Miracle-dz/UniFAR-FTUs huggingface dataset:
GPU accelerating the FEniCS Project

In the recent years, the graphics processing unit (GPU) has emerged as a popular platform for performing general purpose calculations. The high computational power of the GPU has made it an attractive accelerator for achieving increased performance of computer programs. Although GPU programming has become more tangible over the years, it is still challenging to program GPUs efficiently to achieve good performance. The FEniCS Project is a collection of software components for the automated solution of partial differential equations. It allows users to specify input problems in a high-level, domain specific language. Novel techniques such as code generation and just-in-time compilation is used to automate the implementation of complicated code. This ensures computational efficiency of the software while retaining a high-level user interface that accepts a wide range of problems as input. To further increase the performance of the software, it is of interest to accelerate certain parts of it via GPUs. This thesis presents a GPU-accelerated implementation of the FEniCS Project. By integrating GPU-accelerated libraries for linear algebra, the solution of linear systems of equations is accelerated. With this implementation, the rate of floating point operations performed on the GPU is up to six times higher than that of the CPU. This leads to significant decreases in the time required to solve the linear systems. Throughout, emphasis was placed on keeping the resulting implementation clean and easy to maintain for the software developers. In the spirit of the FEniCS Project, the user interface remains easy to use, with simple parameters for activating GPU acceleration. The distribution and compilation of the software is kept simple by extending the FEniCS build system. Through this implementation, it is shown that integrating GPU-accelerated libraries in an existing software system is a viable approach to increase the system’s performance. It makes it possible to keep the overall structure and layout of the system intact while still utilizing the computational power of the GPU.
Anaphoric Relations in the Copenhagen Dependency Treebanks

The Copenhagen Dependency Treebanks (CDT) are a set of parallel treebanks for Danish, English, German, Italian, and Spanish. One of the main objectives of the CDT is to arrive at a unified description and annotation system for syntax, morphology, discourse, and anaphora. The treebanks are currently in the process of being annotated for these levels in all five languages. After a brief discussion of the subdivisions of the so-called bridging anaphors proposed by different scholars, we describe the classification and terminology adopted in the CDT. The main distinction here is the very common one between coreferential and associative anaphors, special attention being given to the latter group. Resumptive and evolving anaphors are treated as special subgroups of the coreferential anaphors. A list of the associative relations proposed by the CDT with authentic examples concludes the paper.
Aspects of change in the syntax of Māori - A corpus-based study

In the current climate of Māori language revitalisation, there is ample anecdotal evidence to suggest that not only the vocabulary, but also the syntax of modern Māori is markedly different from its traditional roots, and that it shows significant influence from English syntax. However, syntactic change in Māori has not hitherto been rigorously studied. This thesis aims to provide material evidence of change in Māori syntax, through a corpus-based study of grammatical change in te reo Māori over the period of contact with English. My methodology involved the compilation and comparison of two synchronic corpora representing the two ends of the contact period to provide a diachronic perspective on the language. Each corpus consists of approximately 102,000 running words of material written originally in Māori. The early corpus contains items published pre-1900. The modern material was written post-1990. The thesis is not only an exploration of the possibility of documenting syntactic change through the use of such corpora, but also tests whether it is possible to do this using corpora significantly smaller than the multi-million word corpora typical in corpus linguistics. The scope of this methodology is tested by examining three distinct types of grammatical features: a grammatical particle (the preposition mō), a pair of semantically related lexemes that appear to be undergoing a process of grammaticalisation (the verbs taea and āhei), and a widespread grammatical construction (certain types of relative clauses). In each instance, the two corpora are compared for features such as the frequency of occurrence, the associated constructions, and the contexts of use. In relation to the methodological questions, the thesis concludes that while these corpora are too small to provide adequate data on individual lexical items like taea and āhei, the methodology did make it possible to document change in the other, relatively high-frequency grammatical features. The thesis also raises the questions of whether the changes identified result from the direct adoption of English usages and constructions, whether they result from insufficient exposure to traditional Māori as a result of the dominance of English, or whether they are perhaps instead the result of internally-motivated Māori language evolution. This leads to a discussion of the likely implications of the changes documented here for the future of the language and the language community. I argue that acceptance of all such change as natural and unavoidable is likely to be detrimental to the future of te reo Māori.
Handbook of Molecular and Cellular Methods in Biology and Medicine

