Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of proteasome cleavage motifs by neural networks.

We present a predictive method that can simulate an essential step in the antigen presentation in higher vertebrates, namely the step involving the proteasomal degradation of polypeptides into fragments which have the potential to bind to MHC Class I molecules. Proteasomal cleavage prediction algorithms published so far were trained on data from in vitro digestion experiments with constitutive proteasomes. As a result, they did not take into account the characteristics of the structurally modified proteasomes--often called immunoproteasomes--found in cells stimulated by gamma-interferon under physiological conditions. Our algorithm has been trained not only on in vitro data, but also on MHC Class I ligand data, which reflect a combination of immunoproteasome and constitutive proteasome specificity. This feature, together with the use of neural networks, a non-linear classification technique, make the prediction of MHC Class I ligand boundaries more accurate: 65% of the cleavage sites and 85% of the non-cleavage sites are correctly determined. Moreover, we show that the neural networks trained on the constitutive proteasome data learns a specificity that differs from that of the networks trained on MHC Class I ligands, i.e. the specificity of the immunoproteasome is different than the constitutive proteasome. The tools developed in this study in combination with a predictor of MHC and TAP binding capacity should give a more complete prediction of the generation and presentation of peptides on MHC Class I molecules. Here we demonstrate that such an approach produces an accurate prediction of the CTL the epitopes in HIV Nef. The method is available at www.cbs. dtu.dk/services/NetChop/.
Masked Hypertension: A Review

Masked hypertension is defined as a normal blood pressure (BP) in the clinic or office (<140/90 mmHg), but an elevated BP out of the clinic (ambulatory daytime BP or home BP>135/85 mmHg). It may occur in as many as 10% of the general population, and is important because it is not diagnosed by routine medical examinations, but carries an adverse prognosis, both in terms of increased target organ damage and cardiovascular events. Possible characteristics of individuals with masked hypertension are: relatively young age, male sex, stress or increased physical activity during the daytime, and smoking or drinking habits. Masked hypertension has also been described in treated hypertensive patients (in whom the prognosis is worse than predicted from the clinic pressure) and in children, in whom it may be a precursor of sustained hypertension. It may be suspected in individuals who have a history of occasional high BP readings, but who are apparently normotensive when checked in the office. One practical point is that we should continue to follow such people rather than dismissing them, and encourage out-of-clinic monitoring of BP. This would apply particularly to smokers and those with BP in the prehypertensive range. The potential implications of masked hypertension are huge, but the optimal strategy for detecting the condition in the general population is not yet clear.
Comparative Genome Analysis of Fusobacterium nucleatum

Abstract Fusobacterium nucleatum is considered to be a key oral bacterium in recruiting periodontal pathogens into subgingival dental plaque. Currently F. nucleatum can be subdivided into five subspecies. Our previous genome analysis of F. nucleatum W1481 (referred to hereafter as W1481), isolated from an 8-mm periodontal pocket in a patient with chronic periodontitis, suggested the possibility of a new subspecies. To further investigate the biology and relationships of this possible subspecies with other known subspecies, we performed comparative analysis between W1481 and 35 genome sequences represented by the five known Fusobacterium subspecies. Our analyses suggest that W1481 is most likely a new F. nucleatum subspecies, supported by evidence from phylogenetic analyses and maximal unique match indices (MUMi). Interestingly, we found a horizontally transferred W1481-specific genomic island harboring the tripartite ATP-independent (TRAP)-like transporter genes, suggesting this bacterium might have a high-affinity transport system for the C4-dicarboxylates malate, succinate, and fumarate. Moreover, we found virulence genes in the W1481 genome that may provide a strong defense mechanism which might enable it to colonize and survive within the host by evading immune surveillance. This comparative study provides better understanding of F. nucleatum and the basis for future functional work on this important pathogen.
Analysis and Calculation of DC-Link Current and Voltage Ripples for Three-Phase Inverter With Unbalanced Load

In this paper, an analysis and calculation of the dc-link current and voltage ripples are presented for a three-phase inverter with unbalanced load. A comparison of the dc-link average and root-mean-square (rms) currents between considering and ignoring high frequency harmonics of the output current is drawn. It is shown that high frequency harmonic currents have little effect on the dc-link current, and therefore, they can be ignored. Based on the symmetrical components method, the dc-link average and harmonic rms currents are derived, and the dc-link voltage ripple is compared between the balanced and unbalanced loads. It can be found that the dc-link current and voltage ripples consist of not only high frequency harmonics but also the double fundamental frequency harmonic, and the voltage ripple is independent of the positive-sequence component and determined by the negative-sequence component, under the unbalanced load. Experimental results are shown to verify the accuracy of the theoretical analysis.
Linear Array Synthesis to Obtain Broadside and Endfire Beam Patterns Using Element-Level Pattern Diversity

