Realism about PDB

Schierz,A.C., L. Soldatova, R.D. King. Realism about PDB. Nature Biotechnology, 25, No. 8, August 2007, p846. Sponsorship: Project IQ, EU IST-FET FP6-516169 BBSRC Project 2/BEP17028

Using a logical model to predict the growth of yeast

Whelan, K. E. and King, R. D. Using a logical model to predict the growth of yeast. BMC Bioinformatics 2008, 9:97

Locational distribution of gene functional classes in Arabidopsis thaliana

Riley, M. C., Clare, A., King, R. D. (2007). Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics 8, Article No: 112 Sponsorship: EPSRC / RAEng

The EXACT description of biomedical protocols

Soldatova, L. N., Aubrey, W., King, R. D., Clare, A. J. (2008). The EXACT description of biomedical protocols. Bioinformatics, 24 (13), i295-i303 Sponsorship: BBSRC / RAEng / EPSRC specialissue: ISMB

Project Sanitarium: gaming TB: a serious game for a serious problem

Collaborative projects between Industry and Academia provide excellent opportunities for learning. Throughout the academic year 2014-2015 undergraduates from the School of Arts, Media and Computer Games at Abertay University worked with academics from the Infection Group at the University of St Andrews and industry partners Microsoft and DeltaDNA. The result was a serious game prototype that utilized game design techniques and technology to demystify and educate players about the diagnosis and treatment of one of the world's oldest and deadliest diseases, Tuberculosis (TB). Project Sanitarium is a game incorporating a mathematical model that is based on data from real-world drug trials. This paper discusses the project design and development, demonstrating how the project builds on the successful collaborative pedagogical model developed by academic staff at Abertay University. The aim of the model is to provide undergraduates with workplace simulation, wider industry collaboration and access to academic expertise to solve challenging and complex problems.

Zasada racji dostatecznej w kontekście semantycznej kontrowersji realizm–antyrealizm

"Principle of sufficient reason in the context of the realism-antirealism semantic controversy". The topic of this article is the cognitive and semantic status of Michael Dummett’s principle C. According to the principle, if a statement is true, there must be something in virtue of which it is true. The author suggests the interpretation of principle C in terms of the sufficient reason principle as a contemporary, weaker and semantic counterpart of the classical version of the principle. Considerations include such problems as: the distinction between the reason-consequence relationship and cause-effect relationship; the reductionism and justificationism in the context of the realism-antirealism semantic controversy; the reversibility of reason-consequence relationship and the question of a search for ultimate reasons. The author also distinguishes three forms of the sufficient reason principle: metaphysical, ontological and propositional.

Why do Nigerian manufacturing firms take action on AIDS?

Objective: To identify differences between manufacturing firms in Nigeria that have undertaken HIV/AIDS prevention activities and those that have not as a step toward improving the targeting of HIV policies and interventions. Methods: A survey of a representative sample of registered manufacturing firms in Nigeria, stratified by location, workforce size, and industrial sector. The survey was administered to managers of 232 firms representing most major industrial areas and sectors in March-April 2001. Results: 45.3 percent of the firms’ managers received information about HIV/AIDS from a source outside the firm in 2000; 7.7 percent knew of an employee who was HIV-positive at the time of the survey; and 13.6 percent knew of an employee who had left the firm and/or died in service due to AIDS. Only 31.7 percent of firms took any action to prevent HIV among employees in 2000, and 23.9 percent had discussed the epidemic as a potential business concern. The best correlates of having taken action on HIV were knowledge of an HIV-positive employee or having lost an employee to AIDS (odds ratio [OR] 6.36, 95% confidence interval [CI]: 2.30, 17.57) and receiving information about the disease from an outside source (OR 7.83, 95% CI: 3.46, 17.69). Conclusions: Despite a nationwide HIV seroprevalence of 5.8 percent, as of 2001 most Nigerian manufacturing firm managers did not regard HIV/AIDS as a serious problem and had neither taken any action on it nor discussed it as a business issue. Providing managers with accurate, relevant information about the epidemic and practical prevention interventions might strengthen the business response to AIDS in countries like Nigeria.

