Miracle-dz/UniFAR-FTUs huggingface dataset:
Using UML in a Risk-Driven Development Process

Risk-driven development focus on identifying and treating risks as an integrated part of the development process. One then obtain an adequate security level by treating security issues at the right time for the correct cost throughout the development. The EU IST-project CORAS has developed an integrate risk management and system development process for security-critical systems based on AS/NZS 4360, RUP, and RM–ODP. However, trials have shown that the efficiency and applicability of the integrated process depends on having an experienced risk analyst present during development. In this paper we present a refinement of the context identification phase of CORAS and provide detailed description on how to employ UML according to each of the RM– ODP viewpoints in each phase of the development. The refinements are described through a set of guidelines that where developed applying the CORAS integrated process on an example system. These guidelines reflects the experiences gained in a set of trials performed within the CORAS project.
Chapter 5 Nominalisation and rhetorical structure

A study of a small corpus of pharmaceutical leaflets supports the hypothesis that a subset of Mann and Thompson’s Rhetorical Relations may hold within as well as between clauses, with one or more propositional arguments nominalised. This paper summarises the main results of this study and outlines a formal account of the phenomenon within a framework of discourse generation, whereby nominalisation of propositions is licensed as a by-product of explicit realisation of the relations as verbs or propositions. 5.1 Rhetorical Structure Rhetorical Structure Theory (Mann & Thompson 1987) claims that a small set of rhetorical relations (RRs) hold between adjacent text units in a discourse, and that recognition of these relations may enable the hearer/reader to recover information or semantic content which is not explicitly conveyed by the components of the text. The list of relations in (M & T op cit) is not claimed to be exhaustive, but the relations can be classified into two types: on the one hand informational or semantic such as Cause and Condition, on the other hand intentional (presentational, pragmatic) such as Evidence and Justify. A typical pair of text units is said to consist of a Nucleus and Satellite, the former being more “central to the writer’s purposes”1 A full list of RRs from (Mann & Thompson 1987) is shown in Table 5.1. 5.1. 1 Background RST originally assumed that there is a single preferred relation holding between two adjacent units, even in cases of ambiguity. Moore and Pollack (1992) challenge this assumption, and argue in particular that it is not desirable for informational and intentional relations to be in competition. They propose that both types of relation may hold simultaneously, for example Evidence and Volitional-Cause in example (1): The nucleus+satellite pattern is in fact one of five “schemas” identified by M & T but these distinctions are not relevant to the issues discussed in this paper.
MUZZEUM — Augmented Reality and QR codes enabled mobile platform with digital library, used to Guerrilla open the National Museum of Serbia

Serbian National Museum has been closed for past 10 years for renovation. Furthermore, certain inadequate actions of the Government and national cultural institutions have been made. A group of activists decided to make a statement and perform a virtual exhibition in front of the National museum by using QR codes and Augmented Reality. This paper focuses on technical and social implications of consumption and implementation of QR codes and Augmented Reality in terms of museology, cultural heritage, objects and relationship they create with people who are their potential consumers. In the case study, we are tackling here, we investigate the transformation in definitions of space, artifacts, visitor and the power of representation in terms of museology. Since the artifacts which represent the Serbian national heritage of the highest rank are being held in museum depots far from the eyes of the public for such a long time, the project team has produced QR codes which will bring some of the masterpieces back to its audience. The objects from different museums will be represented by special ARQR codes outside of the museum building, reachable by smartphones. This socially engaged project sends direct message to the wider public that usage of IT, mobile technologies, Augmented Reality and QR codes can potentially transform the way we communicate cultural heritage.
The Appetitive Aggression Scale—development of an instrument for the assessment of human's attraction to violence.

Background : Several instruments, notably Buss and Perry's Aggression Questionnaire, have been developed for the assessment of aggressive behavior. However, in these instruments, the focus has been on reactive rather than instrumental forms of aggression, even though men in particular may find aggressive behavior attractive. A questionnaire or structured interview for the systematic assessment of the attraction to violence is not yet available. Objective : We, therefore, developed a freely available short form for the assessment of a person's attraction to violent and planned forms of aggression based on reports of former combatants on the attraction to violence and the characteristics of instrumental aggression described in the literature. Method : The Appetitive Aggression Scale (AAS) was administered to nine samples drawn from different populations, with a total of 1,632 former combatants and participants from war-affected regions (1,193 male and 439 female respondents). Results : From the initial set of 31 items, a selection of 15 items was extracted to improve the scale's psychometric properties and assess the construct of appetitive aggression validly with respect to content. Cronbach's Alpha coefficient of 0.85 was appropriate. All items loaded significantly on a single factor accounting for 32% of the total variance. Further analysis revealed that the scale measures a specific construct that can be distinguished from other concepts of human aggression. Conclusions : With the AAS, we present an easily administrable tool for the assessment of the attraction to violence.
Scrambling query plans to cope with unexpected delays

