Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Literature Review on the Quality of UML Models

The quality of conceptual models directly affects the quality of the understanding of the application domain and the quality of the final software products that are ultimately based upon them. The field of research into conceptual modelling research is still young and is still evolving. This paper describes a systematic literature review (SLR) of peer-reviewed conference and journal articles published between 1997 and 2007 on this topic so that we may understand the state-of-the-art and then identify any gaps in current research. Six digital libraries were searched, and 193 papers dealing with the quality of UML models were identified and classified into five dimensions: type of model quality, type of evidence, type of research result, type of diagram and research goal. The results indicate that the field is indeed still young and evolving with a great deal of research dedicated to semantic consistency and to improving the understandability of UML diagrams. However, much more empirical research is needed to develop a theoretical understanding of conceptual model quality. The classification scheme developed in this paper can serve as a guide for both researchers and practitioners.
RSP-QL Semantics: A Unifying Query Model to Explain Heterogeneity of RDF Stream Processing Systems

RDF and SPARQL are established standards for data interchange and querying on the Web. While they have been shown to be useful and applicable in many scenarios, they are not sufficiently adequate for dealing with streams of data and their intrinsic continuous nature. In the last years data and query languages have been proposed to extend both RDF and SPARQL for streams and continuous processing, under the name of RDF Stream Processing-RSP. These efforts resulted in several models and implementations that, at a first look, appear to propose alternative syntaxes but equivalent semantics. However, when asked to continuously answer the same queries on the same data streams, they provide different answers at disparate moments due to the heterogeneity of their operational semantics. These discrepancies render the process of understanding and comparing continuous query results complex and misleading. In this work, the authors propose RSP-QL, a comprehensive model that formally defines the semantics of an RSP system. RSP-QL makes explicit the hidden assumptions of currently available RSP systems, allows defining a formal notion of correctness for RSP query results and, thus, explains why available implementations provide different answers at disparate moments.
Anonymous Multi-Receiver Identity-Based Authenticated Encryption with CCA Security

In a multi-receiver encryption system, a sender chooses a set of authorized receivers and sends them a message securely and efficiently, as the message is well encrypted and only one ciphertext corresponding to the message is generated no matter how many receivers the sender has chosen. It can be applied to video conferencing systems, pay-per-view channels, remote education, and so forth. Due to privacy considerations, an authorized receiver may not expect that his identity is revealed. In 2010, anonymous multi-receiver identity-based (ID-based) encryption was first discussed, and furthermore, many works on the topic have been presented so far. Unfortunately, we find that all of those schemes fail to prove the chosen ciphertext attacks (CCA) security in either confidentiality or anonymity. In this manuscript, we propose the first anonymous multi-receiver ID-based authenticated encryption scheme with CCA security in both confidentiality and anonymity. In the proposed scheme, the identity of the sender of a ciphertext can be authenticated by the receivers after a successful decryption. In addition, the proposed scheme also is the first CCA-secure one against insider attacks. Moreover, only one pairing computation is required in decryption.
Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks

Deletions encompassing the BP1-2 region at 15q11.2 increase schizophrenia and epilepsy risk, but only some carriers have either disorder. To investigate the role of CYFIP1, a gene within the region, we performed knockdown experiments in human neural progenitors derived from donors with 2 copies of each gene at the BP1-2 locus. RNA-seq and cellular assays determined that knockdown of CYFIP1 compromised cytoskeletal remodeling. FMRP targets and postsynaptic density genes, each implicated in schizophrenia, were significantly overrepresented among differentially expressed genes (DEGs). Schizophrenia and/or epilepsy genes, but not those associated with randomly selected disorders, were likewise significantly overrepresented. Mirroring the variable expressivity seen in deletion carriers, marked between-line differences were observed for dysregulation of disease genes. Finally, a subset of DEGs showed a striking similarity to known epilepsy genes and represents novel disease candidates. Results support a role for CYFIP1 in disease and demonstrate that disease-related biological signatures are apparent prior to neuronal differentiation.
Spherical Harmonic Analysis of the PSCz Galaxy Catalogue: Redshift distortions and the real-space power spectrum