A reconsideration of the theological conception of sin in the light of the psychoanalytic conceptions of shame and guilt

Boston University Graduate School of Arts and Sciences. Department of Religion.

The influence of neoliberal thought on contemporary politics: an examination of the interrelationships between ideological hegemony, neoliberal thought and contemporary politics

This thesis critically assesses the impact of neoliberal ideology on liberal thought and contemporary politics specifically examining the question, To what extent has neoliberalism, as elucidated originally by Hayek affected change in contemporary politics? This question is crucial to understanding the nature, role, influence and impact of neoliberal ideas. This investigation required a broad engagement with the literature, identifying and discussing the relationships within neoliberalism allowing a clearer understanding of the role of ideas in neoliberalism’s continuing hegemony. The methodological approach adopted a social constructivist character that encompassed an individual centric emphasis, acknowledging the breadth and complexity of Neoliberalization through the use of interpretive repertoires. The initial chapters examine the ideational process and the role of particular understanding in motivating political conduct. In this context of the transfer of ideas through their everyday resonance eventually becoming ‘stubborn social facts’ (Habermas 2006:413) is highlighted. Later chapters discuss the historical and economic context of Neoliberalization focussing on the role of the hegemon and its influence, outlining and evaluating the contribution of Hayek to liberal thought. The penultimate chapter deals with the contemporary situation and the irony associated with Hayek’s original ideas. Concluding, several findings emerged contributing by combining available knowledge in a uniquely fresh way and generating originality by linking old ideas, new ideas and new facts. The results are grouped as, - Pragmatic, recognising that political pragmatism trumps ideological aspiration where liberal democratic processes require politicians are held to account. - Realistic, recognising the contrast and irony between political action and ideological insight reflected in the operationalization of neoliberalism. - General, recognising Hayek’s on-going but increasingly indirect influence. The thesis finishes with a short aside on ideational change within the context of the current crisis and advocates an introspective approach that includes entrepreneurial spirit, good conscience and duty as part of future deliberations.

Surface plasmon resonance in nanostructured metal films under the Kretschmann configuration

We systematically investigated the surface plasmon resonance in one-dimensional (1D) subwavelength nanostructured metal films under the Kretschmann configuration. We calculated the reflectance, transmittance, and absorption for varying the dielectric fill factor, the period of the 1D nanostructure, and the metal film thickness. We have found that the small dielectric slits in the metal films reduce the surface plasmon resonance angle and move it toward the critical angle for total internal reflection. The reduction in surface plasmon resonance angle in nanostructured metal films is due to the increased intrinsic free electron oscillation frequency in metal nanostructures. Also we have found that the increasing the spatial frequency of the 1D nanograting reduces the surface plasmon resonance angle, which indicates that less momentum is needed to match the momentum of the surface plasmon-polariton. The variation in the nanostructured metal film thickness changes the resonance angle slightly, but mainly remains as a mean to adjust the coupling between the incident optical wave and the surface plasmon-polariton wave. © 2009 American Institute of Physics.

