Miracle-dz/UniFAR-FTUs huggingface dataset:
Automated gui testing guided by usage profiles

Most software developed in recent years has a graphical userinterface (GUI). The only way for the end-user to interact with the software application is through the GUI. Hence, acceptance and system testing of the software requires GUI testing. This paper presents a new technique for testing of GUI applications. Information on the actual usage of the application, in the form of "usage profiles," is used to ensure that a new version of the application will function correctly. Usage profiles, sequences of events that end-users execute on a GUI, are used to develop a probabilistic usage model of the application. An algorithm uses the model to generate test cases that represent events the user is most likely to execute. Reverse engineering methods are used to extract the underlying structure of the application. An empirical study on four open source GUI applications reveals that test suites generated from the probabilistic model are 0.2-22% of the size of test suites produced directly from usage profiles. Furthermore, the test suites generated from the model detect more faults per test case than those detected directly from the usage profiles, and detect faults not detected by the original profiles
Reversal of Neurofibrillary Tangles and Tau-Associated Phenotype in the rTgTauEC Model of Early Alzheimer's Disease

Neurofibrillary tangles (NFTs), a marker of neuronal alterations in Alzheimer's disease (AD) and other tauopathies, are comprised of aggregates of hyperphosphorylated tau protein. We recently studied the formation of NFTs in the entorhinal cortex (EC) and their subsequent propagation through neural circuits in the rTgTauEC mouse model (de Calignon et al., 2012). We now examine the consequences of suppressing transgene expression with doxycycline on the NFT-associated pathological features of neuronal system deafferentation, NFT progression and propagation, and neuronal loss. At 21 months of age we observe that EC axonal lesions are associated with an abnormal sprouting response of acetylcholinesterase (AChE)-positive fibers, a phenotype reminiscent of human AD. At 24 months, NFTs progress, tau inclusions propagate to the dentate gyrus, and neuronal loss is evident. Suppression of the transgene expression from 18 to 24 months led to reversal of AChE sprouting, resolution of Gallyas-positive and Alz50-positive NFTs, and abrogation of progressive neuronal loss. These data suggest that propagation of NFTs, as well as some of the neural system consequences of NFTs, can be reversed in an animal model of NFT-associated toxicity, providing proof in principle that these lesions can be halted, even in established disease.
Validation of a Novel Biomarker Panel for the Detection of Ovarian Cancer

Background: Ovarian cancer is the most lethal gynecological malignancy. Our integrated -omics approach to ovarian cancer biomarker discovery has identified kallikrein 6 (KLK6) and folate-receptor 1 (FOLR1) as promising candidates but these markers require further validation. Methods: KLK6, FOLR1, CA125, and HE4 were investigated in three independent serum cohorts with a total of 20 healthy controls, 150 benign controls, and 216 ovarian cancer patients. The serum biomarker levels were determined by ELISA or automated immunoassay. Results: All biomarkers demonstrated elevations in the sera of ovarian cancer patients compared with controls (P < 0.01). Overall, CA125 and HE4 displayed the strongest ability (AUC 0.80 and 0.82, respectively) to identify ovarian cancer patients and the addition of HE4 to CA125 improved the sensitivity from 36% to 67% at a set specificity of 95%. In addition, the combination of HE4 and FOLR1 was a strong predictor of ovarian cancer diagnosis, displaying comparable sensitivity (65%) to the best-performing CA125-based models (67%) at a set specificity of 95%. Conclusions: The markers identified through our integrated -omics approach performed similarly to the clinically approved markers CA125 and HE4. Furthermore, HE4 represents a powerful diagnostic marker for ovarian cancer and should be used more routinely in a clinical setting. Impact: The implications of our study are 2-fold: (i) we have demonstrated the strengths of HE4 alone and in combination with CA125, lending credence to increasing its usage in the clinic; and (ii) we have demonstrated the clinical utility of our integrated -omics approach to identifying novel serum markers with comparable performance to clinical markers. Cancer Epidemiol Biomarkers Prev; 25(9); 1333–40. ©2016 AACR.
Hepatocyte Growth Factor Production by Neutrophils Infiltrating Bronchioloalveolar Subtype Pulmonary Adenocarcinoma : Role in Tumor Progression and Death 1

