperative device-to-device (D2D) communications framework in order to combat the problem of congestion in crowded communication environments. The idea is to allow a D2D transmitter to act as an in-band relay for a cellular link and at the same time transmit its own data by employing superposition coding in the downlink. Cooperation between the cellular link and D2D transmitter eases down the requirement on the interference. The main benefit of the proposed method is in increasing the number of connections per unit area with the same spectrum usage. It could also be beneficial to offload over-loaded cells. We formulate our problem to minimize the assigned power for cooperation while making sure the cellular user's performance does not degrade. Our results show that cooperation possibilities and improvement in overall cell capacity increase with the number of cellular users within the cell as well as the cell size.
The influence of non-DNA-targeted effects on carbon ion–induced low-dose hyper-radiosensitivity in MRC-5 cells

Low-dose hyper-radiosensitivity (LDHRS) is a hot topic in normal tissue radiation protection. However, the primary causes for LDHRS still remain unclear. In this study, the impact of non-DNA-targeted effects (NTEs) on high-LET radiation–induced LDHRS was investigated. Human normal lung fibroblast MRC-5 cells were irradiated with high-LET carbon ions, and low-dose biological effects (in terms of various bio-endpoints, including colony formation, DNA damage and micronuclei formation) were detected under conditions with and without gap junctional intercellular communication (GJIC) inhibition. LDHRS was observed when the radiation dose was <0.2 Gy for all bio-endpoints under investigation, but vanished when the GJIC was suppressed. Based on the probability of cells being hit and micro-dose per cell calculation, we deduced that the LDHRS phenomenon came from the combined action of direct hits and NTEs. We concluded that GJIC definitely plays an important role in cytotoxic substance spreading in high-LET carbon ion–induced LDHRS.
UvA-DARE (Digital Academic Repository) Correlated timing and spectral variations of the soft X-ray transient Aquila X-1: evidence for an atoll classification

Based on Rossi X-Ray T iming Explorer data, we discuss the classiÐcation of the soft X-ray transient Aquila X-1 in the Z/atoll scheme and the relation of its kilohertz quasi-periodic oscillations (kHz QPOs) properties to the X-ray colors. The color-color diagram shows one elongated (““ banana ÏÏ) structure and several ““ islands ÏÏ of data points. The power spectra of the island are best represented by a broken power law whereas those of the banana by a power law below D1 Hz plus an exponentially cuto† component at intermediate frequencies (30È60 Hz). The parameters of these two components change in correlation with the position of the source in the color-color diagram. Based on the pattern that the source shows in the color-color diagram and its aperiodic variability, we conclude that Aquila X-1 is an atoll source. We have also investigated the possible correlation between the frequency of the kHz QPOs and the position of the source in the color-color diagram. The complexity seen in the frequency versus count rate diagram is reduced to a single track when the frequency is plotted against hard or soft color. Subject headings : accretion, accretion disks È stars : individual (Aquila X-1) È stars : neutron È X-rays : stars
The Market for Corporate Subsidiaries in Japan : An empirical study of trades among listed firms USHIJIMA

We investigate the economic role of trades in corporate subsidiaries in Japan between 1996 and 2010, in terms of valuation and performance effects. By pairing both sides to each deal, we show differences in firm characteristics, returns, and subsequent performance of buying and selling firms. Unlike mergers among whole firms, most subsidiary deals straddled different industries. Most sellers were larger, more diversified and less profitable than the buyers. Our event study reveals that abnormal returns were positive for buyers yet insignificantly different from zero for sellers, with the notable exception of subsidiary sales in the core business, which earned negative returns, the more so the larger the deal. An analysis of ex-post operating results shows that the performance of sellers often declined after the trade, in particular for firms that divested a core-related subsidiary. We conclude that subsidiary trades in Japan in this period contributed importantly to strategic repositioning and a more efficient use of corporate assets.
Ultra-Low Background DNA Cloning System

Yeast-based in vivo cloning is useful for cloning DNA fragments into plasmid vectors and is based on the ability of yeast to recombine the DNA fragments by homologous recombination. Although this method is efficient, it produces some by-products. We have developed an “ultra-low background DNA cloning system” on the basis of yeast-based in vivo cloning, by almost completely eliminating the generation of by-products and applying the method to commonly used Escherichia coli vectors, particularly those lacking yeast replication origins and carrying an ampicillin resistance gene (Ampr). First, we constructed a conversion cassette containing the DNA sequences in the following order: an Ampr 5′ UTR (untranslated region) and coding region, an autonomous replication sequence and a centromere sequence from yeast, a TRP1 yeast selectable marker, and an Ampr 3′ UTR. This cassette allowed conversion of the Ampr-containing vector into the yeast/E. coli shuttle vector through use of the Ampr sequence by homologous recombination. Furthermore, simultaneous transformation of the desired DNA fragment into yeast allowed cloning of this DNA fragment into the same vector. We rescued the plasmid vectors from all yeast transformants, and by-products containing the E. coli replication origin disappeared. Next, the rescued vectors were transformed into E. coli and the by-products containing the yeast replication origin disappeared. Thus, our method used yeast- and E. coli-specific “origins of replication” to eliminate the generation of by-products. Finally, we successfully cloned the DNA fragment into the vector with almost 100% efficiency.