Accessing data from numerous widely distributed sources poses significant new challenges for query optimization and execution. Congestion and failures in the network can introduce highly variable response times for wide area data access. The paper is an initial exploration of solutions to this variability. We introduce a class of dynamic, run time query plan modification techniques that we call query plan scrambling. We present an algorithm that modifies execution plans on-the-fly in response to unexpected delays in obtaining initial requested tuples from remote sources. The algorithm both reschedules operators and introduces new operators into the query plan. We present simulation results that demonstrate how the technique effectively hides delays by performing other useful work while waiting for missing data to arrive.
Light-weight, Conservative, yet Effective: Scalable Real-time Tweet Summarization

Microblogging platforms and Twitter speciﬁcally have become a major resource for exploring diverse topics of interest that vary from the world’s breaking news to other topics such as sports, science, religion and even personal daily updates. Nevertheless, one by herself cannot easily follow her topics of interest while tackling the challenges that stem from the Twitter timeline nature. Among those challenges is the huge amount of posted tweets that are either not interesting, noisy, or redundant. Additionally, one cannot survive with manual techniques to summarize tweets related to topics that are discussed on the stream and are developed rapidly. In this paper, we tackle the problem of summarizing a stream of tweets given a pre-deﬁned set of topics in the context of Qatar University’s participation in TREC-2016 Real-Time Summarization (RTS) track. We participated in both push notiﬁcation and e-mail digest scenarios. Given a set of users’ interest proﬁles, our RTS system for push notiﬁcations scenario adopts a light-weight and conservative ﬁltering strategy that monitors the continuous stream of tweets over a pipeline of multiple stages, while maintaining a scalable processing of a large number of interest pro-ﬁles. For the e-mail digest scenario, we adopted a similar but even simpler approach. At the end of each day, a list of potentially relevant tweets is retrieved using a query of topic title terms that is issued against an index of all streamed tweets of that day. Our push-notiﬁcation runs exhibited the best performance among all submitted automatic runs in the push notiﬁcation task this year. Moreover, our best-performing email-digest run was the second-best among all submitted automatic runs in the email-digest task
A Simplified Method for Quantifying Cell Migration/Wound Healing in 96-Well Plates

Cell migration plays a key role in both normal physiological and pathological conditions. The study of cell migration and its underlying mechanisms is of great significance in various fields of research, including basic biology and pharmaceutical development. The cell migration or scratch wounding assay is an easy and economical in vitro method that allows researchers to assess a large number of testing compounds. Even though this simple assay has been used for decades, researchers are still trying to modify such experimental protocols and wounding devices. In this study, an 8-channel mechanical “wounder” was designed for performing a cell migration assay, particularly in a 96-well culture plate format. With special designs of a guiding bar and adjustable pins for use with disposable pipette tips, this wounder confined the scratch area within the center of each well to ensure a perfect contact between the pins and the well surface. As a result, this mechanical wounder produces a uniform denudation of a cell monolayer in a 96-well plate with a wound size of around 600 µm. Using this improved wounding device, the effects of epidermal growth factor and DL-α-difluoromethylornithine on the reepithelialization of rat intestinal epithelial cells (IEC-6) and serum on the wound recovery of human umbilical vein endothelial cells were demonstrated. This wounder facilitates cell migration study and can be applicable for multiple sample analysis.
Diversity-based Information Exchange among Multiple Swarms in Particle Swarm Optimization

This paper proposes a method to exchange information among multiple swarms in particle swarm optimization. The provided algorithm is developed to solve problems that have landscapes with a high number of local optima. Each swarm provides two sets of particles; one set is the particles to be sent to another swarm, while the other set is the particles to be replaced by individuals from other swarms. Proposed algorithm also provides a new paradigm to search for neighboring swarms in order to share common interests in the swarm's neighborhood. The particle's movement is according to one variation of PSO with three basic terms, each one to lead the particles toward the best particle in the swarm, in the neighborhood, and in the whole population. Demonstrated through a suite of benchmark test functions, the proposed algorithm is shown competitive performance with improved convergence speed.
DGCR14 Induces Il17a Gene Expression through the RORγ/BAZ1B/RSKS2 Complex