Selected Solo Music for Saxophone by United States Composers: 1975-2005

This dissertation project identifies important works for solo saxophone by United States composers between 1975 and 2005. The quality, variety, expressiveness, and difficulty of the solo saxophone repertoire during these thirty years is remarkable and remedies, to some extent, the fact that the saxophone had been a largely neglected instrument in the realm of classical music. In twentieth-century music, including Jazz, the saxophone developed, nevertheless, a unique and significant voice as is evident in the saxophone repertoire that expands immensely in many instrumental settings, including the orchestra, solo works, and a wide variety of chamber ensembles. Historically, the saxophone in the United States first found its niche in Vaudeville, military bands, and jazz ensembles, while in Europe composers such as Debussy, D'Indy, Schmitt, Ibert, Glazounov, Heiden, and Desenclos recognized the potential of the instrument and wrote for it. The saxophone is well suited to the intimacy and unique timbral explorations of the solo literature, but only by the middle twentieth century did the repertoire allow the instrument to flourish into a virtuosic and expressive voice presented by successive generations of performers – Marcel Mule, Sigurd Rascher, Cecil Leeson, Jean-Marie Londeix, Fred Hemke, Eugene Rousseau, and Donald Sinta. The very high artistic level of theses soloists was inspiring and dozens of new compositions were commissioned. Through the 1960’s American composers such as Paul Creston, Leslie Bassett, Henry Cowell, Alec Wilder, and others produced eminent works for the saxophone, to be followed by an enormous output of quality compositions between 1975 and 2005. The works chosen for performance were selected from thousands of compositions between 1975 and 2005 researched for this project. The three recital dates were: April 6, 2005, in Gildenhorn Recital Hall, December 4, 2005, in Ulrich Recital Hall, and April 15, 2006, in Gildenhorn Recital Hall. Recordings of these recitals may be obtained in person or online from the Michelle Smith Performing Arts Library of the University of Maryland, College Park.

Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV

Proteins are essential components of cells and are crucial for catalyzing reactions, signaling, recognition, motility, recycling, and structural stability. This diversity of function suggests that nature is only scratching the surface of protein functional space. Protein function is determined by structure, which in turn is determined predominantly by amino acid sequence. Protein design aims to explore protein sequence and conformational space to design novel proteins with new or improved function. The vast number of possible protein sequences makes exploring the space a challenging problem.

Computational structure-based protein design (CSPD) allows for the rational design of proteins. Because of the large search space, CSPD methods must balance search accuracy and modeling simplifications. We have developed algorithms that allow for the accurate and efficient search of protein conformational space. Specifically, we focus on algorithms that maintain provability, account for protein flexibility, and use ensemble-based rankings. We present several novel algorithms for incorporating improved flexibility into CSPD with continuous rotamers. We applied these algorithms to two biomedically important design problems. We designed peptide inhibitors of the cystic fibrosis agonist CAL that were able to restore function of the vital cystic fibrosis protein CFTR. We also designed improved HIV antibodies and nanobodies to combat HIV infections.

Nurse-led behavioral management of diabetes and hypertension in community practices: a randomized trial.

BACKGROUND: Several trials have demonstrated the efficacy of nurse telephone case management for diabetes (DM) and hypertension (HTN) in academic or vertically integrated systems. Little is known about the real-world potency of these interventions. OBJECTIVE: To assess the effectiveness of nurse behavioral management of DM and HTN in community practices among patients with both diseases. DESIGN: The study was designed as a patient-level randomized controlled trial. PARTICIPANTS: Participants included adult patients with both type 2 DM and HTN who were receiving care at one of nine community fee-for-service practices. Subjects were required to have inadequately controlled DM (hemoglobin A1c [A1c] ≥ 7.5%) but could have well-controlled HTN. INTERVENTIONS: All patients received a call from a nurse experienced in DM and HTN management once every two months over a period of two years, for a total of 12 calls. Intervention patients received tailored DM- and HTN- focused behavioral content; control patients received non-tailored, non-interactive information regarding health issues unrelated to DM and HTN (e.g., skin cancer prevention). MAIN OUTCOMES AND MEASURES: Systolic blood pressure (SBP) and A1c were co-primary outcomes, measured at 6, 12, and 24 months; 24 months was the primary time point. RESULTS: Three hundred seventy-seven subjects were enrolled; 193 were randomized to intervention, 184 to control. Subjects were 55% female and 50% white; the mean baseline A1c was 9.1% (SD = 1%) and mean SBP was 142 mmHg (SD = 20). Eighty-two percent of scheduled interviews were conducted; 69% of intervention patients and 70% of control patients reached the 24-month time point. Expressing model estimated differences as (intervention--control), at 24 months, intervention patients had similar A1c [diff = 0.1 %, 95 % CI (-0.3, 0.5), p = 0.51] and SBP [diff = -0.9 mmHg, 95% CI (-5.4, 3.5), p = 0.68] values compared to control patients. Likewise, DBP (diff = 0.4 mmHg, p = 0.76), weight (diff = 0.3 kg, p = 0.80), and physical activity levels (diff = 153 MET-min/week, p = 0.41) were similar between control and intervention patients. Results were also similar at the 6- and 12-month time points. CONCLUSIONS: In nine community fee-for-service practices, telephonic nurse case management did not lead to improvement in A1c or SBP. Gains seen in telephonic behavioral self-management interventions in optimal settings may not translate to the wider range of primary care settings.