We apply the formalism of spherical harmonic decomposition to the galaxy density field of the IRAS PSCz redshift survey. The PSCz redshift survey has almost all-sky coverage and includes IRAS galaxies to a flux limit of 0.6 Jy. Using maximum likelihood methods to examine (to first order) the distortion of the galaxy pattern resulting from redshift coordinates, we have measured the parameter β≡Ω{0.6}/b. We also simultaneously measure either (a) the undistorted amplitude of perturbations in the galaxy distribution when a parametrized power spectrum is assumed, or (b) the shape and amplitude of the real-space power spectrum if the band-power in a set of passbands is measured in a step-wise fashion. These methods are extensively tested on a series of CDM, Λ CDM and MDM simulations and are found to be unbiased. We obtain consistent results for the subset of the PSCz catalogue with flux above 0.75 Jy, but inclusion of galaxies to the formal flux limit of the catalogue gives variations which are larger than our internal errors. For the 0.75-Jy catalogue we find, in the case of a parametrized power spectrum, β=0.58±0.26 and the amplitude of the real-space power measured at wavenumber k=0.1h Mpc−1 is Δ0. 1=0.42±0.03. Freeing the shape of the power spectrum we find that β=0.47±0.16 (conditional error) and Δ0. 1=0.47±0.03. The shape of the real-space power spectrum is consistent with a Γ=0.2 CDM-like model, but does not strongly rule out a number of other models. Finally by combining our estimate of the amplitude of galaxy clustering and the distortion parameter we find the amplitude of mass fluctuations on a scale k=0.1h Mpc−1 is Δρ=0.24Ω0−0.6, with an uncertainty of 50 per cent.
Pediatric Emotional Dysregulation and Behavioral Disruptiveness Treated With Hypnosis: A Time-Series Design

Abstract A case of pediatric oppositional defiant disorder (ODD) with concomitant emotional dysregulation and secondary behavioral disruptiveness was treated with hypnosis by means of the hypnotic hold, a method adapted by the authors. An A-B-A-B time-series design with multiple replications was employed to measure the relationship of the hypnotic treatment to the dependent measure: episodes of emotional dysregulation with accompanying behavioral disruptiveness. The findings indicated a statistically significant relationship between the degree of change from phase to phase and the treatment. Follow-up at 6 months indicated a significant reduction of the frequency of targeted episodes of emotional dysregulation and behavioral disruptiveness at home.
Clustering the topics using TF-IDF for model fusion

Users tend to express their queries in various ways: sometimes they use more general terms, sometimes more specific terms. Information retrieval systems need to be able to accommodate this variety of user needs. Some retrieval models perform better when the queries are general, others perform better when the queries are more specific, and others when a combination is available. In this paper we are looking for a system that will perform well in all these cases, we present a new method for combining the results of different models in order to improve the performance on a difficult task: Information Retrieval from spontaneous speech. Our technique is based on clustering the training topics according to their tf-idf (term frequency-inverse document frequency) properties, and selecting the best models for each cluster. When the system runs on a test topic, the cluster of the topic needs to be determined and the combination of models of this cluster is used. We report improvements on the Malach collection used at CLEF-CLSR 2007.
Empirical validation of the involvement component of the pervasive GameFlow model

This paper presents an empirical investigation into the question of involvement in pervasive games. The study is motivated by the Pervasive GameFlow model and its involvement component. The main research question is whether aspects of involvement in desktop computer games are also valid for the immersion and enjoyment of players of pervasive games. In order to address this question, two empirical studies were performed: the first explored the possible correlations between several aspects of involvement and the enjoyment and immersion of players. The second compared two versions of an outdoor game, one with and the other without digital augmentations, in order to explore which version provided a higher degree of involvement and enjoyment. The results of these studies suggest that becoming less aware of everyday life is not a relevant aspect of the immersion and enjoyment of players of pervasive games and that there is no significant difference in these elements of the gaming experience (immersion and enjoyment) when comparing the digitally and non-digitally augmented versions of the outdoor game. These results suggest that the involvement experienced by players of pervasive games is not characterised by a sense of being transported into the virtual world of the game; instead, in these types of games the virtual world of the digital application is the one which is drawn out into the physical world. The paper proposes that an embodied view of game-play can explain these results in a coherent manner.
Intellectual Property Rights and Food Security

The book under review seeks to provide a fundamental understanding of one of the most hotly-debated topics at International level – “Intellectual Property Rights (IPRs) and Food Security” in all its aspects. The book offers a well-researched defence and examines the tasks including the international bond linking IPRs, agricultural biotechnology, and access to biological resources, food security and globalization, paying meticulous attention to suggestions for the protection of Farmers’ Rights, traditional knowledge, GM crops and the impact of competition laws. It advises a number of proposals for action in installing IPRs in order to reach greater food security internationally.
An Observational Perspective of Low-Mass Dense Cores I: Internal Physical and Chemical Properties

Low-mass dense cores represent the state of molecular gas associated with the earliest phases of low-mass star formation. Such cores are called "protostellar" or "starless," depending on whether they do or do not contain compact sources of luminosity. In this chapter, the first half of the review of low-mass dense cores, we describe the numerous inferences made about the nature of starless cores as a result of recent observations, since these reveal the initial conditions of star formation. We focus on the identification of isolated starless cores and their internal physical and chemical properties, including morphologies, densities, temperatures, kinematics, and molecular abundances. These objects display a wide range of properties since they are each at different points on evolutionary paths from ambient molecular cloud material to cold, contracting, and centrally concentrated configurations with significant molecular depletions and, in rare cases, enhancements.
Transmembrane Movement of Exogenous Long-Chain Fatty Acids: Proteins, Enzymes, and Vectorial Esterification

