Miracle-dz/UniFAR-FTUs huggingface dataset:
Herpesviral regulation of the RAE-1 family of NKG2D ligands

Author(s): Greene, Trever T. | Advisor(s): Coscoy, Laurent | Abstract: Natural Killer (NK) cells are essential for control of viral infection and cancer. NK cells express NKG2D, an activating receptor that directly recognizes NKG2D ligands. These are expressed at low level on healthy cells, but are induced by stresses like infection and transformation. The physiological events that drive NKG2D ligand expression during infection are still poorly understood. Given the observation that the mouse cytomegalovirus (MCMV) encoded protein m18 is necessary and sufficient to drive expression of the RAE-1 family of NKG2D ligands I investigate m18, how it induces NKG2D ligand expression, and how the biology of NKG2D ligand regulation relates to the biology of herpesviruses. I demonstrate that RAE-1 is transcriptionally repressed by histone deacetylase inhibitor 3 (HDAC3) in healthy cells, and m18 relieves this repression by directly interacting with Casein Kinase II and preventing it from activating HDAC3. Accordingly, I found that HDAC inhibiting proteins from human herpesviruses induce human NKG2D ligand ULBP-1. Thus my findings indicate that virally mediated HDAC inhibition can act as a signal for the host to activate NK-cell recognition. Additionally, I characterize two unique proteins produced from the m18 ORF, and demonstrate tone of them is necessary and sufficient to induce the expression of RAE-1 ligands. Finally, I investigate a similarity between the reactivation control promoters of y-herpesviruses and NKG2D ligands, and investigate the potential of a drug that blocks NKG2D ligand induction to block y-herpesvirus reactivation.
Design and Security Impact on Consumers’ Intention To Use Single Platform E-Payment

This paper summarizes an explorative study of the novel design and security that contribute to consumers’ adoption of an integrated, single platform payment system encompassing card, Internet and mobile technologies in the ASEAN. The attempt to survey these areas in an integrated fashion is a novel approach that differs from existing studies that mainly focus on adoption factors of these technologies in isolation as well as focuses on the novel design and the security elements. The empirical results from the quantitative analysis suggest that design, security, perceived usefulness as well as perceived ease of use are significant factors that contribute to consumers’ intention to utilize a single platform payment System. Organizations will be able to utilize the study information for developing products and services that meet the consumers’ single platform E-payment system while also fulfil their objective of corporate social responsibility.
Detection of Genes Related to Resistance to Silver Nanoparticles in Bacteria from Secondary Endodontic Infections

Introduction. Silver nanoparticles are used in endodontics due to their antimicrobial activity, although it is considered that bacteria are unable to develop resistance to silver nanoparticles. Silver resistance genes have been related to resistance to nanoparticles and antibiotics. The presence of these resistance genes has not been studied in endodontic bacteria. The objective of this study is to report the prevalence of silver resistance genes in endodontic bacteria. Methods. The selected teeth were isolated using a rubber dam and any restoration, post, or caries was eliminated. The operative field was disinfected, and the root-filling material was removed. The samples were obtained using three sterile paper points to absorb the fluid of the root canal. The DNA from the samples and the control organism was extracted, and the detection of the silCBA resistance genes was carried out by PCR. Results. The results of this study show a high prevalence (73.3%) of silCBA silver resistance genes. The Spearman rank correlation coefficient was utilized to identify correlations between the presence of genes and clinical variables. Conclusions. This study reports a high frequency of silver resistance genes related to nanoparticle resistant from bacteria.
Satellite inference of water vapour and above-cloud aerosol combined effect on radiative budget and cloud-top processes in the southeastern Atlantic Ocean

