Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Detection of Incomplete Instances of Structural Patterns in UML Class Diagrams

An approach for the detection of structural patterns based on UML class diagrams is presented. By using a fuzzy-like evaluation mechanism the introduced approach is able to recognize not only entire patterns but also incomplete instances.Referring to structural patterns in general the knowledge about used patterns assists a developer not only while maintaining or reverse engineering existing software, but already while designing or implementing new software. The information about the instantiation status is essential for a developer using, for example, specialization patterns that guide the extension of a particular framework. The developer can be supported by information about already instantiated patterns as well as partial instances which obviously occur rather often while developing.
Effect of interferon-α on cortical glutamate in patients with hepatitis C: a proton magnetic resonance spectroscopy study

Background The development of depressive symptomatology is a recognized complication of treatment with the cytokine interferon-α (IFN-α) and has been seen as supporting inflammatory theories of the pathophysiology of major depression. Major depression has been associated with changes in glutamatergic activity and recent formulations of IFN-induced depression have implicated neurotoxic influences that could also lead to changes in glutamate function. The present study used magnetic resonance spectroscopy (MRS) to measure glutamate and its major metabolite glutamine in patients with hepatitis C who received treatment with pegylated IFN-α and ribavirin. Method MRS measurements of glutamate and glutamine were taken from a 25 × 20 × 20 mm voxel including the pregenual anterior cingulate cortex in 12 patients before and after 4–6 weeks of treatment with IFN. Results IFN treatment led to an increase in cortical levels of glutamine (p = 0.02) and a significant elevation in the ratio of glutamine to glutamate (p < 0.01). Furthermore, changes in glutamine level correlated significantly with ratings of depression and anxiety at the time of the second scan. Conclusions We conclude that treatment with IFN-α is associated with MRS-visible changes in glutamatergic metabolism. However, the changes seen differ from those reported in major depression, which suggests that the pathophysiology of IFN-induced depression may be distinct from that of major depression more generally.
Microstructural models for diffusion MRI in breast cancer and surrounding stroma: an ex vivo study

The diffusion signal in breast tissue has primarily been modelled using apparent diffusion coefficient (ADC), intravoxel incoherent motion (IVIM) and diffusion tensor (DT) models, which may be too simplistic to describe the underlying tissue microstructure. Formalin‐fixed breast cancer samples were scanned using a wide range of gradient strengths, durations, separations and orientations. A variety of one‐ and two‐compartment models were tested to determine which best described the data. Models with restricted diffusion components and anisotropy were selected in most cancerous regions and there were no regions in which conventional ADC or DT models were selected. Maps of ADC generally related to cellularity on histology, but maps of parameters from more complex models suggest that both overall cell volume fraction and individual cell size can contribute to the diffusion signal, affecting the specificity of ADC to the tissue microstructure. The areas of coherence in diffusion anisotropy images were small, approximately 1 mm, but the orientation corresponded to stromal orientation patterns on histology.
A Review on Teaching Approaches and Content of College English over the Past Ten Years

This review attempts to reveal the research situation in Teaching Approaches and Content of College English over the past 10 years.The analysis is based on the articles published in 10 foreign language research CSSCI( 2014-2015) journals.It is found that much focus has been laid by Chinese researchers on the research of teaching approaches and content of College English,which has been developing from a state of superficiality to complication,and then to simplicity.Generally speaking,problems lie in the imbalanced attention of research,inadequacy in depth and lack of relevance with classroom teaching.Specifically,too much attention has been paid to the research of writing skill and lexical knowledge while less to the research of teaching listening,speaking and general cultural knowledge.Therefore,future studies are expected to fill these gaps.
Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks

Achieving a real understanding of animal development obviously requires a comprehensive rather than partial identification of the genes working in each developmental process. Recent decoding of genome sequences will enable us to perform such studies. An ascidian, Ciona intestinalis, one of the animals whose genome has been sequenced, is a chordate sharing a basic body plan with vertebrates, although its genome contains less paralogs than are usually seen in vertebrates. In the present study, we discuss the genomewide approach to networks of developmental genes in Ciona embryos. We focus on transcription factor genes and some major groups of signal transduction genes. These genes are comprehensively listed and examined with regard to their embryonic expression by in situ hybridization (http://ghost.zool.kyoto-u.ac.jp/tfst.html). The results revealed that 74% of the transcription factor genes are expressed maternally and that 56% of the genes are zygotically expressed during embryogenesis. Of these, 34% of the transcription factor genes are expressed both maternally and zygotically. The number of zygotically expressed transcription factor genes increases gradually during embryogenesis. As an example, and taking advantage of this comprehensive description of gene expression profiles, we identified transcription factor genes and signal transduction genes that are expressed at the early gastrula stage and that work downstream of β-catenin, FoxD and/or Fgf9/16/20. Because these three genes are essential for ascidian endomesoderm specification, transcription factor genes and signal transduction genes involved in each of the downstream processes can be deduced comprehensively using the present approach.
The Economic Value of A Passport: A Model of Citizenship and the Social Dividend in a Global Economy