SUMMARY The processes that govern the regulated transport of long-chain fatty acids across the plasma membrane are quite distinct compared to counterparts involved in the transport of hydrophilic solutes such as sugars and amino acids. These differences stem from the unique physical and chemical properties of long-chain fatty acids. To date, several distinct classes of proteins have been shown to participate in the transport of exogenous long-chain fatty acids across the membrane. More recent work is consistent with the hypothesis that in addition to the role played by proteins in this process, there is a diffusional component which must also be considered. Central to the development of this hypothesis are the appropriate experimental systems, which can be manipulated using the tools of molecular genetics. Escherichia coli and Saccharomyces cerevisiae are ideally suited as model systems to study this process in that both (i) exhibit saturable long-chain fatty acid transport at low ligand concentrations, (ii) have specific membrane-bound and membrane-associated proteins that are components of the transport apparatus, and (iii) can be easily manipulated using the tools of molecular genetics. In both systems, central players in the process of fatty acid transport are fatty acid transport proteins (FadL or Fat1p) and fatty acyl coenzyme A (CoA) synthetase (FACS; fatty acid CoA ligase [AMP forming] [EC 6.2.1.3]). FACS appears to function in concert with FadL (bacteria) or Fat1p (yeast) in the conversion of the free fatty acid to CoA thioesters concomitant with transport, thereby rendering this process unidirectional. This process of trapping transported fatty acids represents one fundamental mechanism operational in the transport of exogenous fatty acids.
Contrasting genomic properties of free-living and particle-attached microbial assemblages within a coastal ecosystem

The Columbia River (CR) is a powerful economic and environmental driver in the US Pacific Northwest. Microbial communities in the water column were analyzed from four diverse habitats: (1) an estuarine turbidity maximum (ETM), (2) a chlorophyll maximum of the river plume, (3) an upwelling-associated hypoxic zone, and (4) the deep ocean bottom. Three size fractions, 0.1–0.8, 0.8–3, and 3–200 μm were collected for each habitat in August 2007, and used for DNA isolation and 454 sequencing, resulting in 12 metagenomes of >5 million reads (>1.6 Gbp). To characterize the dominant microorganisms and metabolisms contributing to coastal biogeochemistry, we used predicted peptide and rRNA data. The 3- and 0.8-μm metagenomes, representing particulate fractions, were taxonomically diverse across habitats. The 3-μm size fractions contained a high abundance of eukaryota with diatoms dominating the hypoxic water and plume, while cryptophytes were more abundant in the ETM. The 0.1-μm metagenomes represented mainly free-living bacteria and archaea. The most abundant archaeal hits were observed in the deep ocean and hypoxic water (19% of prokaryotic peptides in the 0.1-μm metagenomes), and were homologous to Nitrosopumilus maritimus (ammonia-oxidizing Thaumarchaeota). Bacteria dominated metagenomes of all samples. In the euphotic zone (estuary, plume and hypoxic ocean), the most abundant bacterial taxa (≥40% of prokaryotic peptides) represented aerobic photoheterotrophs. In contrast, the low-oxygen, deep water metagenome was enriched with sequences for strict and facultative anaerobes. Interestingly, many of the same anaerobic bacterial families were enriched in the 3-μm size fraction of the ETM (2–10X more abundant relative to the 0.1-μm metagenome), indicating possible formation of anoxic microniches within particles. Results from this study provide a metagenome perspective on ecosystem-scale metabolism in an upwelling-influenced river-dominated coastal margin.
The Neuroprotective Properties of the Amyloid Precursor Protein Following Traumatic Brain Injury

Despite the significant health and economic burden that traumatic brain injury (TBI) places on society, the development of successful therapeutic agents have to date not translated into efficacious therapies in human clinical trials. Injury to the brain is ongoing after TBI, through a complex cascade of primary and secondary injury events, providing a valuable window of opportunity to help limit and prevent some of the severe consequences with a timely treatment. Of note, it has been suggested that novel treatments for TBI should be multifactorial in nature, mimicking the body’s own endogenous repair response. Whilst research has historically focused on the role of the amyloid precursor protein (APP) in the pathogenesis of Alzheimer’s disease, recent advances in trauma research have demonstrated that APP offers considerable neuroprotective properties following TBI, suggesting that APP is an ideal therapeutic candidate. Its acute upregulation following TBI has been shown to serve a beneficial role following trauma and has lead to significant advances in understanding the neuroprotective and neurotrophic functions of APP and its metabolites. Research has focused predominantly on the APP derivative sAPPα, which has consistently demonstrated neuroprotective and neurotrophic functions both in vitro and in vivo following various traumatic insults. Its neuroprotective activity has been narrowed down to a 15 amino acid sequence, and this region is linked to both heparan binding and growth-factor-like properties. It has been proposed that APP binds to heparan sulfate proteoglycans to exert its neuroprotective action. APP presents us with a novel therapeutic compound that could overcome many of the challenges that have stalled development of efficacious TBI treatments previously.
Chunking in Spatial Memory 1 Running head : CHUNKING IN SPATIAL MEMORY Chunking in Spatial Memory