A linear array synthesis method using element-level pattern diversity (ELPD) is presented. Compared with conventional array, the ELPD array provides one more degree of freedom in antenna synthesis. The advantages and limitations of the ELPD in the linear array synthesis are discussed through three examples of broadside flat-topped, dual beam patterns, and endfire low sidelobe beam pattern. The tolerance analysis of the ELPD array is given. The practical application of a dual beam array with three elements was designed by using the full-wave solver and was tested. The 11% impedance bandwidth at a center frequency of 5.8 GHz with a −10 dB return loss and the measured maximum gain of 10.1 dBi at the beam-pointing angle of ±49° are achieved. The measured results agree well with the simulated ones.
Classification and Ontology Maintenance in Agent-Based Knowledge Management Frameworks: A Prototypical Approach

Being able to create views on the document space via grouping the documents is a key functionality in intelligent document management in view of browsing and querying. Hierarchically grouped sets of Documents can be viewed as simple extensionally defined ontological concepts. In an example Knowledge Management system (KnowCat) developed at UAM, Madrid, we investigate how agents for the maintenance of this ontology (these document groupings) can be constructed. We discuss two examples: A classification agent and a maintenance agent support users and administrators of the system to keep the ontology tight and functional. The agents are tested, developed targeted toward Spanish natural language documents, which requires adapted NLP techniques.
Interlingual Machine Translation

Summary: The first part of this paper considers some of the reasons why mechanical translation via a logically formalized interlingua is worth pursuing. The interlingua described consists of a network of bonded semantic elements, the bonds being either homogeneous, corresponding to a generalized notion of qualification, or heterogeneous, for dyadic relations. The translation procedure involves a basic program applicable to any input language (P) and any output language ( Q ), and P -interlingua and interlingua-Q mechanical dictionaries. The essence of the program is the construction of an array of symbols, grammatical, syntactic and semantic, containing all the information required for translation. The interlingual translation of the input in P is then derived by successive eliminations, usually involving comparisons either across the rows of the array or down the columns. Similar treatment of a second array suffices to translate from the interlingua to the output Q.
On Probabilistic Checking in Perfect Zero Knowledge

We present the first constructions of single-prover proof systems that achieve perfect zero knowledge (PZK) for languages beyond NP, under no intractability assumptions: 1. The complexity class #P has PZK proofs in the model of Interactive PCPs (IPCPs) [KR08], where the verifier first receives from the prover a PCP and then engages with the prover in an Interactive Proof (IP). 2. The complexity class NEXP has PZK proofs in the model of Interactive Oracle Proofs (IOPs) [BCS16,RRR16], where the verifier, in every round of interaction, receives a PCP from the prover. Our constructions rely on succinct simulators that enable us to "simulate beyond NP", achieving exponential savings in efficiency over [BCGV16]. These simulators crucially rely on solving a problem that lies at the intersection of coding theory, linear algebra, and computational complexity, which we call the succinct constraint detection problem, and consists of detecting dual constraints with polynomial support size for codes of exponential block length. Our two results rely on solutions to this problem for fundamental classes of linear codes: * An algorithm to detect constraints for Reed--Muller codes of exponential length. * An algorithm to detect constraints for PCPs of Proximity of Reed--Solomon codes [BS08] of exponential degree. The first algorithm exploits the Raz--Shpilka [RS05] deterministic polynomial identity testing algorithm, and shows, to our knowledge, a first connection of algebraic complexity theory with zero knowledge. Along the way, we give a perfect zero knowledge analogue of the celebrated sumcheck protocol [LFKN92], by leveraging both succinct constraint detection and low-degree testing. The second algorithm exploits the recursive structure of the PCPs of Proximity to show that small-support constraints are "locally" spanned by a small number of small-support constraints.
An adaptable sketch-based modeling system

In this paper, we propose a novel approach for inferring a closed smooth surface from sketched contours and deforming it by the following sketch-based gestures. Once the contours are drawn, smooth distance fields are computed within the contours, which are then transformed into height fields. A closed smooth surface is obtained upon the contours and the inferred height fields. The smooth surface can be further deformed by the four deformation gestures defined in the system. Though simple in idea, the system is able to create moderately complex models very quickly and intuitively.
Supporting maintenance tasks on transformational code generation environments

