Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterizing the informal knowledge contained in systems

Program comprehension of legacy systems is a highly knowledge-intensive task. One of the goals of reverse engineering is to propose automated help to relate application domain concepts to all their implementation instances. It is generally accepted that to do so would require analyzing such documentation as identifiers or comments. However, before attempting to perform this difficult analysis, it would be useful to know precisely what information the documentation contains and if it is worth trying. In this paper, we present the results of a study of the knowledge contained in two sources of documentation for the Mosaic system. This knowledge is categorized into various domains, and the relative proportions of these domains are discussed. Among other things, the results highlight the high frequency with which application domain concepts are used, which could provide the means to identify them.
Supporting viewpoint-oriented enterprise architecture

Increasingly, organisations establish what is called an enterprise architecture. The enterprise architecture combines and relates all architectures describing some aspect of the organization, such as the business process architecture, the information architecture, and the application architecture. It is a blueprint of the organisation, which serves as a starting point for analysis, design and decision making. Viewpoints define abstractions on the set of models representing the enterprise architecture, each aimed at a particular type of stakeholder and addressing a particular set of concerns. The use of viewpoints is widely advocated for managing the inherent complexity in enterprise architecture. Viewpoints can both be used to view certain aspects in isolation, and for relating two or more aspects. However, in order to make such a viewpoint-oriented approach practically feasible, architects require a tool environment, which supports the definition, generation, editing and management of architectural views. Moreover, such an environment should work in concert with existing domain-specific modelling tools. We present the design of such a tool environment for viewpoint-oriented enterprise architecture.
From Prion Diseases to Prion-Like Propagation Mechanisms of Neurodegenerative Diseases

Prion diseases are fatal neurodegenerative sporadic, inherited, or acquired disorders. In humans, Creutzfeldt-Jakob disease is the most studied prion disease. In animals, the most frequent prion diseases are scrapie in sheep and goat, bovine spongiform encephalopathy in cattle, and the emerging chronic wasting disease in wild and captive deer in North America. The hallmark of prion diseases is the deposition in the brain of PrPSc, an abnormal β-sheet-rich form of the cellular prion protein (PrPC) (Prusiner 1982). According to the prion hypothesis, PrPSc can trigger the autocatalytic conversion of PrPC into PrPSc, presumably in the presence of cofactors (lipids and small RNAs) that have been recently identified. In this review, we will come back to the original works that led to the discovery of prions and to the protein-only hypothesis proposed by Dr. Prusiner. We will then describe the recent reports on mammalian synthetic prions and recombinant prions that strongly support the protein-only hypothesis. The new concept of “deformed templating” regarding a new mechanism of PrPSc formation and replication will be exposed. The review will end with a chapter on the prion-like propagation of other neurodegenerative disorders, such as Alzheimer's and Parkinson's disease and tauopathies.
The challenge of chronic lung disease in HIV-infected children and adolescents

Until recently, little attention has been given to chronic lung disease (CLD) in HIV‐infected children. As the HIV epidemic matures in sub‐Saharan Africa, adolescents who acquired HIV by vertical transmission are presenting to health services with chronic diseases. The most common is CLD, which is often debilitating.
A fine-grained evaluation framework for machine translation system development

Intelligibility and fidelity are the two key notions in machine translation system evaluation, but do not always provide enough information for system development. Detailed information about the type and number of errors of each type that a translation system makes is important for diagnosing the system, evaluating the translation approach, and allocating development resources. In this paper, we present a fine-grained machine translation evaluation framework that, in addition to the notions of intelligibility and fidelity, includes a typology of errors common in automatic translation, as well as several other properties of source and translated texts. The proposed framework is informative, sensitive, and relatively inexpensive to apply, to diagnose and quantify the types and likely sources of translation error. The proposed fine-grained framework has been used in two evaluation experiments on the LMT English-Spanish machine translation system, and has already suggested one important architectural improvement of the system.
Hantaan Virus Infection Induces Both Th1 and ThGranzyme B+ Cell Immune Responses That Associated with Viral Control and Clinical Outcome in Humans