Increased numbers of tumor-infiltrating neutrophils are linked to poorer outcome in patients with adenocarcinoma of the bronchioloalveolar carcinoma (BAC) subtype. Hepatocyte growth factor (HGF) is a pleiotropic cytokine operating through activation of the proto-oncogene c-met and is a factor of poor prognosis in various cancers. Reports that neutrophils produce HGF led us to investigate their participation in the aerogenous spread of tumor cells and the prognosis of BAC, through the effect of HGF on c-met-expressing tumor cells. Immunoreactive HGF was detected in bronchoalveolar lavage fluid (BALF) supernatants from 34 of 36 patients, whereas it was undetectable in BALF from healthy controls. The HGF thus detected was locally produced, because HGF mRNA was expressed by the patients’ fresh alveolar cells, and HGF protein was detected in 24-h culture supernatants. In immunocytochemical studies of BALF cytospin preparations and tumor specimens from the patients, neutrophils were always HGF-positive, whereas alveolar macrophages and tumor cells gave inconsistent results. Alveolar neutrophil-derived HGFs induced significant, concentration-dependent migration of BACderived tumor cells in vitro, and this effect was inhibited by anti-HGF neutralizing antibodies. Granulocyte-macrophage colony-stimulating factor and tumor necrosis factor (present in the lung tumor microenvironment) provoked HGF release from neutrophil intracellular stocks, and the capacity of blood neutrophils from BAC patients to produce HGF was unaltered. Immunochemical studies of c-met expression in BALF cytospin preparations and tumor sections showed that most HGF receptor-bearing cells were tumor cells. High HGF levels in BALF supernatants were significantly associated with poorer outcome in patients with BAC and were an independent predictor of clinical outcome in multivariate analysis. Altogether, our results support the notion that BAC generates a local environment that attracts functionally normal neutrophils from peripheral blood and leads to neutrophil release of biologically active HGF on contact with HGF receptor-expressing tumor cells, thereby contributing to poorer patient outcome.
Virtual reality

Although the terms cyberspace and virtual reality have been around for years, virtual reality as an industry is in its infancy. The term virtual reality is credited to Jaron Lanier, founder of VPL Research; earlier experimenters, like Myron Krueger in the mid-1970s, used phrases like artificial reality. William Gibson coined cyberspace in his 1984 science fiction novel. Neuromancer. Few technologies in recent years have evoked such fiery discussions in the technical community, and fewer still have sparked such passionate involvement of the humanities and the cultural sector. Maybe the humanities community reacts because the VR interaction is so tightly coupled to the human senses. Perhaps the cultural sector clamours for a role in the evolution of VR because the technology is finally interfacing with the human, rather than the human interfacing with the technology. Whatever the reasons, VR is more a convergence of previously disparate disciplines than a whole new branch of technology. It simply takes a fresh look at human interaction. Evolving from user interface design, flight and visual simulation, and telepresence technologies, VR is unique in its emphasis on the experience of the human participant. VR focuses the user's attention on the experience while suspending disbelief about the method of creating it. We feel that neither the devices used nor the level of interactiveness or fidelity determine whether a system is VR. The quality of the experience is crucial. To stimulate creativity and productivity. the virtual experience must be credible. The reality must both react to the human participants in physically and perceptually appropriate ways, and conform to their personal cognitive representations of the microworld in which they are engrossed. The experience does not necessarily have to be realistic/spl minus/just consistent. <<ETX>>
The protein arginine methyltransferases CARM1 and PRMT1 cooperate in gene regulation

