Predicting class II MHC-Peptide binding:a kernel based approach using similarity scores

Background - Modelling the interaction between potentially antigenic peptides and Major Histocompatibility Complex (MHC) molecules is a key step in identifying potential T-cell epitopes. For Class II MHC alleles, the binding groove is open at both ends, causing ambiguity in the positional alignment between the groove and peptide, as well as creating uncertainty as to what parts of the peptide interact with the MHC. Moreover, the antigenic peptides have variable lengths, making naive modelling methods difficult to apply. This paper introduces a kernel method that can handle variable length peptides effectively by quantifying similarities between peptide sequences and integrating these into the kernel. Results - The kernel approach presented here shows increased prediction accuracy with a significantly higher number of true positives and negatives on multiple MHC class II alleles, when testing data sets from MHCPEP [1], MCHBN [2], and MHCBench [3]. Evaluation by cross validation, when segregating binders and non-binders, produced an average of 0.824 AROC for the MHCBench data sets (up from 0.756), and an average of 0.96 AROC for multiple alleles of the MHCPEP database. Conclusion - The method improves performance over existing state-of-the-art methods of MHC class II peptide binding predictions by using a custom, knowledge-based representation of peptides. Similarity scores, in contrast to a fixed-length, pocket-specific representation of amino acids, provide a flexible and powerful way of modelling MHC binding, and can easily be applied to other dynamic sequence problems.

Discourses of friendship between heterosexual women and gay men:mythical norms and an absence of desire

Gay men and heterosexual women may share some common interests in critiquing hetero-patriarchy. However feminism and gay liberationist politics do not always coincide and the role of individual subjectivities in recognising oppressive discourses of normativity remains debated. Interviews were conducted with seven friendship dyads of heterosexual women and gay men. Transcripts were subjected to discourse analysis, which suggested extensive management of heterosexist norms in the friends' accounts of friendship. The analysis highlighted ambiguity over the 'male' status of gay men, a concern with constructing the friendships as legitimately asexual, and the use of parody in the face of homophobia to disrupt normative assumptions. Although we primarily considered the role of heterosexist discourses, there is also evidence that other dimensions of non-normativity (for example, gender and ethnicity) are implicated in friendships constructed around shared otherness and mutual non-normativity. © 2010 SAGE.

An improved conflicting evidence combination approach based on a new supporting probability distance

To avoid counter-intuitive result of classical Dempster's combination rule when dealing with highly conflict information, many improved combination methods have been developed through modifying the basic probability assignments (BPAs) of bodies of evidence (BOEs) by using a certain measure of the degree of conflict or uncertain information, such as Jousselme's distance, the pignistic probability distance and the ambiguity measure. However, if BOEs contain some non-singleton elements and the differences among their BPAs are larger than 0.5, the current conflict measure methods have limitations in describing the interrelationship among the conflict BOEs and may even lead to wrong combination results. In order to solve this problem, a new distance function, which is called supporting probability distance, is proposed to characterize the differences among BOEs. With the new distance, the information of how much a focal element is supported by the other focal elements in BOEs can be given. Also, a new combination rule based on the supporting probability distance is proposed for the combination of the conflicting evidences. The credibility and the discounting factor of each BOE are generated by the supporting probability distance and the weighted BOEs are combined directly using Dempster's rules. Analytical results of numerical examples show that the new distance has a better capability of describing the interrelationships among BOEs, especially for the highly conflicting BOEs containing non-singleton elements and the proposed new combination method has better applicability and effectiveness compared with the existing methods.

Policy ideas through the prism of knowledge regimes and framing

Policymakers are often confronted with problems that involve ambiguity and uncertainty (Zahariadis, 2003). In order to make sense of such problems and to identify possible solutions, they are on the lookout for policy ideas.