Isolation and Purification of DNA Isolation and Purification of RNA Extraction and Purification of Proteins Preparation of Nucleic Acid Probes Southern Blot Hybridization Northern Blot Hybridization Preparation of Monoclonal and Polyclonal Antibodies against Specific Protein(s) Western Blot Hybridization cDNA Libraries Genomic DNA Libraries DNA Sequencing Analysis DNA Mutagenesis DNA Footprinting and Gel Retardation Assay Differential Display Functional Genomics and DNA Microarray Technology Translation of mRNA(s) and Analysis of Proteins by Gel Electrophoresis Plant Tissue and Cell Culture Gene Transfer and Expression in Animals Gene Transfer and Expression in Plants Inhibition of Gene Expression Light, Scanning Electron, Environmental Scanning Electron, Transmission Electron, and Confocal Microscopy Localization of Gene Expression Bioseparation Techniques and Their Applications Combinatorial Techniques Computational Data Mining Methods Applied to Combinatorial Chemistry Libraries Subject Index
SUPERVISED ONTOLOGY TO DOCUMENT INTERLINKING

All rights reserved. However, in accordance with the Copyright Act of Canada, this work may be reproduced, without authorization, under the conditions for Fair Dealing. Therefore, limited reproduction of this work for the purposes of private study, research, criticism, review and news reporting is likely to be in accordance with the law, particularly if cited appropriately. ABSTRACT The value from the growing availability of online documents and ontologies will increase significantly once these two resources become deeply interlinked at the semantic level. We focus our investigation on the automated identification and the linking of concepts and relations mentioned in a document that are (or should be) in a domain-specific ontology. Such semantic information can allow for improved navigation of the information space: users can more quickly retrieve documents that mention the relations sought; Ontology engineers can enhance concepts with relations extracted from the literature; and more advanced natural language-based applications such as text summarization, textual entailment, and machine reading become ever more possible. In this thesis, we present the task of supervised semantic interlinking of documents to an ontology. We also propose a supervised algorithm that identifies and links concept mentions that are (or should be) in the ontology, and also identify mentions of binary relations that are (or should be) in the ontology. The resulting system, SDOI, is tested on a novel corpus and ontology from the data mining field on intrinsic measures such as accuracy, and extrinsic measures such time saved by the annotator in the annotation process. One day many high-value documents and ontologies will be interlinked to each other. This thesis presents a principled step towards that outcome.
The review of the modeling methods and numerical analysis software for nanotechnology in material science

Due to the high demand for building materials with universal set of properties which extend their application area the research efforts are focusing on nanotechnology in material science. The rational combination of theoretical studies, mathematical modeling and simulation can favour reduced resource and time consumption when nanomodified materials are being developed. The development of composite material is based on the principles of system analysis which provides for the necessity of criteria determination and further classification of modeling methods. In this work the criteria of spatial scale, dominant type of interaction and heterogeneity are used for such classification. The presented classification became a framework for analysis of methods and software which can be applied to the development of building materials. For each of selected spatial levels from atomistic one to macrostructural level of constructional coarsegrained composite – existing theories, modeling algorithms and tools have been considered. At the level of macrostructure which is formed under influence of gravity and exterior forces one can apply probabilistic and geometrical methods to study obtained structure. The existing models are suitable for packing density analysis and solution of percolation problems at the macroscopic level, but there are still no software tools which could be applied in nanotechnology to carry out systematic investigations. At the microstructure level it’s possible to use particle method along with probabilistic and statistical methods to explore structure formation but available software tools are partially suitable for numerical analysis
Survey of Large-scale Hierarchical Classification

