Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation.

BACKGROUND: Fitness costs and slower disease progression are associated with a cytolytic T lymphocyte (CTL) escape mutation T242N in Gag in HIV-1-infected individuals carrying HLA-B*57/5801 alleles. However, the impact of different context in diverse HIV-1 strains on the fitness costs due to the T242N mutation has not been well characterized. To better understand the extent of fitness costs of the T242N mutation and the repair of fitness loss through compensatory amino acids, we investigated its fitness impact in different transmitted/founder (T/F) viruses. RESULTS: The T242N mutation resulted in various levels of fitness loss in four different T/F viruses. However, the fitness costs were significantly compromised by preexisting compensatory amino acids in (Isoleucine at position 247) or outside (glutamine at position 219) the CTL epitope. Moreover, the transmitted T242N escape mutant in subject CH131 was as fit as the revertant N242T mutant and the elimination of the compensatory amino acid I247 in the T/F viral genome resulted in significant fitness cost, suggesting the fitness loss caused by the T242N mutation had been fully repaired in the donor at transmission. Analysis of the global circulating HIV-1 sequences in the Los Alamos HIV Sequence Database showed a high prevalence of compensatory amino acids for the T242N mutation and other T cell escape mutations. CONCLUSIONS: Our results show that the preexisting compensatory amino acids in the majority of circulating HIV-1 strains could significantly compromise the fitness loss due to CTL escape mutations and thus increase challenges for T cell based vaccines.

NAFTA and the apparel commodity chain: Corporate strategies, interfirm networks, and industrial upgrading

The apparel industry is one of the oldest and largest export industries in the world, with global trade and production networks that connect firms and workers in countries at all levels of economic development. This chapter examines the impact of the North American Free Trade Agreement (NAFTA) as one of the most recent and significant developments to affect patterns of international trade and production in the apparel and textile industries. Tr ade policies are changing the institutional environment in which firms in this industry operate, and companies are responding to these changes with new strategies designed to increase their profitability and strengthen their control over the apparel commodity chain. Our hypothesis is that lead firms are establishing qualitatively different kinds of regional production networks in North America from those that existed prior to NAFTA, and that these networks have important consequences for industrial upgrading in the Mexican textile and apparel industries. Post-NAFTA crossborder production arrangements include full-package networks that link lead firms in the United States with apparel and textile manufacturers, contractors, and suppliers in Mexico. Full-package production is increasing the local value added provided by the apparel commodity chain in Mexico and creating new opportunities for Mexican firms and workers. The chapter is divided into four main sections. The first section uses trade and production data to analyze shifts in global apparel flows, highlighting the emergence and consolidation of a regional trade bloc in North America. The second section discusses the process of industrial upgrading in the apparel industry and introduces a distinction between assembly and full-package production networks. The third section includes case studies based on published industry sources and strategic interviews with several lead companies whose strategies are largely responsible for the shifting trade patterns and NAFTA-inspired cross-border production networks discussed in the previous section. The fourth section considers the implications of these changes for employment in the North American apparel industry. © 2009 by Temple University Press. All rights reserved.

Economic and Social Upgrading in Global Value Chains and Industrial Clusters: Why Governance Matters

© 2014, Springer Science+Business Media Dordrecht.The burgeoning literature on global value chains (GVCs) has recast our understanding of how industrial clusters are shaped by their ties to the international economy, but within this context, the role played by corporate social responsibility (CSR) continues to evolve. New research in the past decade allows us to better understand how CSR is linked to industrial clusters and GVCs. With geographic production and trade patterns in many industries becoming concentrated in the global South, lead firms in GVCs have been under growing pressure to link economic and social upgrading in more integrated forms of CSR. This is leading to a confluence of “private governance” (corporate codes of conduct and monitoring), “social governance” (civil society pressure on business from labor organizations and non-governmental organizations), and “public governance” (government policies to support gains by labor groups and environmental activists). This new form of “synergistic governance” is illustrated with evidence from recent studies of GVCs and industrial clusters, as well as advances in theorizing about new patterns of governance in GVCs and clusters.

The tithe: Public research university STEM faculty perspectives on sponsored research indirect costs