Abstract. Aerosols have a direct effect on the Earth's radiative budget and can also affect cloud development and lifetime, and the aerosols above clouds (AAC) are particularly associated with high uncertainties in global climate models. Therefore, it is a prerequisite to improve the description and understanding of these situations. During the austral winter, large loadings of biomass burning aerosols originating from fires in the southern African subcontinent are lifted and transported westwards, across the southeastern Atlantic Ocean. The negligible wet scavenging of these absorbing aerosols leads to a near-persistent smoke layer above one of the largest stratocumulus cloud decks on the planet. Therefore, the southeastern Atlantic region is a very important area for studying the impact of above-cloud absorbing aerosols, their radiative forcing and their possible effects on clouds. In this study we aim to analyse and quantify the effect of smoke loadings on cloud properties using a synergy of different remote sensing techniques from A-Train retrievals (methods based on the passive instruments POLDER and MODIS and the operational method of the spaceborne lidar CALIOP), collocated with ERA-Interim re-analysis meteorological profiles. To analyse the possible mechanisms of AAC effects on cloud properties, we developed a high and low aerosol loading approach, which consists in evaluating the change in radiative quantities (i.e. cloud-top cooling, heating rate vertical profiles) and cloud properties with the smoke loading. During this analysis, we account for the variation in the meteorological conditions over our sample area by selecting the months associated with one meteorological regime (June–August). The results show that the region we focus on is primarily under the energetic influence of absorbing aerosols, leading to a significant positive shortwave direct effect at the top of the atmosphere. For larger loads of AACs, clouds are optically thicker, with an increase in liquid water path of 20 g m−2 and lower cloud-top altitudes by 100 m. These results do not contradict the semi-direct effect of above-cloud aerosols, explored in previous studies. Furthermore, we observe a strong covariance between the aerosol and the water vapour loadings, which has to be accounted for. A detailed analysis of the heating rate profiles shows that within the smoke layer, the absorbing aerosols are 90 % responsible for warming the ambient air by approximately 5.7 K d−1. The accompanying water vapour, however, has a longwave effect at distance on the cloud top, reducing its cooling by approximately 4.7 K d−1 (equivalent to 7 %). We infer that this decreased cloud-top cooling in particular, in addition with the higher humidity above the clouds, might modify the cloud-top entrainment rate and its effect, leading to thicker clouds. Therefore, smoke (the combination of aerosol and water vapour) events would have the potential to modify and probably reinforce the underlaying cloud cover.
Security--Reliability Tradeoff for Untrusted and Selfish Relay-Assisted D2D Communications in Heterogeneous Cellular Networks for IoT

This paper investigates security–reliability tradeoff for untrusted and selfish two-way relay-assisted device-to-device (D2D) communications in heterogeneous cellular networks for the Internet of Things (IoT). On one hand, the relay is untrusted and may try to extract useful information during the relaying process. On the other hand, the relay is selfish and is only willing to use the harvesting energy from the sources’ signals for relaying. Both instantaneous and statistical security–reliability tradeoffs are taken into consideration. For instantaneous model, the security and the reliability are characterized by the secrecy rate and the data rate, respectively. We aim at maximizing the tradeoff function of a tradeoff factor subject to a total transmit power constraint. For statistical model, the security and the reliability are characterized by the secrecy outage probability (SOP) and the data outage probability (DOP), respectively. An SOP optimization problem is developed with a DOP constraint and a total transmit power constraint. For both the problems, closed-form solutions are achieved. Simulation results show that both instantaneous and statistical security–reliability tradeoffs can achieve the Pareto optimal front.
End-to-End Automatic Speech Recognition with a Reconstruction Criterion Using Speech-to-Text and Text-to-Speech Encoder-Decoders

In this paper, we present a novel end-to-end automatic speech recognition (ASR) method that considers whether an input speech can be reconstructed from a generated text or not. A speech-to-text encoder-decoder model is one of the most powerful end-to-end ASR methods since it does not make any conditional independence assumptions. However, encoder-decoder models often suffer from a problem that is caused from a gap between the teacher forcing in a training phase and the free running in a testing phase. In fact, there is no guarantee that texts can be generated correctly when some generation errors occur in conditioning contexts. In order to mitigate this problem, our proposed method utilizes not only a generation probability of the text computed from a speech-to-text encoder-decoder but also a reconstruction probability of the speech computed from a text-to-speech encoder-decoder on the basis of a maximum mutual information criterion. We can expect that considering the reconstruction criterion can impose a constraint against generation errors. In addition, in order to compute the reconstruction probability, we introduce a mixture density network into the text-to-speech encoder-decoder. Our experiments on Japanese lecture ASR tasks demonstrate that considering the reconstruction criterion can yield ASR performance improvements.
Semantic Embeddings for OWL 2 Ontologies

While semantic technologies and the use of ontologies is one of the proposed solutions to the heterogeneity problem in database systems, the independent generation of ontologies leaves us with another heterogeneity problem. We need to match ontologies to allow active co-operation of different systems. This matching can often not be done by human effort alone because of the size and complexity of the ontologies. Thus automatic ontology matching systems are indispensable. We evaluate the usefulness of embeddings, more specifically ontology embeddings both for analytical tasks and for ontology alignment tasks. We further propose OWL2Vec as a framework to create such embeddings. The embeddings are created by projecting the ontology to an RDFgraph, conducting a series of walks on the graph and collect them in a walks document. Natural language embeddings systems such as word2vec are used to train the embeddings. To leverage ontology matching, we propose to create joint embeddings in the same vector space for two (or more ontologies). The user must then provide the system with anchors. The results are promising for analytical tasks such as clustering and partitioning of the ontology into related concepts. We demonstrate that by using the embeddings and the provided anchors, it is possible to find new mappings between two ontologies. We also demonstrate that the structural similarities provided by the embeddings can give ontology matching systems an additional similarity score that could help such systems to decide if a potential mapping is valid.
The serum level alterations of Acute-phase proteins, serum alpha-1-acid glycoprotein, haptoglobin and alpha-2-Macroglobulin in the Patients with Stage I of Multiple Myeloma