Large-scale classification taxonomies have thousands of classes, deep hierarchies and skewed category distribution over documents. Hierarchical classification can speed up the classification process because problem is sub divided into smaller sub problems, and each of which can be efficiently and effectively managed. Most commonly used method for multiclass classification is one versus rest method. It is inflexible due to computational complexity. The top down method is usually accepted, but it has an error propagation problem. The metaclassification method solves error propagation problem. In this paper, several challenges for hierarchical document classification such as scalability, complexity, and misclassification are reviewed. The questions concerning about the learning and the classification processes are reviewed.
Morphodynamic modelling of a shoreface nourishment at Egmond-aan-Zee, The Netherlands

This study aims at investigating the morphodynamic effect of the shoreface nourishment using profile (2DV) and area (3D) DELFT3D – MOR modelling approaches. The research model is based on the engineering sand transport formulations of TRANSPOR2004 model, which include both wave-related and current-related components, with a numerical intra-wave approach. Tide and wave schematizations are defined to minimize the computation time of the simulation, and to enable the use of a morphological factor, which assists in dealing with the difference in time-scales between hydrodynamic and morphological developments. Calibrated models are applied to support the design of future shoreface nourishments. The efficiency of three different nourishment designs is evaluated. The application suggests that the more appropriate design consists of nourishing the seaward slope of the outer bar with a height of -5 m.
Game contingent claims

AbstractGame contingent claims (GCCs), as introduced by Kifer (2000), are a generalization of American contingent claims where the writer has the opportunity to terminate the contract, and must then pay the intrinsic option value plus a penalty. In complete markets, GCCs are priced using no-arbitrage arguments as the value of a zero-sum stochastic game of the type described in Dynkin (1969). In incomplete markets, the neutral pricing approach ofKallsen and Kuhn (2004) can be used.In Part I of this thesis, we introduce GCCs and their pricing, and also cover some basics of mathematical finance. In Part II, we present a new algorithm for valuing game contingent claims. This algorithm generalises the least-squares Monte-Carlo method for pricing American options of Longstaff and Schwartz (2001). Convergence proofs are obtained, and the algorithm is tested against certain GCCs. A more efficient algorithm is derived from the first one using the computational complexity analysis technique of Chen and Shen (2003). The algorithms were found to give good results with reasonable time requirements. Reference implementations of both algorithms are available for download from the author’s Github page https://github.com/del/ Game-option-valuation-library
Role of cartridge -based nucleic acid amplification test (CBNAAT) for early diagnosis of pulmonary tuberculosis in HIV

Background: Pulmonary Tuberculosis (PTB) is the commonest opportunistic infection and leading cause of death among people living with HIV (PLHIV). The role of cartridge based nucleic acid amplification test (CBNAAT) has potential to diagnose PTB and rifampicin resistance within two hours in PLHIV is promising. Methodology: 100 PLHIV patients with age of >18years having signs and symptoms greater than or equal to two weeks of duration and / or Chest X-ray findings suggestive of pulmonary tuberculosis who are attending to the department of Pulmonary Medicine, Guntur Medical College, Guntur from November 2016 to October 2017 are included in the study. Sputum samples sent for CBNAAT, AFB stain. Positive samples of CBNAAT and AFB stain are sent for conventional culture. Results: Out of 100 sputum samples, 45 were positive in CBNAAT, and 16 were AFB smear positive. All these 16 smear positive samples have 100% sensitivity in CBNAAT. These positive samples (45) were sent for culture. In culture out of 16 smear positive samples 15 are culture positive 1 is culture negative, which is false positive in CBNAAT also. In culture out of 45 CB-NAAT positive samples 29 culture positive, 16 culture negative. Sensitivity, specificity, PPV, NPV of smear in sputum samples are 46.88%, 98.5%, 93.75%, 79.76%, while that of CB-NAAT are 90.6%, 76.47%, 64. 44%, 94.55% respectively. Primary rifampicin resistance was detected in 1 case (2.22%) in CBNAAT and culture. Conclusions: CBNAAT is a rapid, reliable tool with least bio-safety concern and requires minimally trained staff, is best alternative to conventional methods of tubercular diagnosis and detects rifampicin resistance simultaneously within 2 hours. Keywords: CBNAAT; Sputum; TB.
Visual Analysis of Expert Systems for Smart Grid Monitoring