ABSTRACT The Dgcr14/Es2 gene is located in a chromosomal region the loss of which has been associated with DiGeorge syndrome, a cause of immunodeficiency, heart defects, and skeletal abnormalities. However, the role of DGCR14 protein remains to be elucidated. Here, I found that DGCR14 protein acts as a coactivator of RORγt in TH17 cells. Biochemical purification of the RORγ coregulator complex allowed me to identify the associated DGCR14 protein by matrix-assisted laser desorption ionization–time of flight mass spectrometry. Overexpression of Dgcr14 mRNA enhanced RORγt-mediated transcriptional activity and facilitated TH17 cell differentiation. Furthermore, knockdown of Dgcr14 reduced Il17a mRNA expression. I also found that DGCR14 associated with ribosomal S6 kinase 2 (RSK2, also called RpS6ka3) and BAZ1B, both of which were recruited to the Il17a promoter during TH17 cell differentiation. Knockdown of Baz1b or RpS6ka3 also reduced Il17a mRNA expression, and Baz1b knockdown increased transcriptional suppressive histone marks (histone H3K9me3) on the Il17a promoter. My findings showed the roles of DGCR14, RSK2, and BAZ1B in the transcriptional regulation of Il17a mRNA during TH17 cell differentiation.
Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution

Significance Orotidine 5′-monophosphate decarboxylase has attracted intense enzymological interest, because it achieves a very large rate enhancement (∼1017) without the use of cofactors. Previous studies provided evidence that substrate destabilization and vinyl anion intermediate stabilization contribute to the rate enhancement. Using in vitro translation, we generated a backbone amide to ester substitution to evaluate the importance of the hydrogen bond between a backbone amide and the substrate in intermediate stabilization. The hydrogen bond contributes modestly (≤102), suggesting that the intermediate is primarily stabilized by electrostatic interactions with the active site. This study establishes a versatile method for generation of backbone amide to ester substitutions in sufficient quantities to investigate the importance of backbone amide hydrogen bonding interactions in enzyme-catalyzed reactions. Hydrogen bonds between backbone amide groups of enzymes and their substrates are often observed, but their importance in substrate binding and/or catalysis is not easy to investigate experimentally. We describe the generation and kinetic characterization of a backbone amide to ester substitution in the orotidine 5′-monophosphate (OMP) decarboxylase from Methanobacter thermoautotrophicum (MtOMPDC) to determine the importance of a backbone amide–substrate hydrogen bond. The MtOMPDC-catalyzed reaction is characterized by a rate enhancement (∼1017) that is among the largest for enzyme-catalyzed reactions. The reaction proceeds through a vinyl anion intermediate that may be stabilized by hydrogen bonding interaction between the backbone amide of a conserved active site serine residue (Ser-127) and oxygen (O4) of the pyrimidine moiety and/or electrostatic interactions with the conserved general acidic lysine (Lys-72). In vitro translation in conjunction with amber suppression using an orthogonal amber tRNA charged with l-glycerate (HOS) was used to generate the ester backbone substitution (S127HOS). With 5-fluoro OMP (FOMP) as substrate, the amide to ester substitution increased the value of Km by ∼1.5-fold and decreased the value of kcat by ∼50-fold. We conclude that (i) the hydrogen bond between the backbone amide of Ser-127 and O4 of the pyrimidine moiety contributes a modest factor (∼102) to the 1017 rate enhancement and (ii) the stabilization of the anionic intermediate is accomplished by electrostatic interactions, including its proximity of Lys-72. These conclusions are in good agreement with predictions obtained from hybrid quantum mechanical/molecular mechanical calculations.
Structured smoking cessation training for health professionals on cardiology wards: a prospective study

Background Smoking is a major cardiovascular risk factor, and smoking cessation is imperative for patients hospitalized with a cardiovascular event. This study aimed to evaluate a systems-based approach to helping hospitalized smokers quit and to identify implementation barriers. Design Prospective intervention study followed by qualitative analysis of staff interviews. Methods The prospective intervention study assessed the effects of implementing standard operating procedures (SOPs) for the provision of counselling and pharmacotherapy to smokers admitted to cardiology wards on counselling frequency. In addition, a qualitative analysis of staff interviews was undertaken to examine determinants of physician and nurse behaviour; this sought to understand barriers in terms of motivation, capability, and/or opportunity. Results A total of 150 smoking patients were included in the study (75 before and 75 after SOP implementation). Before the implementation of SOPs, the proportion of patients reporting to have received cessation counselling from physicians and nurses was 6.7% and 1.3%, respectively. Following SOP implementation, these proportions increased to 38.7% (p < 0.001) and 2.7% (p = 0.56), respectively. Qualitative analysis revealed that lack of motivation, e.g. role incongruence, appeared to be a major barrier. Conclusions Introduction of a set of standard operating procedures for smoking cessation advice was effective with physicians but not nurses. Analysis of barriers to implementation highlighted lack of motivation rather than capability or opportunity as a major factor that would need to be addressed.
How to Sign Digital Streams