Background & Aims: Acute phase proteins are mainly synthesized by the liver and macrophages in inflammatory conditions as a result of various traumas and malignancies. Increased levels of these proteins have been reported in many tumors like multiple myeloma as an important indicator for the prognosis of malignancies. We investigated the serum levels of acute phase proteins in multiple myeloma cancer patients in stage one due to the important role of these proteins in malignancies. Materials & Methods: The serum levels of acute phase proteins (alpha 1-acid glycoprotein, haptoglobin and alpha-2-Macroglobulin) were measured in 30 patients with stage I of multiple myeloma and 30 healthy persons as the control group. The average age of population was 69 years. Measurement of the serum levels of proteins was done using Capillary zone electrophoresis and high resolution (HR). Total protein amounts were measured by biuret method, as well. The data were analyzed by SPSS method. Results: The values obtained from results of the test and statistical calculations in the groups of study suggested that the serum levels of examined acute phase proteins decreased significantly in the patients compared to the control group. (P<0.001) Conclusion: The results of this study indicated the reduction of serum alpha-1-acid glycoprotein, haptoglobin and alpha-2Macroglobulin in stage I patients compared to the control group, which is inconsistent with previous studies. These proteins may be considered as specific prognostic and diagnostic factors in multiple myeloma stage I. However, further studies are needed to assess accurate results.
Cartography: Visualization of Geospatial Data

Contents Preface Acknowledgements Chapter 1 Georgraphic information science and maps 1.1 The map as an interface 1.2 Geospatial data 1.3 Geographic information systems 1.4 Geospatial analysis operations 1.5 The spatial infrastructure and maps Chapter 2 Data acquisition 2.1 The need to know acquisition methods 2.2 Vector file characteristics 2.3 Raster file characteristics 2.4 Deriving data from existing maps 2.5 Working with digital data 2.6 Control and accuracy Chapter 3 Map characteristics 3.1 Maps are unique 3.2 Definitions of cartography 3.3 The cartographic communication process 3.4 Map functions and map types Chapter 4 GIS applications: which map to use? 4.1 Maps and the nature of GIS applications 4.2 Cadastre and utilitites: use of large-scale maps 4.3 Geospatial analysis in geography: use of small-scale maps 4.4 Geospatial, thematic and temporal comparisons Chapter 5 Map design and production 5.1 Introduction 5.2 Symbols to portray data related to points, lines, areas and volumes 5.3 Graphic variables 5.4 Conceptual and design aspects of text on the map 5.5 Requiremenets for the cartographic component of GIS packages Chapter 6 Topography 6.1 Georeferencing 6.2 Map projections 6.3 Geometric transformations 6.4 Generalization 6.5 Relief 6.6 Topographic data: mapping and charting organizations 6.7 Geographical names Chapter 7 Statistical mapping 7.1 Statistical surveys 7.2 Data analysis 7.3 Data classification 7.4 Catographical data analysis 7.5 Mapping methods Chapter 8 Mapping time 8.1 Introduction 8.2 Mapping change 8.3 Animation 8.4 Dynamic variables Chapter 9 Maps at work: presenting and using geospatial data in maps and atlases 9.1 Introduction 9.2 Paper atlases 9.3 Electronic atlases 9.4 Maps at work: map use functions 9.5 Working with (web-based) electronic atlases Chapter 10 Maps at work: analysis and geovisualisation 10.1 10.2 Geovisual analytics Chapter 11 Cartography at work: maps as decision tools 11.1 Again: why maps? 11.2 Management and documentation of spatial information 11.3 Outdated data: at work with the Digital Chart of the World 11.4 Acessibility: Cartography, GIS and geospatial information policy 11.5 Copyright and liability 11.6 Map use and usability 11.7 Maps and GIScience revisited References Index
Stimulating critical thinking about the self-sustaining network of relations which reinforce smartphone use: a Critical Design study

The design of the smartphone has not changed drastically over the past decade. This project aimed to uncover the structures which maintain the position the smartphone through Participatory Design workshops and stimulate debate about these structures through Critical Design. The PD workshops indicated that the smartphone has become central to most daily activities of the participants, changing how they interact both in the virtual world and the ''real'' world. The two CD artifacts build on and change its aspects, one by making virtual world ``real'' by projecting it around the user, the other by making the implicit behavioural rules explicit by connecting them to the school system. The final reflection combined the results with the theories of Embodied Interaction. It is argued that the user and the smartphone are part of a network of relations, which it is hard to break out off. First, this network is blackboxed, second, many functionalities are delegated to the smartphone, and finally, by stepping out of the network individually a (non)user becomes isolated. Thus, design changes should be supported on a larger scale, which could be stimulated through Critical Design. The project showed a promising method of challenging smartphone use through CD artifacts.
Network Based Intrusion Detection Using the UNSW-NB15 Dataset