Hantaviruses infection causing severe emerging diseases with high mortality rates in humans has become public health concern globally. The potential roles of CD4+T cells in viral control have been extensively studied. However, the contribution of CD4+T cells to the host response against Hantaan virus (HTNV) infection remains unclear. Here, based on the T-cell epitopes mapped on HTNV glycoprotein, we studied the effects and characteristics of CD4+T-cell responses in determining the outcome of hemorrhagic fever with renal syndrome. A total of 79 novel 15-mer T-cell epitopes on the HTNV glycoprotein were identified, among which 20 peptides were dominant target epitopes. Importantly, we showed the presence of both effective Th1 responses with polyfunctional cytokine secretion and ThGranzyme B+ cell responses with cytotoxic mediators production against HTNV infection. The HTNV glycoprotein-specific CD4+T-cell responses inversely correlated with the plasma HTNV RNA load in patients. Individuals with milder disease outcomes showed broader epitopes targeted and stronger CD4+T-cell responses against HTNV glycoproteins compared with more severe patients. The CD4+T cells characterized by broader antigenic repertoire, stronger polyfunctional responses, better expansion capacity and highly differentiated effector memory phenotype(CD27-CD28-CCR7-CD45RA-CD127hi) would elicit greater defense against HTNV infection and lead to much milder outcome of the disease. The host defense mediated by CD4+T cells may through the inducing antiviral condition of the host cells and cytotoxic effect of ThGranzyme B+ cells. Thus, these findings highlight the efforts of CD4+T-cell immunity to HTNV control and provide crucial information to better understand the immune defense against HTNV infection.
High speed LED based visible light communication networks for beyond 10Gb/s wireless access

Visible light communication (VLC) has been considered as a promising technique for broadband wireless access. In this paper, we propose and experimentally demonstrate a novel high-speed LED based VLC local area network to provide beyond 10Gb/s optical wireless access for massive users based on star topology architecture. Fiber link is used as the bidirectional transmission backbone of the VLC network and directly connected to the LED lamps. Frequency division multiplexing (FDM) is used for the downlink, while for the uplink, we respectively utilize FDM and time division multiplexing (TDM) as the uplink access schemes. A full-duplex VLC network for 4 users has been successfully demonstrated with the overall throughput of 4Gb/s. The measured bit error rates (BERs) of downlink and uplink for all the users are under 7% pre-forward error correction (FEC) limit of 3.8×10-3 over 25km standard single mode fiber (SSMF) and 65cm free space, clearly validating the promising potential of the proposed VLC network architecture for future 40Gb/s and 100Gb/s wireless access.
Methodology for hyperspectral image classification using novel neural network

A novel feed forward neural network is used to classify hyperspectral data from the AVIRIS sensor. The network applies an alternating direction singular value decomposition technique to achieve rapid training times. Very few samples are required for training. 100 percent accurate classification is obtained using test data sets. The methodology combines this rapid training neural network together with data reduction and maximal feature separation techniques such as principal component analysis and simultaneous diagonalization of covariance matrices, for rapid and accurate classification of large hyperspectral images. The results are compared to those of standard statistical classifiers.
Arbuscular mycorrhizal symbiosis increases relative apoplastic water flow in roots of the host plant under both well-watered and drought stress conditions.

BACKGROUND AND AIMS The movement of water through mycorrhizal fungal tissues and between the fungus and roots is little understood. It has been demonstrated that arbuscular mycorrhizal (AM) symbiosis regulates root hydraulic properties, including root hydraulic conductivity. However, it is not clear whether this effect is due to a regulation of root aquaporins (cell-to-cell pathway) or to enhanced apoplastic water flow. Here we measured the relative contributions of the apoplastic versus the cell-to-cell pathway for water movement in roots of AM and non-AM plants. METHODS We used a combination of two experiments using the apoplastic tracer dye light green SF yellowish and sodium azide as an inhibitor of aquaporin activity. Plant water and physiological status, root hydraulic conductivity and apoplastic water flow were measured. KEY RESULTS Roots of AM plants enhanced significantly relative apoplastic water flow as compared with non-AM plants and this increase was evident under both well-watered and drought stress conditions. The presence of the AM fungus in the roots of the host plants was able to modulate the switching between apoplastic and cell-to-cell water transport pathways. CONCLUSIONS The ability of AM plants to switch between water transport pathways could allow a higher flexibility in the response of these plants to water shortage according to the demand from the shoot.
Convergence Rate of Frank-Wolfe for Non-Convex Objectives

We give a simple proof that the Frank-Wolfe algorithm obtains a stationary point at a rate of $O(1/\sqrt{t})$ on non-convex objectives with a Lipschitz continuous gradient. Our analysis is affine invariant and is the first, to the best of our knowledge, giving a similar rate to what was already proven for projected gradient methods (though on slightly different measures of stationarity).
A Review of Literature on Knowledge Management using ICT in Higher Education

The paper aims to survey the role of Knowledge Management (KM) using Information and Communication Technology (ICT) in higher education by conducting literature review and classification of articles from 2000 to 2012 in order to explore how KM technologies and applications have been developed in this period. The emergence of Information and Communication Technologies (ICT) in the last decade has opened new avenues in Knowledge Management that could play important roles in meeting the prevailing challenges related to sharing, exchanging and disseminating knowledge and technologies in the higher education. This paper provides a high level overview of KM using Information and Communication Technology (ICT) in higher education. A critical analysis is done by studying attempts made by professionals to implement KM using ICT in higher education .
Experience with KRL-0: One Cycle of a Knowledge Representation Language