In order to gain insight into the nature of human spatial representations, the current study examined how those representations are affected by blind rotation. Evidence was sought that while certain environmental aspects may be updated independently of one another, other aspects may be grouped (or chunked) together and updated as a unit. Participants learned the locations of an array of objects around them in a room, then were blindfolded and underwent a succession of passive, whole-body rotations. After each rotation, participants pointed to remembered target locations. Targets were located more precisely relative to each other if they were 1) separated by smaller angular distances 2) contained within the same regularly configured arrangement, or 3) corresponded to parts of a common object. A hypothesis is presented describing the roles played by egocentric and allocentric information within the spatial updating system. Results are interpreted in terms of an existing neural systems model, elaborating the model’s conceptualization of how parietal (egocentric) and medial temporal (allocentric) representations interact.
Controlling Seizure-Like Events by Perturbing Ion Concentration Dynamics with Periodic Stimulation

We investigate the effects of adding periodic stimulation to a generic, conductance-based neuron model that includes ion concentration dynamics of sodium and potassium. Under conditions of high extracellular potassium, the model exhibits repeating, spontaneous, seizure-like bursting events associated with slow modulation of the ion concentrations local to the neuron. We show that for a range of parameter values, depolarizing and hyperpolarizing periodic stimulation pulses (including frequencies lower than 4 Hz) can stop the spontaneous bursting by interacting with the ion concentration dynamics. Stimulation can also control the magnitude of evoked responses to modeled physiological inputs. We develop an understanding of the nonlinear dynamics of this system by a timescale separation procedure that identifies effective nullclines in the ion concentration parameter space. Our results suggest that the manipulation of ion concentration dynamics via external or endogenous stimulation may play an important role in neuronal excitability, seizure dynamics, and control.
How the Camel Lost Its Hump: The Impact of Object Typicality on Event-related Potential Signals in Object Decision

Using an object decision task, event-related potentials (ERPs), and minimum norm current source estimates, we investigated early spatiotemporal aspects of cortical activation elicited by line drawings that were manipulated on two dimensions: authenticity and typicality. Authentic objects were those that match real-world experience, whereas nonauthentic objects were doctored by deletion or addition of features (e.g., a camel with its hump removed, a hammer with two handles). The main manipulation of interest for both authentic and nonauthentic objects was the degree of typicality in the object's structure: typical items are composed of parts that have tended to co-occur across many different objects in the perceiver's experience. The ERP pattern revealed a significant typicality effect at 116 msec after stimulus onset. Both atypical authentic objects (e.g., a camel with its hump) and atypical nonauthentic objects (e.g., a jackal with a hump) elicited stronger brain activation than did objects with typical structure. A significant effect of authenticity was observed at 480 msec, with stronger activation for the nonauthentic objects. The factors of typicality and authenticity interacted at 160 and 330 msec. The most prominent source of the typicality effect was the bilateral occipitotemporal cortex, whereas the interaction and the authenticity effects were mainly observed in the more anterior bilateral temporal cortex. These findings support the hypothesis that within the first few hundred milliseconds after stimulus presentation onset, visual-form-related perceptual and conceptual processes represent distinct but interacting stages in object recognition.
Discrimination, Vulnerability, and Justice in the Face of Risk

Recent research finds that perceived risk is closely associated with race and gender. In surveys of the American public a subset of white males stand out for their uniformly low perceptions of environmental health risks, while most nonwhite and nonmale respondents reveal higher perceived risk. Such findings have been attributed to the advantageous position of white males in American social life. This article explores the linked possibility that this demographic pattern is driven not simply by the social advantages or disadvantages embodied in race or gender, but by the subjective experience of vulnerability and by sociopolitical evaluations pertaining to environmental injustice. Indices of environmental (in)justice and social vulnerability were developed as part of a U.S. National Risk Survey (n= 1,192) in order to examine their effect on perceived risk. It was found that those who regarded themselves as vulnerable and supported belief statements consistent with the environmental justice thesis offered higher risk ratings across a range of hazards. Multivariate analysis indicates that our measures of vulnerability and environmental (in)justice predict perceived risk but do not account for all of the effects of race and gender. The article closes with a discussion of the implications of these findings for further work on vulnerability and risk, risk communication, and risk management practices generally.