In a world of fully mobile capital and highly immobile labour, citizenship is effectively an entitlement to the ‘dividend’ arising from the social infrastructure accumulated in a particular country of birth. The paper opens with the reasons why the passport (ie citizenship) can in consequence be considered as an economic asset with a value that can in principle be determined analytically. A simple endogenous growth model is set up which defines the level and growth of per capita income in a world economy where capital is fully mobile and labour is fully immobile, and where governments set a rate of taxation such as to achieve the optimal balance between the stocks of private capital and social infrastructure. The ‘passport value’ is then defined as the difference between national income net of capital charges, wage costs and taxes when divided equally among the population; and is shown to depend on per capita income, the rate of growth and the parameters of the production function. A preliminary estimate of the main variables in the model, and the scale of expenditure on social infrastructure, for a wide range of countries suggests what the order of magnitude of the ‘value of a passport’ might be. A brief section on the wider implications of the findings concludes.
Activation of Multiple Interleukin-1β Converting Enzyme Homologues in Cytosol and Nuclei of HL-60 Cells during Etoposide-induced Apoptosis*

Recent genetic and biochemical studies have implicated cysteine-dependent aspartate-directed proteases (caspases) in the active phase of apoptosis. In the present study, three complementary techniques were utilized to follow caspase activation during the course of etoposide-induced apoptosis in HL-60 human leukemia cells. Immunoblotting revealed that levels of procaspase-2 did not change during etoposide-induced apoptosis, whereas levels of procaspase-3 diminished markedly 2-3 h after etoposide addition. At the same time, cytosolic peptidase activities that cleaved DEVD-aminotrifluoromethylcoumarin and VEID-aminomethylcoumarin increased 100- and 20-fold, respectively; but there was only a 1.5-fold increase in YVAD-aminotrifluoromethylcoumarin cleavage activity. Affinity labeling with N-(Nα-benzyloxycarbonylglutamyl-Nε-biotinyllysyl)aspartic acid [(2,6-dimethylbenzoyl)oxy]methyl ketone indicated that multiple active caspase species sequentially appeared in the cytosol during the first 6 h after the addition of etoposide. Analysis on one- and two-dimensional gels revealed that two species comigrated with caspase-6 and three comigrated with active caspase-3 species, suggesting that several splice or modification variants of these enzymes are active during apoptosis. Polypeptides that comigrate with the cytosolic caspases were also labeled in nuclei of apoptotic HL-60 cells. These results not only indicate that etoposide-induced apoptosis in HL-60 cells is accompanied by the selective activation of multiple caspases in cytosol and nuclei, but also suggest that other caspase precursors such as procaspase-2 are present but not activated during apoptosis.
Reinterpretation of disturbance observer as an add-on controller

In the paper, the reinterpretation of a disturbance observer formulated in the transfer function domain is considered. Recalling that the disturbance observer produces an additional disturbance suppresion performance to the existing closed-loop system, the idea of this paper is that the disturbance observer can be an add-on controller only to suppress the disturbances. By inducing the equivalent block diagram from generalized disturbance observer based control system [9], we obtain the equivalent feedback controller and the equivalent open-loop transfer function. Then, the role of a disturbance observer as an add-on controller is newly analyzed. Also, the reason of robust stability margin reduction phenomenon is explaned with the equivalent open-loop transfer function. The reinterpretation of a disturbance observer as an add-on controller is shown by a simple minimum-phase plant.
Cloud architecture for tight interaction with the real world and deep sensor-data aggregation mechanism

The next-generation cloud computing systems are expected to be connected to the real world more tightly by massive amounts of sensors and actuators. Today's clouds, however, are not capable of handling massive sensor data or giving fast feedback to the real world because of the long latency and limited bandwidth of WANs. We propose a cloud architecture that allows fast response to the real world in spite of floods of sensor data. We also present a deep sensor-data aggregation mechanism for the proposed cloud architecture to compress sensor data by an order of magnitude. Our evaluation results show that the deep sensor-data aggregation at the edges of clouds is effective in reducing network traffic sent over cloud networks.
An analysis of alcohol consumption status and alcohol related-factors in the Pearl River Delta area in China