This application paper introduces the combination of an expert system with a visualization system, speciﬁcally designed for SmartGrid control rooms. It supports operators in the efﬁcient monitoring of electric grids with a focus on distributed, small-scale power generation. A rule-based expert system ﬁlters the stream of a large amount of incoming events, searching for potential problems. A multiple, coordinated view environment provides the required situational awareness for the user and presents the analysis results in a details-on-demand manner. Being a critical infrastructure, the electric grid is highly sensitive and any modiﬁcation must be well justiﬁed. Our visualization system therefore also provides insight into the expert system enabling the user to validate and verify the expert system’s analysis process. This provides the required decision support to assist the operator in keeping the grid in stable operating condition.
Neural networks for energy flows prediction in facility systems

A procedure for the short-term prediction of the thermal energy consumption of a hospital is shown in this paper. First, linear ARX models are built in order to obtain information on the influence of the input variables on the output of the system. Therefore, nonlinear models based on feedforward neural networks (NNARX) are built using the information provided by the linear estimate. The results obtained from the ARX and NNARX models are compared, concluding that NNARX models provide better results than ARX models, but the analysis of ARX models is necessary to obtain guidelines in the choice of the best regression vector as input for the neural models.
The Use of Axial Based Superficial Temporal Artery Frontal Branch Island Flap in Reconstruction of Full Thickness Extensive Lateral Canthus and Eyelid Defects

Amac: Lateral kantus da dahil olmak uzere tam kat ve genis goz kapagi defekti rekonstruksiyonu, karma-sik ve kompleks yapinin bir sonucu olarak zordur. Bu bolge defektlerini kapatmak, basarili fonksiyonel ve estetik sonuclar elde etmek icin iyi vaskularize cilt ve yumusak doku onemli bir rol oynamaktadir. Hasta ve yontem: Calismaya Manisa Celal Bayar Universitesi Tip Fakultesi Hastanesi'nde Mayis 2014-Aralik 2015 tarihleri arasinda aksiyel superfisyal temporal arter frontal dal ada flebi ile rekonstruksiyon yapilan tam kalinlikta goz kapagi ve lateral kantus defekti olan toplam 7 hasta dahil edildi. Bulgular: Bu teknikle 7 hasta ameliyat edildi. Dort tanesi kadindi. Ortalama yas 64.4 ve ortalama takip suresi 13 ay idi. Uc hastada bazal hucreli karsinom, 2 hastada skuamoz hucreli karsinom, bir hastada tri-koblastik karsinom tespit edildi. Bir hasta defekti ise travmaya sekonder idi. Bu teknikle toplam 4 alt ka-pak total tam kat defekti, 2 lateral kantus defekti ve bir total tam kat ust kapak defekti rekonstrukte edildi. Iki hastada flep donor alani, kismi kalinlikta deri grefti ile onarildi. Bir hasta ameliyattan 6 ay sonra lateral kantal fissurun genisletilmesi icin lateral kantoplastiye ihtiyac duydu. Bir hasta ise ameliyattan 6 ay sonra hafif ektropiyona sekonder lateral kantopeksiye gereksinim duydu. Sonuc: Yuzeysel temporal arterin terminal frontal dali bazli ada flebi, palpebral konjonktiva rekonstruksi-yonu icin mukoza grefti ve tars rekonstruksiyonu icin kikirdak grefti gerekmeksizin kabul edilebilir este-tik ve fonksiyonel onarim icin guvenilir ve degerli bir secenektir.
IFN-γ and TNF-α aggravate endothelial damage caused by CD123-targeted CAR T cell