We present a new efficient paradigm for signing digital streams. The problem of signing digital streams to prove their authenticity is substantially different from the problem of signing regular messages. Traditional signature schemes are message oriented and require the receiver to process the entire message before being able to authenticate its signature. However, a stream is a potentially very long (or infinite) sequence of bits that the sender sends to the receiver and the receiver is required to consumes the received bits at more or less the input rate and without excessive delay. Therefore it is infeasible for the receiver to obtain the entire stream before authenticating and consuming it. Examples of streams include digitized video and audio files, data feeds and applets. We present two solutions to the problem of authenticating digital streams. The first one is for the case of a finite stream which is entirely known to the sender (say a movie). We use this constraint to devise an extremely efficient solution. The second case is for a (potentially infinite) stream which is not known in advance to the sender (for example a live broadcast). We present proofs of security of our constructions. Our techniques also have applications in other areas, for example, efficient authentication of long files when communication is at a cost and signature based filtering at a proxy server.
Analytical and Numerical Elements of a Supersolid Model

In this article, the main properties of a model of supersolid in the frame of a Gross–Pitaevskii equation is reviewed. It was developed mainly by the author with Pomeau, Josserand and Sepulveda. Emphasis is placed on the numerical details and tools that are absent in our previous publications and maybe useful for authors who are eventually interested in the model. The model exhibits superfluid properties like nonclassical moment of inertia at T = 0K, quantized vortices and persistent currents without the presence of defects, moreover, only a transient flow is allowed by defects, akin to plastic flow in ordinary solids.
Exploring oral nanoemulsions for bioavailability enhancement of poorly water-soluble drugs

Introduction : More than 40% of new chemical entities discovered are poorly water soluble and suffer from low oral bioavailability. In recent years, nanoemulsions are receiving increasing attention as a tool of delivering these low-bioavailable moieties in an efficient manner. Areas covered : This review gives a brief description about how oral nanoemulsions act as a tool to improve the bioavailability of poorly water-soluble drugs. The recurrent confusion found in the literature regarding the theory behind the formation of nanoemulsions is clarified, along with the difference between nanoemulsion and lyotropic ‘microemulsion' phase. This paper gives a clear-cut idea about all possible methods for the preparation of nanoemulsions and the advantages and disadvantages of each method are described. A description of the stability problems of nanoemulsions and their prevention methods is also provided, in addition to a comprehensive update on the patents and research works done in the arena of oral nanoemulsions. Expert opinion : Low-energy emulsification techniques can also produce stable nanoemulsions. It is guaranteed that oral nanoemulsions can act as a potential tool for the delivery of poorly water-soluble therapeutic moieties in a very efficient manner.
Cell resolved, multiparticle model of plastic tissue deformations and morphogenesis

We propose a three-dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue plasticity is modeled by a stochastic process consisting of a connectivity change (addition or removal of a single link) followed by a complete relaxation to mechanical equilibrium. In particular, we assume that (i) two non-connected, but adjacent particles can form a new link; and (ii) the lifetime of links is reduced by tensile forces. We demonstrate that the proposed model yields a realistic macroscopic elasto-plastic behavior and we establish how microscopic model parameters determine material properties at the macroscopic scale. Based on these results, microscopic parameter values can be inferred from tissue thickness, macroscopic elastic modulus and the magnitude and dynamics of intercellular adhesion forces. In addition to their mechanical role, model particles can also act as simulation agents and actively modulate their connectivity according to specific rules. As an example, anisotropic link insertion and removal probabilities can give rise to local cell intercalation and large scale convergent extension movements. The proposed stochastic simulation of cell activities yields fluctuating tissue movements which exhibit the same autocorrelation properties as empirical data from avian embryos.
Suicide by Burning: Epidemiological and Clinical Profiles

Self-immolation constitutes a rare form of suicide in developed countries, though it accounts for unique injury characteristics in the burn intensive care unit. The aim of this study was to present the epidemiological and clinical features of patients burned during a suicidal attempt seen in a North Rhine-Westphalia burn intensive care unit (BICU). To address this aim, we undertook a 21-year retrospective study involving patients with thermal injuries admitted to the largest burn unit in Germany. A total of 125 suicide-related burn victims were identified in the study period (9.4%). Comparing the self-immolation group with the rest burn patient cohort, suicide victims were more likely to be single and to act under the influence of alcohol. The suicidal group had a larger extent of burns, higher incidence of inhalation injury, required more surgical procedures, catecholamines, blood transfusions, and a longer BICU stay. Their clinical course was complicated by prolonged intubation period, higher rate of multiple drug-resistant bacteria acquisition and sepsis, leading to a higher mortality rate. Although the proportion of self-immolation victims among all burned patients is not high, the markedly higher severity of their burns and their poorer quality of outcomes makes them an important clinical subgroup for further study.