ObjectiveTo understand alcohol consumption status and alcohol related-factors in the total amount of alcohol use of people living in the Pearl River delta. MethodsBy cluster sampling, 3340 community residents aged 15 years old or older were interviewed by psychiatrists with structural questionnaires provided by WHO. ResultsThe total alcohol dependence rate is 6.0%, and the rate in male is 8.1%, while in female is (3.6)%. The results of single variable analysis revealed that numerous variables were related factors for alcohol dependence, including heavy physical labor, peasants, less education level, unemployed and retired people, intelligent labors and administrators, younger, divorcer and separationer, while family income was junior to alcohol dependence. In Logistic regression analysis, the factors including annual alcohol consumption,employee, education level, marriage, sex, age, family income entry the equation for alcohol dependence continuously. ConclusionThe situation of alcohol consumption in the Pearl River delta is very serious, alcohol consumption and its related problems impact severely on the drinkers' health, especially in heavy drinkers, measures must be taken by the government to prohibit alcohol or reducing alcohol consumption in high-risk population.
On the Dehydrocoupling of Alkenylacetylenes Mediated by Various Samarocene Complexes: A Charming Story of Metal Cooperativity Revealing a Novel Dual Metal σ-Bond Metathesis Type of Mechanism (DM|σ-BM)

The prevailing reductive chemistry of Sm(II) has been accessed and explored mostly by the use of samarocene precursors. The highly reducing character of these congeners, along with their Lewis acidity and predominantly ionic bonding, allows for the relatively facile activation of C–H bonds, as well as peculiar transformations of unsaturated substrates (e.g., C–C couplings). Among other important C–C coupling reactions, the reaction of phenylacetylene with different mono- or bimetallic samarocene complexes affords trienediyl complexes of the type {[(C5Me5)2Sm]2(µ-η2:η2-PhC4Ph)}. In contrast, when t-butylacetylene is used, uncoupled monomers of the type (C5Me5)2Sm(C≡C–tBu) were obtained. Although this type of reactivity may appear to be simple, the mechanism underlying these transformations is complex. This conclusion is drawn from the density functional theory (DFT) mechanistic studies presented herein. The operating mechanistic paths consist of: (i) the oxidation of each samarium center and the concomitant double reduction of the alkyne to afford a binuclear intermediate; (ii) the C–H scission of the acetylinic bond that lies in between the two metals; (iii) a dual metal σ-bond metathesis (DM|σ-SBM) process that releases H2; and eventually (iv) the C–C coupling of the two bridged μ-alkynides to give the final bimetallic trienediyl complexes. For the latter mechanistic route, the experimentally used phenylacetylene was considered first as well as the aliphatic hex-1-yne. More interestingly, we shed light into the formation of the mono(alkynide) complex, being the final experimental product of the reaction with t-butylacetylene.
Mus81 nuclease and Sgs1 helicase are essential for meiotic recombination in a protist lacking a synaptonemal complex

Mus81 resolvase and Sgs1 helicase have well-established roles in mitotic DNA repair. Moreover, Mus81 is part of a minor crossover (CO) pathway in the meiosis of budding yeast, plants and vertebrates. The major pathway depends on meiosis-specific synaptonemal complex (SC) formation, ZMM proteins and the MutLγ complex for CO-directed resolution of joint molecule (JM)-recombination intermediates. Sgs1 has also been implicated in this pathway, although it may mainly promote the non-CO outcome of meiotic repair. We show in Tetrahymena, that homologous chromosomes fail to separate and JMs accumulate in the absence of Mus81 or Sgs1, whereas deletion of the MutLγ-component Mlh1 does not affect meiotic divisions. Thus, our results are consistent with Mus81 being part of an essential, if not the predominant, CO pathway in Tetrahymena. Sgs1 may exert functions similar to those in other eukaryotes. However, we propose an additional role in supporting homologous CO formation by promoting homologous over intersister interactions. Tetrahymena shares the predominance of the Mus81 CO pathway with the fission yeast. We propose that in these two organisms, which independently lost the SC during evolution, the basal set of mitotic repair proteins is sufficient for executing meiotic recombination.
Logical definability and query languages over unranked trees

Unranked trees, that is, trees with no restriction on the number of children of nodes, have recently attracted much attention, primarily as an abstraction of XML (Extensible Markup Language) documents. In this paper, we study logical definability over unranked trees, as well as collections of unranked trees, that can be viewed as databases of XML documents. The traditional approach to definability is to view each tree as a structure of a fixed vocabulary, and study the expressive power of various logics on trees. A different approach, based on model theory, considers a structure whose universe is the set of all trees, and studies definable sets and relations; this approach extends smoothly to the setting of definability over collections of trees. We study the latter, model-theoretic approach. We find sets of operations on unranked trees that define regular tree languages, and show that some natural restrictions correspond to logics studied in the context of XML pattern languages. We then look at relational calculi over collections of unranked trees, and obtain quantifier-restriction results that give us bounds on the expressive power and complexity. As unrestricted relational calculi can express problems complete for each level of the polynomial hierarchy, we look at their restrictions, corresponding and find several calculi with low (NC/sup 1/) data complexity that can express important XML properties like DTD validation and XPath evaluation.
Anterolateral Prefrontal Cortex Mediates the Analgesic Effect of Expected and Perceived Control over Pain