Protein arginine methyltransferases (PRMT) have been implicated in the regulation of transcription. They are recruited to promoters via interaction with transcription factors and exert their coactivator function by methylating arginine residues in histones and other chromatin proteins. Here, we employ an unbiased approach to identify novel target genes, which are under the control of two members of the enzyme family, PRMT1 and CARM1/PRMT4 (coactivator associated arginine methyltransferase 1). By using cDNA microarray analysis, we find that the siRNA-mediated single knockdown of neither CARM1 nor PRMT1 causes significant changes in gene expression. In contrast, double knockdown of both enzymes results in the deregulated expression of a large group of genes, among them the CITED2 gene. Cytokine-stimulated expression analysis indicates that transcriptional activation of CITED2 depends on STAT5 and the coactivation of both PRMTs. ChIP analysis identifies the CITED2 gene as a direct target gene of STAT5, CARM1 and PRMT1. In reporter gene assays, we show that STAT5-mediated transcription is cooperatively enhanced by CARM1 and PRMT1. Interaction assays reveal a cytokine-induced association of STAT5 and the two PRMTs. Our data demonstrate a widespread cooperation of CARM1 and PRMT1 in gene activation as well as repression and that STAT5-dependent transcription of the CITED2 gene is a novel pathway coactivated by the two methyltransferases.
IL-27 Signaling Is Crucial for Survival of Mice Infected with African Trypanosomes via Preventing Lethal Effects of CD4+ T Cells and IFN-γ

African trypanosomes are extracellular protozoan parasites causing a chronic debilitating disease associated with a persistent inflammatory response. Maintaining the balance of the inflammatory response via downregulation of activation of M1-type myeloid cells was previously shown to be crucial to allow prolonged survival. Here we demonstrate that infection with African trypanosomes of IL-27 receptor-deficient (IL-27R-/-) mice results in severe liver immunopathology and dramatically reduced survival as compared to wild-type mice. This coincides with the development of an exacerbated Th1-mediated immune response with overactivation of CD4+ T cells and strongly enhanced production of inflammatory cytokines including IFN-γ. What is important is that IL-10 production was not impaired in infected IL-27R-/- mice. Depletion of CD4+ T cells in infected IL-27R-/- mice resulted in a dramatically reduced production of IFN-γ, preventing the early mortality of infected IL-27R-/- mice. This was accompanied by a significantly reduced inflammatory response and a major amelioration of liver pathology. These results could be mimicked by treating IL-27R-/- mice with a neutralizing anti-IFN-γ antibody. Thus, our data identify IL-27 signaling as a novel pathway to prevent early mortality via inhibiting hyperactivation of CD4+ Th1 cells and their excessive secretion of IFN-γ during infection with African trypanosomes. These data are the first to demonstrate the essential role of IL-27 signaling in regulating immune responses to extracellular protozoan infections.
Estimating the Effects of Global Patent Protection in Pharmaceuticals: A Case Study of Quinolones in India

Under the Agreement on Trade-Related Intellectual Property Rights, the World Trade Organization members are required to enforce product patents for pharmaceuticals. In this paper we empirically investigate the welfare effects of this requirement on developing countries using data for the fluoroquinolones subsegment of the systemic anti-bacterials segment of the Indian pharmaceuticals market. Our results suggest that concerns about the potential adverse welfare effects of TRIPS may have some basis. We estimate that the withdrawal of all domestic products in this subsegment is associated with substantial welfare losses to the Indian economy, even in the presence of price regulation. The overwhelming portion of this welfare loss derives from the loss of consumer welfare.
CDKN1C (p57KIP2) Is a Direct Target of EZH2 and Suppressed by Multiple Epigenetic Mechanisms in Breast Cancer Cells

CDKN1C (encoding tumor suppressor p57KIP2) is a cyclin-dependent kinase (CDK) inhibitor whose family members are often transcriptionally downregulated in human cancer via promoter DNA methylation. In this study, we show that CDKN1C is repressed in breast cancer cells mainly through histone modifications. In particular, we show that CDKN1C is targeted by histone methyltransferase EZH2-mediated histone H3 lysine 27 trimethylation (H3K27me3), and can be strongly activated by inhibition of EZH2 in synergy with histone deacetylase inhibitor. Consistent with the overexpression of EZH2 in a variety of human cancers including breast cancer, CDKN1C in these cancers is downregulated, and breast tumors expressing low levels of CDKN1C are associated with a poor prognosis. We further show that assessing both EZH2 and CDKN1C expression levels as a measurement of EZH2 pathway activity provides a more predictive power of disease outcome than that achieved with EZH2 or CDKN1C alone. Taken together, our study reveals a novel epigenetic mechanism governing CDKN1C repression in breast cancer. Importantly, as a newly identified EZH2 target with prognostic value, it has implications in patient stratification for cancer therapeutic targeting EZH2-mediated gene repression.
Finite-block-length analysis in classical and quantum information theory