The goal of the KRL research group is to develop a knowledge representation language with which to bui ld sophisticated systems and theories of language understanding. This is a d i f f i cu l t goal to reach, one that wi l l require a number of years. We are using an iterative strategy with repeated cycles of design, implementation and testing. An in i t ia l design is described in an overview of KRI (Bobrow & Winograd, 1977). The system created in the f i rst cycle is called KRL-o, and this paper describes its implementation, an analysis of what was learned f rom our experiments in using KRL-o, and a brief summary of plans for the second iteration of the cycle (the KRi.-i system). In wr i t ing this paper, we have emphasized our d i f f icul t ies and disappointments more than our successes, because the major lessons learned f rom the iterative cycle were in the form of problems. We mention only br ief ly in the summary of experiments those features of Krelo that we found most satisfactory and useful.
Individual Neighbourhood Exploration in Complex Multi-layered Social Network

Social networks can be extracted from different data about communication or common activities in organizations, companies or various Internet-based services. Different types of data processed may result in creation of separate layers in the complex multilayered social network. Analysis of neighbourhoods of network members and their utilization to social group discovery appears to be an interesting and important research domain. Since there is no measure to evaluate structure of the neighbourhoods in the multilayered social network, a new measure called cross layered multi-layered clustering coefficient (CLMCC) is proposed in the paper. It enables to analyse the density of mutual connections of neighbours that occur in at least a given number of layers in a social network. Additionally, experimental studies on real world data are presented.
Web-Search Ranking with Initialized Gradient Boosted Regression Trees

In May 2010 Yahoo! Inc. hosted the Learning to Rank Challenge. This paper summarizes the approach by the highly placed team Washington University in St. Louis. We investigate Random Forests (RF) as a low-cost alternative algorithm to Gradient Boosted Regression Trees (GBRT) (the de facto standard of web-search ranking). We demonstrate that it yields surprisingly accurate ranking results -- comparable to or better than GBRT. We combine the two algorithms by first learning a ranking function with RF and using it as initialization for GBRT. We refer to this setting as iGBRT. Following a recent discussion by Li et al. (2007), we show that the results of iGBRT can be improved upon even further when the web-search ranking task is cast as classification instead of regression. We provide an upper bound of the Expected Reciprocal Rank (Chapelle et al., 2009) in terms of classification error and demonstrate that iGBRT outperforms GBRT and RF on the Microsoft Learning to Rank and Yahoo Ranking Competition data sets with surprising consistency.
HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods

The binding between the HIV-1 trans-activator of transcription (Tat) and p300/(CREB-binding protein)-associated factor (PCAF) bromodomain is a crucial step in the HIV-1 life cycle. However, the structure of the full length acetylated Tat bound to PCAF has not been yet determined experimentally. Acetylation of Tat residues can play a critical role in enhancing HIV-1 transcriptional activation. Here, we have combined a fully flexible protein-protein docking approach with molecular dynamics simulations to predict the structural determinants of the complex for the common HIV-1BRU variant. This model reproduces all the crucial contacts between the Tat peptide 46SYGR(AcK)KRRQRC56 and the PCAF bromodomain previously reported by NMR spectroscopy. Additionally, inclusion of the entire Tat protein results in additional contact points at the protein-protein interface. The model is consistent with the available experimental data reported and adds novel information to our previous structural predictions of the PCAF bromodomain in complex with the rare HIVZ2 variant, which was obtained with a less accurate computational method. This improved characterization of Tat.PCAF bromodomain binding may help in defining the structural determinants of other protein interactions involving lysine acetylation.
Distributed Software Development: Practices and challenges in different business strategies of offshoring and onshoring

Distributed Software Development involves a number of different business models, and companies intending to embark on the journey of distributed development have difficulty choosing the model(s) that suits their process and current software practice. More literature that presents similarities as well as differences among these models, in terms of processes, practices and challenges that characterize them, is thus becoming critical to software practitioners. This paper intends to bring more knowledge in this direction. We present empirical evidence from a case study of DSD practice in five companies that had projects following one or more of the different DSD business models described in the literature. We discuss the similarities and differences in the challenges faced by the projects in these models, as well as the relationship between the models, development process, and project size and complexity, as reported in the projects studied.
An approach for user authentication on non-keyboard devices using mouse click characteristics and statistical-based classification