This study sought to understand the phenomenon of faculty involvement in indirect cost under-recovery. The focus of the study was on public research university STEM (science, technology, engineering and mathematics) faculty, and their perspectives on, and behavior towards, a higher education fiscal policy. The explanatory scheme was derived from anthropological theory, and incorporated organizational culture, faculty socialization, and political bargaining models in the conceptual framework. This study drew on two key assumptions. The first assumption was that faculty understanding of, and behavior toward, indirect cost recovery represents values, beliefs, and choices drawn from the distinct professional socialization and distinct culture of faculty. The second assumption was that when faculty and institutional administrators are in conflict over indirect cost recovery, the resultant formal administrative decision comes about through political bargaining over critical resources. The research design was a single site, qualitative case study with a focus on learning the meaning of the phenomenon as understood by the informants. In this study the informants were tenured and tenure track research university faculty in the STEM fields who were highly successful at obtaining Federal sponsored research funds, with individual sponsored research portfolios of at least one million dollars. The data consisted of 11 informant interviews, bolstered by documentary evidence. The findings indicated that faculty socialization and organizational culture were the most dominant themes, while political bargaining emerged as significantly less prominent. Public research university STEM faculty are most concerned about the survival of their research programs and the discovery facilitated by their research programs. They resort to conjecture when confronted by the issue of indirect cost recovery. The findings direct institutional administrators to consider less emphasis on compliance and hierarchy when working with expert professionals such as science faculty. Instead a more effective focus might be on communication and clarity in budget processes and organizational decision-making, and a concentration on critical administrative support that can relieve faculty administrative burdens. For higher education researchers, the findings suggest that we need to create more sophisticated models to help us understand organizations dependent on expert professionals.

Interacción genotipo por ambiente sobre caracteres de calidad comercial e industrial en trigo pan (Triticum aestivum L.)

El genotipo (G), el ambiente (A) y la interacción G x A pueden influir de manera diferente sobre las característica que definen la calidad comercial e industrial de trigo pan. Los objetivos de esta tesis fueron: 1) Caracterizar el rendimiento y a sus componentes en cultivares de trigo pertenecientes a diferentes grupos de calidad, expuestos a ofertas de nitrógeno contrastantes. 2) Estudiar el impacto de distinta disponibilidad de nitrógeno sobre los componentes fisiológicos del llenado de los granos (i.e tasa y duración) en distintaas variedades de trigo pan y su posible efecto sobre los parámetros de calidad. 3) Caracterizar y cuantificar la interacción genotipo por ambiente sobre la expresión de los parámetros que determinan el rendimiento y la calidad comercial e industrial del trigo pan en ambientes con diferentes disponibilidades de nitrógeno. Se realizaron ensayos en dos localidades, durante dos años, utilizando seis variedades de distinta aptitud panadera (2 de cada grupo de clasificación por grupo de calidad -GC-), aplicando cuatro tratamientos de fertilización nitrogenadas. Se evaluó el efecto genético, ambiental y la interacción G x A, sobre el rendimiento y sus componentes, el peso de los granos y sus componentes y sobre los parámetros de calidad comercial e industrial. Los resultados mostraron que el rendimiento y sus componentes (número de granos, biomasa aérea, eficiencia de uso de la radiación interceptada acumulada) fueron afectados principalmente por el ambiente y el manejo nutricional dentro de de cada ambiente. Para el peso de los granos y sus componentes (tasa y duración) el efecto del manejo del nitrógeno no fue importante, aunque sí lo fue el efecto genotipo. Para los parámetros de calidad el efecto genotipo fue más importante solo para la tenacidad, mientras que el peso hectolítrico, gluten húmedo, fuerza panadera, la relación de equilibrio (P/L) y volumen de pan fueron modificados principalmente por el efecto ambiente no manejable como son el año y la localidad, en tanto la proteína fue afectada principalmente por el factor ambiental asociado al manejo nutricional. La interacción GxA fue el efecto que explicó en mayor medida las variaciones de rendimiento de harina, absorción de agua y tiempo de amasado. La fuerte interacción GxA observada para la mayoría de los parámetros de calidad determinó que variedades de un determinado GC cambien de grupo asociado principalmente a factores ambientales como la localidad y el año, mientras que el manejo nutricional tuvo un impacto menor

The importance of operating costs about making decisions in farm machine labor contractors services : the case of Cordoba province

p.47-59

Momento de ocurrencia, magnitud y reiteración de lluvias como determinante del lavado del grano de trigo y su efecto en la calidad comercial e industrial

p.45-53

Interacción genotipo por ambiente sobre caracteres de calidad comercial e industrial en trigo pan (Triticum aestivum L.)