Background: CD123-targeted chimeric antigen receptor (CAR) T cell (CART123) for the treatment of acute myeloid leukemia (AML) and blastic plasmacytoid dendritic cell neoplasm has exhibited potential in clinical trials. However, capillary leakage syndrome, which is associated with endothelial cells damage, is under intensive focus in CART123 therapy. Purpose: The present study aimed to explore the change in CD123 in endothelial cells and the injury to endothelial cells caused by CART123. Methods: The expression of CD123 and cytotoxicity were assessed by flow cytometry. Cytokine release was assessed by ELISA. An in vitro co-culture model was designed to mimic the status, wherein CART123 was stimulated and cytokines were released. Results: In the current study, CART123 exhibited cytotoxicity and the effects of cytokine production on endothelium, and the upregulation of CD123 enhanced the cytotoxicity. The addition of interferon (IFN)-γ and tumor necrosis factor (TNF)-α neutralizing antibodies can effectively reverse the upregulation of CD123 on the endothelial cells caused by CART123, while the cytotoxicity of CART123 in AML cell lines was not affected in vitro. Second, we proved that CD123 expresses in CART123 and would be upregulated after activation, putatively causing an overactivated and fratricide effect. Conclusion: In summary, this study identified that the expression of CD123 on endothelial cells could be upregulated when co-cultured with CART123. Furthermore, IFN-γ and TNF-α could aggravate endothelial damage caused by CART123 in vitro.
Executive Functions in Chronic Hepatitis C Virus−Infected Patients

Background. The neuropsychological implications of severe liver dysfunction have been widely discussed in recent neuropsychological literature. However, research has only just begun on the harmful effects of mild liver dysfunction on neurocognitive processes as well as the direct action of the hepatitis C virus (HCV) on the central nervous system. Objectives. The purpose of this study was to investigate the possible existence of alterations in the executive func− tions of HCV patients. Material and Methods. The executive functions were assessed by the administration of the two test batteries relat− ed to frontal lobe functioning: the Behavioral Assessment of the Dysexecutive Syndrome and the Wisconsin Card Sorting Test, to a group of HCV patients (n = 20) and a control group (n = 20). Results. The obtained results suggest the presence of impaired capability to inhibit previous associations and to use feedback in order to correct behavior in the HCV group. Structured planning, conceptualization, organized search, attention supervision, and control in non−routine tasks and maintenance of a non−automatic response are other impaired aspects in these patients. Conclusions. The results were not related to the degree of liver fibrosis, suggesting direct action of the hepatitis C virus on the brain (Adv Clin Exp Med 2008, 17, 1, 53–60).
Extending Design Rationale to Capture An Integrated Design Information Space

DRed is a graphical software tool for design rationale capture that, despite essentially still being a research prototype, has proved robust and useful enough gradually to achieve widespread use in an international aerospace company. The main areas of application up until now have been: (1) in the early stages of design; (2) in the root cause analysis and design of solutions to problems occurring while a product is in service. In order to lay out and navigate freely large interlinked rationales across multiple charts, DRed uses a simple bidirectional hyperlinking approach known as tunnel linking. In this paper we suggest that if it could be made easy for users to create bidirectional hyperlinks between DRed elements and selected locations in a range of external document types, then this might support the capture not just of the rationale, but of a unified, easily navigable information space covering the specification, rationale, calculations, design tasks and the emerging product definition. The objective of this research was to devise a practical way of implementing such a facility, then to explore how integrated design information spaces captured in this way might be structured, and to assess the feasibility of their capture as the design proceeds. To be successful, this will require extending the routine use of DRed from the conceptual into the embodiment design phase. Thus the case study in this paper focuses on the embodiment design of a simple mechanical transmission.