Coding technology is used in several information processing tasks. In particular, when noise during transmission disturbs communications, coding technology is employed to protect the information. However, there are two types of coding technology: coding in classical information theory and coding in quantum information theory. Although the physical media used to transmit information ultimately obey quantum mechanics, we need to choose the type of coding depending on the kind of information device, classical or quantum, that is being used. In both branches of information theory, there are many elegant theoretical results under the ideal assumption that an infinitely large system is available. In a realistic situation, we need to account for finite size effects. The present paper reviews finite size effects in classical and quantum information theory with respect to various topics, including applied aspects.
Development of Filtered Bispectrum for EEG Signal Feature Extraction in Automatic Emotion Recognition Using Artificial Neural Networks

The development of automatic emotion detection systems has recently gained significant attention due to the growing possibility of their implementation in several applications, including affective computing and various fields within biomedical engineering. Use of the electroencephalograph (EEG) signal is preferred over facial expression, as people cannot control the EEG signal generated by their brain; the EEG ensures a stronger reliability in the psychological signal. However, because of its uniqueness between individuals and its vulnerability to noise, use of EEG signals can be rather complicated. In this paper, we propose a methodology to conduct EEG-based emotion recognition by using a filtered bispectrum as the feature extraction subsystem and an artificial neural network (ANN) as the classifier. The bispectrum is theoretically superior to the power spectrum because it can identify phase coupling between the nonlinear process components of the EEG signal. In the feature extraction process, to extract the information contained in the bispectrum matrices, a 3D pyramid filter is used for sampling and quantifying the bispectrum value. Experiment results show that the mean percentage of the bispectrum value from 5 × 5 non-overlapped 3D pyramid filters produces the highest recognition rate. We found that reducing the number of EEG channels down to only eight in the frontal area of the brain does not significantly affect the recognition rate, and the number of data samples used in the training process is then increased to improve the recognition rate of the system. We have also utilized a probabilistic neural network (PNN) as another classifier and compared its recognition rate with that of the back-propagation neural network (BPNN), and the results show that the PNN produces a comparable recognition rate and lower computational costs. Our research shows that the extracted bispectrum values of an EEG signal using 3D filtering as a feature extraction method is suitable for use in an EEG-based emotion recognition system.
Exploring Cancer Worry in Adolescent and Young Adult Survivors of Childhood Cancers.

PURPOSE Adolescent and young adult (AYA) survivors of cancers in childhood experience cancer worry, defined as concerns about cancer-related issues such as relapse and late effects of treatment. Cancer worry is an important determinant of successful transition to long-term follow-up care. The primary aim of this study was to identify patient-, cancer-, and treatment-related factors associated with cancer worry in AYA survivors. A secondary aim was to explore and understand inappropriate cancer worry (e.g., worry of developing a late effect when not at risk) in this population. METHODS Two hundred and fifty AYA survivors, aged 15–26 years, completed a 6-item Cancer Worry Scale. Selection of factors potentially associated with cancer worry was guided by literature and expert opinion for inclusion in univariable and multivariable regression analyses. RESULTS Female survivors reported significantly more cancer worry than males did (b=-9.4; 95% CI -14.4 to -4.5; p < 0.001). Survivors treated with the most intensive therapies reported more cancer worry compared with those who received the least intensive therapies (b=-18.5; 95% CI -31.2 to -5.9; p = 0.004). Thirty-one percent of participants had inappropriate worry regarding infertility and/or secondary malignancy. CONCLUSIONS In AYA survivors, female sex and higher treatment intensity were associated with increased cancer worry. Inappropriate worry was prevalent among survivors and may contribute to unnecessary distress. These findings can help identify survivors who are more likely to worry and support the development of appropriate services to reduce the effect of cancer worry on survivor well-being.
Algorithms for Non-negative Matrix Factorization