Source localization methods

One of the most pressing demands on electrophysiology applied to the diagnosis of epilepsy is the non-invasive localization of the neuronal generators responsible for brain electrical and magnetic fields (the so-called inverse problem). These neuronal generators produce primary currents in the brain, which together with passive currents give rise to the EEG signal. Unfortunately, the signal we measure on the scalp surface doesn't directly indicate the location of the active neuronal assemblies. This is the expression of the ambiguity of the underlying static electromagnetic inverse problem, partly due to the relatively limited number of independent measures available. A given electric potential distribution recorded at the scalp can be explained by the activity of infinite different configurations of intracranial sources. In contrast, the forward problem, which consists of computing the potential field at the scalp from known source locations and strengths with known geometry and conductivity properties of the brain and its layers (CSF/meninges, skin and skull), i.e. the head model, has a unique solution. The head models vary from the computationally simpler spherical models (three or four concentric spheres) to the realistic models based on the segmentation of anatomical images obtained using magnetic resonance imaging (MRI). Realistic models – computationally intensive and difficult to implement – can separate different tissues of the head and account for the convoluted geometry of the brain and the significant inter-individual variability. In real-life applications, if the assumptions of the statistical, anatomical or functional properties of the signal and the volume in which it is generated are meaningful, a true three-dimensional tomographic representation of sources of brain electrical activity is possible in spite of the ‘ill-posed’ nature of the inverse problem (Michel et al., 2004). The techniques used to achieve this are now referred to as electrical source imaging (ESI) or magnetic source imaging (MSI). The first issue to influence reconstruction accuracy is spatial sampling, i.e. the number of EEG electrodes. It has been shown that this relationship is not linear, reaching a plateau at about 128 electrodes, provided spatial distribution is uniform. The second factor is related to the different properties of the source localization strategies used with respect to the hypothesized source configuration.

Delegation in hard times:the financial management of arm's length bodies in the UK

This paper explores the effectiveness of financial management tools in regulating the use of resources by arm’s length bodies (ALBs) in a period of fiscal stress. The paper presents research undertaken into the implementation of a new financial management tool for ALBs in the UK since the 2008 financial crisis. Drawing on conflict ambiguity theory, the paper shows how the effectiveness of such tools is affected by deep-rooted tensions implicit within arm’s length governance. This gives rise to micro-level conflict over the means of achieving fiscal regulation, underpinned by macro-level ambiguity over the logic of governance pursued by the government.

Discovering knowledge structures in mind maps of mental health risks

This thesis addressed the problem of risk analysis in mental healthcare, with respect to the GRiST project at Aston University. That project provides a risk-screening tool based on the knowledge of 46 experts, captured as mind maps that describe relationships between risks and patterns of behavioural cues. Mind mapping, though, fails to impose control over content, and is not considered to formally represent knowledge. In contrast, this thesis treated GRiSTs mind maps as a rich knowledge base in need of refinement; that process drew on existing techniques for designing databases and knowledge bases. Identifying well-defined mind map concepts, though, was hindered by spelling mistakes, and by ambiguity and lack of coverage in the tools used for researching words. A novel use of the Edit Distance overcame those problems, by assessing similarities between mind map texts, and between spelling mistakes and suggested corrections. That algorithm further identified stems, the shortest text string found in related word-forms. As opposed to existing approaches’ reliance on built-in linguistic knowledge, this thesis devised a novel, more flexible text-based technique. An additional tool, Correspondence Analysis, found patterns in word usage that allowed machines to determine likely intended meanings for ambiguous words. Correspondence Analysis further produced clusters of related concepts, which in turn drove the automatic generation of novel mind maps. Such maps underpinned adjuncts to the mind mapping software used by GRiST; one such new facility generated novel mind maps, to reflect the collected expert knowledge on any specified concept. Mind maps from GRiST are stored as XML, which suggested storing them in an XML database. In fact, the entire approach here is ”XML-centric”, in that all stages rely on XML as far as possible. A XML-based query language allows user to retrieve information from the mind map knowledge base. The approach, it was concluded, will prove valuable to mind mapping in general, and to detecting patterns in any type of digital information.

Concept, Measurement, and Ideology of "National Competitiveness"

The author of this paper reviewing the perceptions of competitiveness reveals the origin and ambiguity of the concept of “national competitiveness” which is mostly confused with that of development of countries and competitiveness of their enterprises. He investigates the role of transnational companies and governments in shaping the world economic position of countries, presents a critique on the measurement of “national competitiveness” of countries, and heavily opposes the ideological use of the latter for justifying antisocial measures.

