Sensitivity analysis and experimental design of a stiff signal transduction pathway model

Sensitivity analysis is normally used to analyze how sensitive a system is with respect to the change of parameters or initial conditions and is perhaps best known in systems biology via the formalism of metabolic control analysis [1, 2]. The nuclear factor B (NF-B) signalling pathway is an important cellular signalling pathway, of which protein phosphorylation is a major factor controlling the activation of further downstream events. The NF-κB proteins regulate numerous genes that play important roles in inter- and intra-cellular signalling, cellular stress responses, cell growth, survival, and apoptosis. As such, its specificity and its role in the temporal control of gene expression are of crucial physiological interest

Comment on "Fisheries Management"

The recent article by O’Leary et al. (2011) raises an important question about the relationship between science and those who manage fisheries. They contend that fishery managers do not give due cognisance to scientific advice and consistently set Total Allowable Catches (TACs) above values advised by scientists (which they define as ‘‘political adjustment’’). The authors claim that the consequence of this is that there is a high probability of stock collapse in the next 40 years. They use a simulation model to argue that this probability may exceed 80% at the mean level of political adjustment adopted by managers, depending on the degree of environmental variability and life history strategy of the fish

Study of an attitude control system for the astronaut maneuvering unit final report, dec. 1963 - jul. 1964

Attitude control system for astronaut maneuvering unit

A Different Level of Caring: Navigating the Intersections of Perception of Care in Teaching

This study sought to predict teacher’s perceptions of caring. We surveyed 457 educators using the Caring Abilities Inventory (Nkongho, 1990). Due to the ever increasing diversity of American classrooms, it is critical to determine how to best recognize, recruit, and prepare the next generation of teachers. Findings indicated differences in caring among gender and race. Implications for teacher preparation programs could be a need to gain insight into gendered and racial notions of care

Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Citation: Reppert, M., Kell, A., Pruitt, T., & Jankowiak, R. (2015). Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers. Journal of Chemical Physics, 142(9), 7. doi:10.1063/1.4913685The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(omega) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, omega(sp), for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers. (c) 2015 AIP Publishing LLC

Using TEI for an Endangered Language Lexical Resource: The Nxaʔamxcín Database-Dictionary Project

This paper describes the evolution of a lexical resource project for Nxaʔamxcín, an endangered Salish language, from the project’s inception in the 1990s, based on legacy materials recorded in the 1960s and 1970s, to its current form as an online database that is transformable into various print and web-based formats for varying uses. We illustrate how we are using TEI P5 for data-encoding and archiving and show that TEI is a mature, reliable, flexible standard which is a valuable tool for lexical and morphological markup and for the production of lexical resources. Lexical resource creation, as is the case with language documentation and description more generally, benefits from portability and thus from conformance to standards (Bird and Simons 2003, Thieberger 2011). This paper therefore also discusses standards-harmonization, focusing on our attempt to achieve interoperability in format and terminology between our database and standards proposed for LMF, RELISH and GOLD. We show that, while it is possible to achieve interoperability, ultimately it is difficult to do so convincingly, thus raising questions about what conformance to standards means in practice.National Foreign Language Resource Cente

CWRML: representing crop wild relative conservation and use data in XML

Background Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Results Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. Conclusion CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may be valuable, particularly with regard to the representation of population-specific data and utilisation potential. As crop wild relatives are intrinsically no different to other wild plant species there is potential for the inclusion of CWRML data elements in the emerging standards for representation of biodiversity data