Internet security has become a serious issue for anyone connected to the Internet. To avoid unauthorized people accessing an information system, keystroke dynami-cs-based authentication (KDA) systems combine password knowledge with typing characteristics to enhance the security of general password authentication systems. However, some portable computational devices have no computer keyboard, for example, personal digital assistants and mobile phones. That is, KDA systems cannot successfully work while the enrollment phase is implemented based on a standard desktop keyboard. This reduces the portability of the KDA system. This paper adopts rhythms clicked by a mouse as another identi(cid:12)able factor. Mouse clicks can be replaced by a stylus on non-keyboard device, numeral buttons on mobile phones, or (cid:12)ngers on touch screens to enhance system portability. In our proposed system, the click data are based on the time instances during pressing and releasing the mouse button. Five features based on these time periods are calculated using this data. We invited twenty-(cid:12)ve users to participate in our experiment. The experimental results showed that our authentication system can achieve a good accuracy. Our experiments also showed that the rhythm clicked by a mouse can function as the second identi(cid:12)able factor in general password authentication systems or as the standby identi(cid:12)able factor in KDA systems.
Programming by demonstration - constructing task level plans in hybrid dynamic framework

This paper presents a novel approach to constructing a task level plan for an assembly task from demonstration. A hybrid dynamic system is chosen as an attractive way to model assembly tasks. We propose a framework where the mappings required within the hybrid dynamic system model are extracted from a demonstration. We extract the event path planner mapping, which determines a task level plan. Demonstrated paths are broken down into their base elements, called transitions. A path plan is then constructed from transitions that were well demonstrated. We test the approach by having a robot execute an assembly task using constructed task plans. The framework produces excellent results because: 1) the robot can perform selected paths better than when it simply copies the demonstrator, and 2) it allows flexible path selection so the robot can be given a disposition in how it executes the task.
Energy equilibrium based on corona structure for wireless sensor networks

Although multi-hop routing can reduce communication consumption and extend network scale, energy hole is unavoidable to appear because of the relay nodes being overloaded due to take more tasks. In this paper, we formulate the energy equilibrium problem as an optimal corona division, where data fusion and data slice are both considered in data gathering process. For a circular multi-hop sensor network with uniform node distribution and constant data reporting, we demonstrate that the energy equilibrium of the whole network is unable to be realized no matter whether data fusion and data slice are adopted. However, the maximum energy equilibrium for a given circular area can be achieved only if the area increases in geometric progression from the outer corona to the neighbor inner corona except for the outermost one. Moreover, we use a zone-based allocation scheme to guarantee energy equilibrium of intra-corona. The approach for computing the optimal parameters is presented in terms of maximizing network lifetime. Based on the mathematical model, we propose an energy equilibrium routing based on corona structure (EERCS). Simulating results validate that EERCS can effectively achieve energy equilibrium and prolong the lifetime of network. Copyright © 2010 John Wiley & Sons, Ltd.
Autoradiographic and histological evidence of postnatal hippocampal neurogenesis in rats

In the autoradiograms of young rats injected with thymidine‐H3 many of the granule cells of the dentate gyrus were found labeled. The number of labeled cells declined rapidly with increased age at the time of injection. Histological studies showed the presence in young rats of a large germinal matrix of mitotic cells in the ependymal and subependymal layers of the third and lateral ventricles. The areal extent and cell population of this germinal pool declined rapidly from birth on, with a transient rise with a peak at about 15 days. During this latter period the number of “undifferentiated” cells near the granular layer of the dentate gyrus showed a rapid rise with a subsequent decline. The decline in the number of “undifferentiated” cells was accompanied by a rise in the number of differentiated granule cells. Cell counts in homologous parts of the dentate gyrus indicated a six‐fold increase in the number of differentiated granule cells from birth to three months. We postulated that undifferentiated cells migrate postnatally from the forebrain ventricles to the hippocampus where they become differentiated. The possible functional significance of delayed hippocampal neurogenesis is discussed with reference to our finding of incorporation of testosterone‐H3 by cells of the hippocampus, implicating that they may function as receptors of gonadal hormones.
An Incomplete Settling Technique for Pipelined Analog-to-Digital Converters

This paper presents an incomplete settling design technique for switched-capacitor pipelined analog-to-digital converters (ADCs) to improve conversion rate. An improved multiplying digital-to-analog converter (MDAC) is introduced to eliminate the memory effect between adjacent samples in the conventional MDAC with insufficient settling time. The repeatable interstage gain error and nonlinearity due to incomplete settling are then corrected by a digital background calibration scheme. Behavioral simulations of two 13-bit incomplete settling ADCs, one with the improved MDACs and the other with the conventional MDACs, are performed in MATLAB to verify the proposed technique. The simulation results show that, the first ADC has an almost undegraded dynamic performance until the settling time decreases to 30% of the complete settling time, and at the point of 30% complete settling time, the improvement of SNDR and SFDR over the second one is 36.2dB and 52.4dBc, respectively.