El genotipo (G), el ambiente (A)y la interacción G x A pueden influir de manera diferente sobre las característica que definen la calidad comercial e industrial de trigo pan. Los objetivos de esta tesis fueron: 1)Caracterizar el rendimiento y a sus componentes en cultivares de trigo pertenecientes a diferentes grupos de calidad, expuestos a ofertas de nitrógeno contrastantes. 2)Estudiar el impacto de distinta disponibilidad de nitrógeno sobre los componentes fisiológicos del llenado de los granos (i.e tasa y duración)en distintaas variedades de trigo pan y su posible efecto sobre los parámetros de calidad. 3)Caracterizar y cuantificar la interacción genotipo por ambiente sobre la expresión de los parámetros que determinan el rendimiento y la calidad comercial e industrial del trigo pan en ambientes con diferentes disponibilidades de nitrógeno. Se realizaron ensayos en dos localidades, durante dos años, utilizando seis variedades de distinta aptitud panadera (2 de cada grupo de clasificación por grupo de calidad -GC-), aplicando cuatro tratamientos de fertilización nitrogenadas. Se evaluó el efecto genético, ambiental y la interacción G x A, sobre el rendimiento y sus componentes, el peso de los granos y sus componentes y sobre los parámetros de calidad comercial e industrial. Los resultados mostraron que el rendimiento y sus componentes (número de granos, biomasa aérea, eficiencia de uso de la radiación interceptada acumulada)fueron afectados principalmente por el ambiente y el manejo nutricional dentro de de cada ambiente. Para el peso de los granos y sus componentes (tasa y duración)el efecto del manejo del nitrógeno no fue importante, aunque sí lo fue el efecto genotipo. Para los parámetros de calidad el efecto genotipo fue más importante solo para la tenacidad, mientras que el peso hectolítrico, gluten húmedo, fuerza panadera, la relación de equilibrio (P/L)y volumen de pan fueron modificados principalmente por el efecto ambiente no manejable como son el año y la localidad, en tanto la proteína fue afectada principalmente por el factor ambiental asociado al manejo nutricional. La interacción GxA fue el efecto que explicó en mayor medida las variaciones de rendimiento de harina, absorción de agua y tiempo de amasado. La fuerte interacción GxA observada para la mayoría de los parámetros de calidad determinó que variedades de un determinado GC cambien de grupo asociado principalmente a factores ambientales como la localidad y el año, mientras que el manejo nutricional tuvo un impacto menor

Efecto del pastoreo del trigo sobre el rendimiento y la calidad industrial del grano

p.93-102

Costos de localización en el complejo agroindustrial arrocero argentino, cambios ocurridos en la última década : comparación con la situación en Uruguay

p.13-31

Modelling of industrial multi-physics processes—a key role for computational mechanics.

In the analysis of industrial processes, there is an increasing emphasis on systems governed by interacting continuum phenomena. Mathematical models of such multi-physics processes can only be achieved for practical simulations through computational solution procedures—computational mechanics. Examples of such multi-physics systems in the context of metals processing are used to explore some of the key issues. Finite-volume methods on unstructured meshes are proposed as a means to achieve efficient rapid solutions to such systems. Issues associated with the software design, the exploitation of high performance computers, and the concept of the virtual computational-mechanics modelling laboratory are also addressed in this context.

Bulk synchronous parallelization of industrial electromagentic software

The parallelization of existing/industrial electromagnetic software using the bulk synchronous parallel (BSP) computation model is presented. The software employs the finite element method with a preconditioned conjugate gradient-type solution for the resulting linear systems of equations. A geometric mesh-partitioning approach is applied within the BSP framework for the assembly and solution phases of the finite element computation. This is combined with a nongeometric, data-driven parallel quadrature procedure for the evaluation of right-hand-side terms in applications involving coil fields. A similar parallel decomposition is applied to the parallel calculation of electron beam trajectories required for the design of tube devices. The BSP parallelization approach adopted is fully portable, conceptually simple, and cost-effective, and it can be applied to a wide range of finite element applications not necessarily related to electromagnetics.

Evaluating the effectiveness of Z: The claims made about CICS and where we go from here

There have been few genuine success stories about industrial use of formal methods. Perhaps the best known and most celebrated is the use of Z by IBM (in collaboration with Oxford University's Programming Research Group) during the development of CICS/ESA (version 3.1). This work was rewarded with the prestigious Queen's Award for Technological Achievement in 1992 and is especially notable for two reasons: 1) because it is a commercial, rather than safety- or security-critical, system and 2) because the claims made about the effectiveness of Z are quantitative as well as qualitative. The most widely publicized claims are: less than half the normal number of customer-reported errors and a 9% savings in the total development costs of the release. This paper provides an independent assessment of the effectiveness of using Z on CICS based on the set of public domain documents. Using this evidence, we believe that the case study was important and valuable, but that the quantitative claims have not been substantiated. The intellectual arguments and rationale for formal methods are attractive, but their widespread commercial use is ultimately dependent upon more convincing quantitative demonstrations of effectiveness. Despite the pioneering efforts of IBM and PRG, there is still a need for rigorous, measurement-based case studies to assess when and how the methods are most effective. We describe how future similar case studies could be improved so that the results are more rigorous and conclusive.

Numerical predictions of particle degradation in industrial-scale pneumatic conveyors

This paper presents an Eulerian-based numerical model of particle degradation in dilute-phase pneumatic conveying systems including bends of different angles. The model shows reasonable agreement with detailed measurements from a pilot-sized pneumatic conveying system and a much larger scale pneumatic conveyor. The potential of the model to predict degradation in a large-scale conveying system from an industrial plant is demonstrated. The importance of the effect of the bend angle on the damage imparted to the particles is discussed.