Patient-provider communication, self-reported medication adherence, and race in a postmyocardial infarction population.

OBJECTIVES: Our objectives were to: 1) describe patient-reported communication with their provider and explore differences in perceptions of racially diverse adherent versus nonadherent patients; and 2) examine whether the association between unanswered questions and patient-reported medication nonadherence varied as a function of patients' race. METHODS: We conducted a cross-sectional analysis of baseline in-person survey data from a trial designed to improve postmyocardial infarction management of cardiovascular disease risk factors. RESULTS: Overall, 298 patients (74%) reported never leaving their doctor's office with unanswered questions. Among those who were adherent and nonadherent with their medications, 183 (79%) and 115 (67%) patients, respectively, never left their doctor's office with unanswered questions. In multivariable logistic regression, although the simple effects of the interaction term were different for patients of nonminority race (odds ratio [OR]: 2.16; 95% confidence interval [CI]: 1.19-3.92) and those of minority race (OR: 1.19; 95% CI: 0.54-2.66), the overall interaction effect was not statistically significant (P=0.24). CONCLUSION: The quality of patient-provider communication is critical for cardiovascular disease medication adherence. In this study, however, having unanswered questions did not impact medication adherence differently as a function of patients' race. Nevertheless, there were racial differences in medication adherence that may need to be addressed to ensure optimal adherence and health outcomes. Effort should be made to provide training opportunities for both patients and their providers to ensure strong communication skills and to address potential differences in medication adherence in patients of diverse backgrounds.

SAXOPHONE SONATAS 1980-2010

The purpose of this dissertation project identifies contemporary solo saxophone literature, specifically sonatas between the years 1980 and 2010. The overwhelming majority of repertoire written during these thirty years consisted primarily of either multi-movement or through-composed character pieces. By limiting the selected repertoire to sonatas one can still investigate the breadth of the literature that has helped validate the saxophone in the realm of classical music in a format that has seemingly fallen out of favor with composers. The saxophone had developed a unique voice by the middle of the twentieth century in both Europe and in the United States. European composers such as Claude Debussy, Florent Schmidt, Jacques Ibert, Darius Milhaud, Alexander Glazounov, Erwin Schulhoff and Bernard Heiden recognized the potential and beauty of the instrument, while the saxophone had found quite a different niche in vaudeville, jazz, and military bands in the United States. If not for the dynamic performances by concert saxophonist such as Marcel Mule, Sigurd Rascher, Jean-Marie Londeix, Daniel Deffayet, Cecil Lesson, Larry Teal, Eugene Rousseau, Fredrick Hemke and Donald Sinta, the timbral possibilities and technical virtuosity of the saxophone would not have been discovered. The awe inspiring performances by these soloists led to the commissioning of a multitude of works by composers looking to expand the sonic possibilities of this relatively new instrument. Through the 1970's American composers such as Leslie Bassett, Paul Creston, Henry Brant, Robert Muczynski, and Karel Husa were writing significant works for the saxophone, while European composers such as IngolfDahl, Edison Denisov, Alfred Desenclos, Henri Tomasi and Marius Constant were each making their own contributions, all leading to a significant quantity of repertoire that met the quality demands set by the performers. The compositions chosen for this dissertation project were selected after numerous performance, pragmatic, programming and pedagogical considerations were taken into account. The three recitals occurred on: March 7, 2010, December 10, 2010 and May 1, 2011 in either the Gildenhorn Recital Hall or Lecture Hall 2100.