In this work, we apply a two stage anomaly-based network intrusion detection process using the UNSW-NB15 dataset. We use Recursive Feature Elimination and Random Forests among other techniques to select the best dataset features for the purpose of machine learning; then we perform a binary classification in order to identify intrusive traffic from normal one, using a number of data mining techniques, including Logistic Regression, Gradient Boost Machine, and Support Vector Machine. Results of this first stage classification show that the use of Support Vector Machine reports the highest accuracy (82.11%). We then feed the output of Support Vector Machine to a range of multinomial classifiers in order to improve the accuracy of predicting the type of attacks. Specifically, we evaluate the performance of Decision Trees (C5.0), Naïve Bayes and multinomial Support Vector Machine. Applying C5.0 yielded the highest accuracy (74%) and F1 score (86%), and the two-stage hybrid classification improved the accuracy of results by up to 12% (achieving a multi-classification accuracy of 86.04%). Finally, with the support of our results, we present constructive criticism of the UNSW-NB15 dataset.
Examining Spontaneous Perspective Taking and Fluid Self-to-Data Relationships in Informal Open-Ended Data Exploration

Engaging learners with complex unfamiliar datasets is a known challenge in Data Science education. One promising phenomenon investigated in related work is perspective-taking. A first-person “actor” perspective can help facilitate group and individual sensemaking by mediating observations and actions taken by learners. Here we investigate how museum visitors made use of an actor perspective when exploring an open-ended, interactive data map museum exhibit. We use a mix of qualitative and quantitative empirical methods to explore how actor perspective-taking (APT) may mediate joint sensemaking around data visualizations. By applying interpretive coding to 54 conversations wherein APT naturalistically emerged, we identify 3 distinct self-to-data relationships constructed via APT: role-play, projection, and orientation. A further analysis explores how APT was embedded in joint sensemaking of the visualized data. Twelve APT-mediated sensemaking processes are identified; two (extrapolating and noticing absence) were used in conjunction with multiple APT self-to-data relationships, while the remaining ten (e.g., enacting, spatially characterizing, generalizing) were exclusively used with specific self-to-data APT relationships. We use these empirical findings to generate hypotheses about how APT and associated sensemaking processes may support Data Science learning goals.
Effect of Incorporating Orange Maize Flour into Beef Sausage and Its Associated Quality Attributes

The aim of this study was to incorporate different percentages (0%, 10%, 20%, 30%, and 50%) of orange maize flour (OMF) into beef sausage, and to study the bioactive qualities of the OMF. Also, the physicochemical, microbiological and sensory characteristics of the OMF beef sausages were explored. Results from the bioactive analyses of the OMF indicated it had total carotenoid content of 14.31 µg/g, while the tannin content was 1.52 mg/g. The moisture content of the beef sausages decreased when OMF levels in the sausages were increased. The fat contents of the OMF beef sausages were significantly lower (p<0.05) than that of the control, while the emulsion stability of the 30% OMF beef sausage was not statistically different to that of the control sausages. The iodine values of the OMF beef sausages tended to increase with an increased content of OMF. Salmonella spp. and Staphylococcus aureus were not detected in the sausages. Escherichia coli detected were within the range of 1.0 to 2.0 CFU/g. A consumer preference study showed the most acceptable sausage among the OMF beef sausages contained 20% OMF. This study showed that OMF has the potential to be used as a fat replacer, can maintain the sensory properties of beef sausages and prevent or limit microbial growth on beef sausages formulated with added OMF.
Transferable End-to-End Aspect-based Sentiment Analysis with Selective Adversarial Learning

Joint extraction of aspects and sentiments can be effectively formulated as a sequence labeling problem. However, such formulation hinders the effectiveness of supervised methods due to the lack of annotated sequence data in many domains. To address this issue, we firstly explore an unsupervised domain adaptation setting for this task. Prior work can only use common syntactic relations between aspect and opinion words to bridge the domain gaps, which highly relies on external linguistic resources. To resolve it, we propose a novel Selective Adversarial Learning (SAL) method to align the inferred correlation vectors that automatically capture their latent relations. The SAL method can dynamically learn an alignment weight for each word such that more important words can possess higher alignment weights to achieve fine-grained (word-level) adaptation. Empirically, extensive experiments demonstrate the effectiveness of the proposed SAL method.