Non-negative matrix factorization (NMF) has previously been shown to be a useful decomposition for multivariate data. Two different multiplicative algorithms for NMF are analyzed. They differ only slightly in the multiplicative factor used in the update rules. One algorithm can be shown to minimize the conventional least squares error while the other minimizes the generalized Kullback-Leibler divergence. The monotonic convergence of both algorithms can be proven using an auxiliary function analogous to that used for proving convergence of the Expectation-Maximization algorithm. The algorithms can also be interpreted as diagonally rescaled gradient descent, where the rescaling factor is optimally chosen to ensure convergence.
4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies

A study demonstrating an imaging framework that permits the determination of cell lineages during organogenesis of the posterior lateral line in zebrafish is presented. The combination of Selective Plane Illumination Microscopy and specific fluorescent markers allows retrospective tracking of hair cell progenitors, and hence the derivation of their lineages within the primodium. It is shown that, because of its superior signal‐to‐noise ratio and lower photo‐damaged properties, SPIM can provide significantly higher‐quality images than Spinning Disk Confocal technology. This allows accurate 4D lineage tracing for the hair cells over tens of hours of primordium migration and neuromast development. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Apply Outcomes-Based Framework to Measuring the Quality of Transnational Engineering Education

Transnational education has emerged over the past decade as a strategy for meeting the growing demand for higher education worldwide. Due to rapid expansion of transnational programmes, both governments and parents raise questions about the quality of transnational education. This study transpose the SERVQUAL-TRANS framework which encompasses outcomes and contributory constructs into a measurement instrument for evaluating the quality of transnational engineering education. The findings revealed that the outcomes construct of the SERVQUAL-TRANS explicitly assesses the attributes of students and graduates, and allows the stakeholders to perform backward and forward mapping to sustain growth and development of the education. On the other hand, the contributory construct shows clearly how the practices implemented by educational institutions can affect the quality of education. This study demonstrates the relative ease of using SERVQUAL-TRANS to evaluate the quality of education and it provides a way to assess the standard of the education
The Depression Conundrum and the Advantages of Uncertainty

According to the WHO (2012), the prevalence of unipolar depressive disorders is rising, even in those places where mental health treatments are widely available. The WHO predicts that these disorders will be the leading contributor to the global burden of disease by 2030. This sobering projection fits poorly with how psychological treatments for depression are presented in the mainstream scientific literature: as highly effective therapies, based upon a sound understanding of the causes of distress. There is a clear discrepancy between the rising prevalence figures on the one hand, and the confident claims of this effectiveness research on the other. This discrepancy prompts a set of complex interlinked questions, which we have called ‘The Depression Conundrum. ’ In search of a partial answer, the aim of our study was to critically analyze five meta-analytic studies investigating the effectiveness of psychological EBTs for depression, all of which had been published in high impact factor journals. Our examination established a number of methodological and statistical shortcomings in every study. Furthermore, we argue that the meta-analytic technique is founded upon problematic assumptions. The implications of our analysis are clear: decades of quantitative research might not allow us to conclude that psychological EBTs for depression are effective. The uncertainty and questions raised by our findings might act as a catalyst to broaden the way in which depression and associated therapies are researched. In addition, it might contribute toward a more vigorous and interdisciplinary debate about how to tackle this soon-to-be global public health priority number one.
Study of the Transmission of Subwavelength Metallic Grids in the THz Frequency Range

We report on the transmission of terahertz (THz) electromagnetic waves through gold grids evaporated over a transparent silicon substrate. We observe a near-unity transmission in the subwavelength regime. When the THz wavelength is comparable to the grid periodicity, the grid serves as a grating coupler that allows us to excite guided modes in the device. These guided modes exhibit an intermediate behavior between a surface plasmon mode and modes of a dielectric slab waveguide.