Perceived control attenuates pain and pain-directed anxiety, possibly because it changes the emotional appraisal of pain. We examined whether brain areas associated with voluntary reappraisal of emotional experiences also mediate the analgesic effect of perceived control over pain. Using functional magnetic resonance imaging, we compared self-controlled noxious stimuli with physically identical stimuli that were externally controlled. Self-controlled stimulation was accompanied by less pain and anxiety and higher activation in dorsal anterior cingulate (dACC), right dorsolateral, and bilateral anterolateral prefrontal (alPFC) cortices. Activation in dACC and right alPFC was negatively correlated with pain intensity ratings. For externally controlled pain, activation in right alPFC was inversely correlated with the participants' general belief to have control over their lives. Our results are consistent with a reappraisal view of control and suggest that the analgesic effect of perceived control relies on activation of right alPFC. Failure to activate right alPFC may explain the maladaptive effects of strong general control beliefs during uncontrollable pain.
Critical Evaluation of Linear Dimensionality Reduction Techniques for Cardiac Arrhythmia Classification

Embedding the original high dimensional data in a low dimensional space helps to overcome the curse of dimensionality and removes noise. The aim of this work is to evaluate the performance of three different linear dimensionality reduction techniques (DR) techniques namely principal component analysis (PCA), multi dimensional scaling (MDS) and linear discriminant analysis (LDA) on classification of cardiac arrhythmias using probabilistic neural network classifier (PNN). The design phase of classification model comprises of the following stages: preprocessing of the cardiac signal by eliminating detail coefficients that contain noise, feature extraction through daubechies wavelet transform, dimensionality reduction through linear DR techniques specified, and arrhythmia classification using PNN. Linear dimensionality reduction techniques have simple geometric representations and simple computational properties. Entire MIT-BIH arrhythmia database is used for experimentation. The experimental results demonstrates that combination of PNN classifier (spread parameter, σ = 0.08) and PCA DR technique exhibits highest sensitivity and F score of 78.84% and 78.82% respectively with a minimum of 8 dimensions.
A topological approach to detect conflicts in firewall policies

Packet filtering provides initial layer of security based upon set of ordered filters called firewall policies. It examines the network packets and decides whether to accept or deny them. But when a packet matches two or more filters conflicts arise. Due to the conflicts, some filters are never executed and some filters are occasionally executed. It may results into unintended traffic and it is a tedious job for administrator to detect conflicts. Detection of conflicts through geometrical approach provides a systematic and powerful error classification, but as the filters and key fields of header increase, it demands high memory and computation time. To solve this problem, we propose a topological approach called BISCAL (Bit-vector based spatial calculus) to detect the conflicts in the firewall policies. As because of our approach preserves only the topology of the filters, it can reduce memory usage and computation time to a great extend
A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis[W]

The combination of metabolomics and transcriptomics on Arabidopsis thaliana lines mutated in 10 steps of the lignin pathway provides insight into monolignol biosynthesis and the metabolic network in which it is embedded. In addition, this work reveals novel pathways and genes associated with lignin biosynthesis. Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant’s response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (phenylalanine ammonia-lyase1 [PAL1], PAL2, cinnamate 4-hydroxylase [C4H], 4-coumarate:CoA ligase1 [4CL1], 4CL2, caffeoyl-CoA O-methyltransferase1 [CCoAOMT1], cinnamoyl-CoA reductase1 [CCR1], ferulate 5-hydroxylase [F5H1], caffeic acid O-methyltransferase [COMT], and cinnamyl alcohol dehydrogenase6 [CAD6], two mutant alleles each), were analyzed by transcriptomics and metabolomics. A total of 566 compounds were detected, of which 187 could be tentatively identified based on mass spectrometry fragmentation and many were new for Arabidopsis. Up to 675 genes were differentially expressed in mutants that did not have any obvious visible phenotypes. Comparing the responses of all mutants indicated that c4h, 4cl1, ccoaomt1, and ccr1, mutants that produced less lignin, upregulated the shikimate, methyl-donor, and phenylpropanoid pathways (i.e., the pathways supplying the monolignols). By contrast, f5h1 and comt, mutants that provoked lignin compositional shifts, downregulated the very same pathways. Reductions in the flux to lignin were associated with the accumulation of various classes of 4-O- and 9-O-hexosylated phenylpropanoids. By combining metabolomic and transcriptomic data in a correlation network, system-wide consequences of the perturbations were revealed and genes with a putative role in phenolic metabolism were identified. Together, our data provide insight into lignin biosynthesis and the metabolic network it is embedded in and provide a systems view of the plant’s response to pathway perturbations.