Inmanencia mistica en la obra de Federico Garcia Lorca

The purpose of this dissertation was to analyze the works of Federico García Lorca within the mystic context that dominates their very genesis. The problematic definition of mysticism was explored lest it be confused with traditional mysticism, which implies union with the divine. The historiography of literature speaks of the Mystic Genre, yet it does not address the mystic mode of artistic creation due to its inability to adhere to rational measure. This mode of conception was explored through Lorca's poetic discourse: ‘Lorquian mysticism’ is the result of the poet's cultivation of an innate spiritual potential enhanced by external influences and technical mastery. ^ There is visible influence of Fray Luis of León in Lorca's early Libro de poemas and El maleficio de la mariposa, as well as of Saint John of the Cross in the later Diván del Tamarit, Sonetos de amor and Yerma. However, definitive echoes of poets from the Sufi and other Eastern mystic traditions were also illustrated in these late works. A persistent longing to elide the physical condition, the greatest obstacle of the transcendental quest, is the essence of Lorca's poetic voice. ^ The object of this analysis was Lorca's language, which reaches levels removed from conventional thought. His dazzling metaphors and his particular use of symbols and of paradox compare equitably with those of great mystic poets. Like them, Lorca was faced with the same limitations of language to describe an ineffable experience; he embraced what Octavio Paz describes as ‘sacred language’: there is a linguistic frugality as well as an ambiguity in Lorca's poetic art that result from his realization of supercognitive states. Yet such an interpretation is rejected by the rationalist approach, invoking the age-old debate between faith and reason and signaling the application of psychoanalytical theory. This limited approach was disputed on the basis of reader-response theory. Lorca was truly an eclectic and a modification of the conventional reader's preestablished horizon of expectations is essential in order to seal the gaps in his late works. This innovative perspective placed Lorca within the framework of a new mysticism in the modern world. ^

Ensemble fuzzy belief intrusion detection design

With the rapid growth of the Internet, computer attacks are increasing at a fast pace and can easily cause millions of dollar in damage to an organization. Detecting these attacks is an important issue of computer security. There are many types of attacks and they fall into four main categories, Denial of Service (DoS) attacks, Probe, User to Root (U2R) attacks, and Remote to Local (R2L) attacks. Within these categories, DoS and Probe attacks continuously show up with greater frequency in a short period of time when they attack systems. They are different from the normal traffic data and can be easily separated from normal activities. On the contrary, U2R and R2L attacks are embedded in the data portions of the packets and normally involve only a single connection. It becomes difficult to achieve satisfactory detection accuracy for detecting these two attacks. Therefore, we focus on studying the ambiguity problem between normal activities and U2R/R2L attacks. The goal is to build a detection system that can accurately and quickly detect these two attacks. In this dissertation, we design a two-phase intrusion detection approach. In the first phase, a correlation-based feature selection algorithm is proposed to advance the speed of detection. Features with poor prediction ability for the signatures of attacks and features inter-correlated with one or more other features are considered redundant. Such features are removed and only indispensable information about the original feature space remains. In the second phase, we develop an ensemble intrusion detection system to achieve accurate detection performance. The proposed method includes multiple feature selecting intrusion detectors and a data mining intrusion detector. The former ones consist of a set of detectors, and each of them uses a fuzzy clustering technique and belief theory to solve the ambiguity problem. The latter one applies data mining technique to automatically extract computer users’ normal behavior from training network traffic data. The final decision is a combination of the outputs of feature selecting and data mining detectors. The experimental results indicate that our ensemble approach not only significantly reduces the detection time but also effectively detect U2R and R2L attacks that contain degrees of ambiguous information.

Assessing administrative and political factors in implementing a living wage ordinance

Since 2000, the number of living wage ordinances has steadily increased throughout the country. While most of the current research has focused on the beneficial outcomes of living wages, little has been published on their administrative practices. To address this shortcoming, this study focused on the identification of key administrative and political factors involved impacting the implementation of living wage ordinances in Miami-Dade and Broward Counties. The study utilized a triangulation of interviews, surveys, and direct observation. The author conducted interviews of administrators and members of the living wage oversight boards in both counties and observed the monthly meetings held by each county's oversight board from January 2006 to June 2007. These findings were buttressed with a national survey of senior staff in other living wage communities. The study utilized descriptive statistics, Chi Square, Cronbach's Alpha, and Spearman's Rank Correlation Coefficient (Spearman's rho). Interviews indicated that administrators in Dade and Broward are seriously under-staffed and budgeted. Ambiguities in the enabling ordinances have lead to loopholes that undermine implementation and accountability for participating contractors. Survey results showed that policy ambiguity, organizational politics, and a lack of organizational capacity were significant negative factors in the implementation process while an organizational culture emphasizing consistent enforcement was a positive factor. Without the proper inputs, an organization hinders itself from meeting its outputs and outcomes. This study finds that Broward and Miami-Dade Counties do not provide the necessary administrative support to implement a living wage effectively – in stark contrast to the high hopes and strong political support behind their passage. For a living wage to succeed, it first needs an organizational culture committed to providing the necessary resources for implementation as well as transparent, consistent accountability mechanisms.