At the core of model-driven software development, model-transformation compositions enable automatic generation of executable artifacts from models. Although the advantages of transformational software development have been explored by numerous academics and industry practitioners, adoption of the paradigm continues to be slow, and limited to specific domains. The main challenge to adoption is the fact that maintenance tasks, such as analysis and management of model-transformation compositions and reflecting code changes to model transformations, are still largely unsupported by tools. My dissertation aims at enhancing the field's understanding around the maintenance issues in transformational software development, and at supporting the tasks involved in the synchronization of evolving system features with their generation environments. This paper discusses the three main aspects of the envisioned thesis: (a) complexity analysis of model-transformation compositions, (b) system feature localization and tracking in model-transformation compositions, and (c) refactoring of transformation compositions to improve their qualities.
Existentialist internationalisation and the Chinese student experience in English universities

Much of the ‘internationalisation’ that is currently observed in English universities is driven, whether directly or not, by economic and financial rationales associated with a particular neo‐liberal discourse of globalisation into which higher education has been subsumed. This is particularly true for the recruitment of international students into English universities. We present a case for the recasting of the higher education internationalisation agenda in terms of Sanderson's existential internationalism. Such an agenda promotes inter‐cultural understanding over financial motives and demands a focus on personal engagement with the Cultural Other. We report on the findings of two studies of Chinese students studying at English universities to examine the extent to which their experiences reveal evidence of a context that could support such a personally transformative internationalisation. We find that, far from illustrating the potential for development of genuinely international communities, these students' accounts are commonly of marginalisation, indifference and ‘otherisation’ that lead instead to social and cultural withdrawal into national groups and a heightened sense of national identity.
Performance of Cloud Radio Networks

Cloud radio networks coordinate transmission among base stations (BSs) to reduce the interference effects, particularly for the cell-edge users. In this paper, we analyze the performance of a cloud network with static clustering where geographically close BSs form a cloud network of cooperating BSs. Because, of finite cooperation, the interference in a practical cloud radio cannot be removed and in this paper, the distance based interference is taken into account in the analysis. In particular, we consider centralized zero forcing equalizer and dirty paper precoding for cancelling the interference. Bounds are developed on the signal-to-interference ratio distribution and achievable rate with full and limited channel feedback from the cluster users. The adverse effect of finite clusters on the achievable rate is quantified. We show that, the number of cooperating BSs is more crucial than the cluster area when full channel state information form the cluster is available for precoding. Also, we study the impact of limiting the channel state information on the achievable rate. We show that even with a practically feasible feedback of about five to six channel states from each user, significant gain in mean rate and cell edge rate compared to conventional cellular systems can be obtained.
Extending procedural task models by systematic explicit integration of objects, knowledge and information

Task analysis can be considered as a fundamental component of user centered design methods as it provides a unique way of analyzing in a systematic way users' roles and activities. A widely used way of storing the information gathered during that phase in a structured and exhaustive way is to build task models which are then amenable to verification of properties or to performance evaluation. In widely used notations such as Hierarchical Task Analysis (HTA) or CTT (Concur Task Tree), information or objects manipulated by the users while performing the tasks does not receive a similar treatment as the sequencing of tasks which is usually carefully and exhaustively described. This paper proposes a systematic account for the various concepts manipulated by the users while performing tasks. Such concepts include different types of knowledge (declarative, situational, procedural and strategic), objects (manipulated by the user) and information. These concepts are systematically represented in a set of extensions of the HAMSTERS notation allowing the analysis of concepts-related properties such as learning curve, complexity, information workload,. We demonstrate the application of the approach on the example of a two players game making explicit the connection between these extended task models and the user interface of the game.
Personalized Advertising Strategy for Integrated Social Networking Websites

In addition to provide major funding for many Internet companies, online advertising creates a disutility to consumers, subsequently reducing market share. However, previous works focus only on the topical relevance of ads and, in doing so, neglect consumer attitudes. From the view of text processing, they focus only on the topic dimension of texts, while paying no attention to the sentiment dimension. This work proposes a feature extraction process to match advertisement and targeted users by extracting features from the userpsilas profile and advertisement specification. First, the proposed platform relies on mine characteristics supplied by a user to his avatar including preferred color, style and feeling. Second, the system selects the best matching advertisement based on the userpsilas variable interests (as expressed on his blog). These features are scored and finally these advertisements are conveyed to the target users by product. Experimental results in several topics demonstrate that the proposed framework works well in detecting a userpsilas potential preferences, and in recommending suitable advertisements.
Antimicrobial activity of Anonna mucosa (Jacq.) grown in vivo and obtained by in vitroculture