Space time coding for polynomial phase modulated signals

Polynomial phase modulated (PPM) signals have been shown to provide improved error rate performance with respect to conventional modulation formats under additive white Gaussian noise and fading channels in single-input single-output (SISO) communication systems. In this dissertation, systems with two and four transmit antennas using PPM signals were presented. In both cases we employed full-rate space-time block codes in order to take advantage of the multipath channel. For two transmit antennas, we used the orthogonal space-time block code (OSTBC) proposed by Alamouti and performed symbol-wise decoding by estimating the phase coefficients of the PPM signal using three different methods: maximum-likelihood (ML), sub-optimal ML (S-ML) and the high-order ambiguity function (HAF). In the case of four transmit antennas, we used the full-rate quasi-OSTBC (QOSTBC) proposed by Jafarkhani. However, in order to ensure the best error rate performance, PPM signals were selected such as to maximize the QOSTBC’s minimum coding gain distance (CGD). Since this method does not always provide a unique solution, an additional criterion known as maximum channel interference coefficient (CIC) was proposed. Through Monte Carlo simulations it was shown that by using QOSTBCs along with the properly selected PPM constellations based on the CGD and CIC criteria, full diversity in flat fading channels and thus, low BER at high signal-to-noise ratios (SNR) can be ensured. Lastly, the performance of symbol-wise decoding for QOSTBCs was evaluated. In this case a quasi zero-forcing method was used to decouple the received signal and it was shown that although this technique reduces the decoding complexity of the system, there is a penalty to be paid in terms of error rate performance at high SNRs.

Collective bargaining and faculty unionization: An administrative perspective

The purpose of this qualitative case study was to gain insight into the perspectives of experienced higher education administrators regarding faculty unionization, the collective bargaining process, and the interpersonal relationships between higher education faculty members and administrators. ^ The primary method of data collection was semi-structured face to face interviews with nine administrators from two community colleges and two universities in the south Florida area. All of the study participants worked with unionized faculty members and had direct experience participating in bargaining negotiations. ^ Upon the completion of each interview, the researcher listened to the taped audio recording of the interview several times and then transcribed all of the information from the audiotape into a Word file. Data collection and analysis for each participant were performed concurrently. Using a modified concept mapping approach, the research questions were written on large yellow sticky notes and placed in the middle of a wall in the researcher’s home with nine descriptive categorical themes written on smaller sticky notes placed around the study questions. The highlighted quotes and key phrases were cut from each transcript and placed under each of the descriptive categories. Over the course of a few months repeatedly reviewing the research questions that guided this study, the theory of symbolic interactionism, and relevant literature the categorical descriptive themes were refined and condensed into five descriptive themes. ^ Study findings indicated that the administrators: (a) must have a clear understanding of what it is that the faculty does to be an effective representative at the bargaining table, (b) experienced role ambiguity and role strain related to a lack of understanding as to their role at the bargaining table and a lack of organizational support, (c) were not offered any type of training in preparation for bargaining, (d) perceived a definite “us versus them” mentality between faculty and administration, and (e) saw faculty collective bargaining at public institutions of higher education in Florida as ineffectual. ^

Role Stress, Emotional Exhaustion, and Job Satisfaction in the Hotel Industry: The Moderating Role of Supervisory Support

The purpose of this study is to investigate supervisory support as a moderator of the effects of role conflict and role ambiguity on emotional exhaustion and job satisfaction. This study also examines the moderating role of supervisory support on the relationship between emotional exhaustion and job satisfaction. Data were collected from a sample of frontline hotel employees in Northern Cyprus. The aforementioned relationships were tested based on hierarchical multiple regression analysis. The results demonstrate that supervisory support mitigates the impact of role conflict on emotional exhaustion and further reveal that supervisory support reduces the effect of emotional exhaustion on job satisfaction. There is no empirical support for the rest of the hypothesized relationships. Implications of the empirical results are discussed, and future research directions are offered.

The Influence of Selected Antecedents of Frontline Employee's Perceptions of Service Recovery Performance

The purpose of this study is to determine the potential impact of selected organizational factors on boundary-spanning-role employees’ perceptions of service recovery performance. This study also aims to assess the impact of service recovery performance on the intention to leave the job and extrinsic job satisfaction. This study uses a sample of frontline employees in Belek, Antalya, Turkey. The empirical findings revealed that education, team work and role ambiguity as frontline job perceptions were found to exert positive influences on the service recovery performance, but, empowerment, reward, and organizational commitment were found to have negative effects on the service recovery performance.