Brazilian flora includes numerous species of medicinal importance that can be used to develop new drugs. Plant tissue culture offers strategies for conservation and use of these species allowing continuous production of plants and bioactive substances. Annona mucosa has produced substances such as acetogenins and alkaloids that exhibit antimicrobial activities. The widespread use of antibiotics has led to an increase in multidrug-resistant bacteria, which represents a serious risk of infection. In view of this problem, the aim of this work was to evaluate the antibacterial potential of extracts of A. mucosa obtained by in vitro techniques and also cultured under in vivo conditions. Segments from seedlings were inoculated onto different culture media containing the auxin picloram and the cytokinin kinetin at different concentrations. The calluses obtained were used to produce cell suspension cultures. The materials were subjected to methanol extraction and subsequent fractionation in hexane and dichloromethane. The antimicrobial activity against 20 strains of clinical relevance was evaluated by the macrodilution method at minimum inhibitory and minimum bactericidal concentrations. The extracts showed selective antimicrobial activity, inhibiting the growth of Streptococcus pyogenes and Bacillus thuringiensis at different concentrations. The plant tissue culture methods produced plant materials with antibacterial properties, as well as in vivo grown plants. The antibacterial activity of material obtained through biotechnological procedures of A. mucosa is reported here for the first time.
Automatic recovery of statecharts from procedural code

We have developed a static-analysis algorithm that extracts statecharts from procedural implementations of state machines. The extracted statecharts are semantically-equivalent to the original program, and can be used for further development instead of the procedural code. We have implemented this algorithm in a tool called StatRec. We report on the results of running StatRec on a number of examples, including an implementation of the TCP protocol.
Survival, an Israeli Ju Jutsu school of martial arts

■ Nationalism is the untenable union of the impersonal, mechanistic, bureaucratic logic of the state and the intimate, emotional, organic logic of the nation. While practicing martial arts, the participants at the Israeli Survival School of Ju Jutsu create a utopian Israeliness, using bits of state-national understandings to form a family-like organicity. At the North Indian school of wrestling described by Joseph Alter, too, an organic utopian nationalism is practiced into existence through meticulous care for the body itself. A comparison between those modes of embodying the national, set in very different cultural and national realities, reveals not only different understandings of the national and of its organic nature, but also different uses of semiotic mechanisms. Whereas the Israeli world of the Survival School is based on representation, the Indian one is constructed from the body and the environment, set in dense connectedness forming this world in and of itself.
RULE-BASED CLASSIFICATION OF ALOS/ AVNIR-2 AND PRISM DATA FOR BAMBOO DISTRIBUTION MAPPING

Previously bamboo forests were utilized and maintained to obtain several kinds of product, however, recently the demand has been decreased, so the bamboo forests are not utilized so much, and it is disorderedly expanding in many rural area, in Japan. It has caused serious damage to the ecosystem that expanding bamboo forests are destroying other species. Since the distribution is rapidly expanding, it is very difficult to map the current bamboo distribution with conventional way, such as manually interpretation of aerial photo and satellite data because of required efforts. In this study, we developed a hierarchical algorithm to map bamboo distribution using ALOS /AVNIR-2 and PRISM data. As the first step, land cover is largely classified into vegetated area and nonvegetated area using NDVI. The vegetated area is classified into paddy field and forest area with height of objects, which is derived with surface height calculated with PRISM data and elevation data. Finally, bamboo area is differentiated with discriminant function by using reflectance data estimated from ALOS/AVNIR-2 and PRISM data. By following these rules, finally, landcover is classified into five categories including bamboo forest.
Educators’ perceptions of bringing students to environmental consciousness through engaging outdoor experiences

This paper explores the premise that environmental education involves raising environmental consciousness rather than simply knowing about the environment in a technical-rational manner and acting for it in mechanistic prescribed ways. The paper draws on educational theory and data from a phenomenological case study of educators working together at an outdoor education centre in urban Canada, whose practice of environmental education we believe can best be described as environmental consciousness raising. Based on our study’s findings, we suggest that raising environmental consciousness involves connecting people to their environment, fostering care for the environment, and building agency for the environment. Educating for environmental consciousness also requires providing people with deeply engaging experiences that afford authenticity, multidimensionality and serendipity. Our study shows how these features can work to raise environmental consciousness, by creating epiphanies or moments when sudden expansions of the self, realization and empowerment become possible.