bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson–Boltzmann and linear interaction energy approximations
Authors: Wan Shunzhou , Coveney Peter V , Flower Darren R
Published: July 2005

The binding to the T cell receptor of wild-type and variant HTLV-1 Tax peptide complexed to the major histocompatibility complex has been investigated by means of molecular dynamics simulations. The binding free energy difference is calculated using the molecular mechanics Poisson–Boltzmann surface area and linear interaction energy methods. These methods extract useful information on the binding energetics from simulations of the physical states of the ligands, which are more computationally expedient than the commonly used thermodynamic integration method. The successful reproduction of the relative binding free energies shows that these methods can be useful for free energy calculations and the rational design of drugs and vaccines.
X-ray guided modes produced by Bragg reflections of multilayers: an analytical treatment
Authors: Prudnikov I. R.
Published: July 2005

It is analytically shown that X-ray Bragg reflections from periodical multilayer structures can be used for the excitation of guided modes. The X-ray guided modes in (i) a guiding film embedded in a periodical multilayer and (ii) an air gap between two space-separated multilayers have been considered. In the former case, analytical expressions have been obtained which describe a resonant X-ray intensity enhancement taking place inside the guiding film under the guided mode excitation. Optimal parameters of the waveguide have been found, which are needed to achieve a maximum intensity gain. In the latter case, eigen guided modes arising in the air gap have been determined. Properties of the eigen modes have been studied.
Structure development in aerogel-processed nanocrystalline alkaline earth oxides as revealed by SANS
Authors: Hackley Vincent A. , Stoimenov Peter K. , Ho Derek L. , Sung Li Piin , Klabunde Kenneth J.
Published: July 2005

Nanocrystalline MgO, CaO and SrO were prepared according to a modified aerogel process (AP). Small-angle neutron scattering (SANS) was used to probe the nanoscale structural features of these materials after each stage of the synthetic process, including hydrolysis, supercritical drying and calcining. SANS data were interpreted using a classical analysis involving power-law and Guinier regimes, and by application of the maximum entropy method. Results are compared with previously published structural data based on X-ray diffraction, electron microscopy and gas adsorption. It is found that the gel hydrolysis product suspended in methanol and toluene exhibits rod-like scattering at small length scales. This is consistent with a filiform morphology previously reported for air-dried Mg(OH)2alcogel, yet SANS data for air-dried alcogels tested in this study indicate no evidence for low-dimensional structure on any length scale. A previous assertion of mass fractal structure in the AP aerogels and oxides was not confirmed by the present data. Instead, surface fractal scattering was found to be the most dominant characteristic feature associated with the SANS data for all AP powders examined. Additionally, MgO and CaO exhibited a correlation peak that corresponds to liquid-like ordering at Bragg length scales of 5.9 nm and 20.3 nm, respectively. These values are roughly consistent with previous independent estimates of primary particle size, suggesting that local packing of primary crystallites is facilitated by the calcination/dehydration process. An alternative interpretation treats these features as Guinier scattering regions. Fitting of results using the unified Guinier/power-law equation yields sphere-equivalent radii for the primary particles that are nearly identical to the Bragg lengths calculated from the positions of the maxima. Air-dried alcogels produced very weak maxima that could be interpreted either as correlation peaks or as Guinier regions. No maxima were observed for aerogel samples. Maximum entropy analysis using a spherical shape factor produced interesting but complex results for the calculated volume size distributions of these materials. Overall, the observed trend shows an increase in structural feature size with increasing metal cation size.
Surface morphology of {100} faces ofL-arginine phosphate monohydrate single crystals investigated by atomic force microscopy
Authors: Geng Y. L. , Xu D. , Wang X. Q. , Zhang G. H. , Yu G. W. , Sun D. L.
Published: July 2005

Surface morphology of {100} faces of LAP crystals was investigated by atomic force microscopy (AFM). Both the steps and the two-dimensional nuclei elongate along thebdirection, which is determined by the crystal structure. Fluctuations in the growth conditions could result in the formation of protuberances on the step fronts. Tree-like growth belts are initially observed on LAP crystals. It is assumed that the formation is caused by uneven liquid flow of the mother solution.
Energy calibration and full-pattern refinement for strain analysis using energy-dispersive and monochromatic X-ray diffraction
Authors: Liu J. , Kim K. , Golshan M. , Laundy D. , Korsunsky A. M.
Published: July 2005

Precise channel-to-energy conversion is very important in full-pattern refinement in energy-dispersive X-ray diffraction. Careful examination shows that the channel-to-energy conversion is not entirely linear, which presents an obstacle to obtaining accurate quantitative data for lattice strains by pattern refinement. In order to establish an accurate quadratic channel-to-energy conversion function, aMatlabprogram was written to find the best quadratic coefficient and hence the whole energy conversion function. Then this energy conversion function was used to perform a whole-pattern fitting of the energy-dispersive X-ray diffraction pattern of a Ti64 sample. The strain across the Ti64 bar calculated from the fitting results has been compared with values obtained by single-wavelength X-ray diffraction utilizing a Laue monochromator.
Accountability and accessibility: ensuring the evidence of e‐governance in Australia
Authors: Cunningham Adrian , Phillips Margaret
Published: July 2005

Purpose

To review the challenges associated with ensuring the capture and preservation of and long‐term access to government records and publications in the digital age and to describe how libraries and archives in Australia are responding to the challenge.

Design/methodology/approach

Literature‐ and case‐study‐based conceptual analysis of what makes government online information so vulnerable and initiatives at the National Library of Australia and the National Archives of Australia.

Findings

Democracy, governance, consultation and participation all depend on the availability of authentic and reliable information. Government agencies as well as educational and research institutions are producing increasingly large volumes of information in digital formats only. While Australia has done more than most countries to date to address the need to identify, collect, store and preserve government publications and public records in digital formats, large amounts of information are still at risk of loss.

Research limitations/implications

Focuses on circumstances and initiatives in the Australian Government.

Practical implications

Librarians and archivists need to become more proactive in influencing the behaviour of government agencies to ensure that important evidence of democratic governance is created and managed in ways that facilitate their accessibility and long‐term preservation.

Originality/value

Emphasises the vital role that information management agencies such as libraries and archives have to play in supporting transparent and accountable governance in the digital age, and explores innovative strategies for ensuring the long‐term preservation of this important documentary heritage material for the use of future generations.
The central role of leaders in public libraries
Authors: Mullins John , Linehan Margaret
Published: July 2005

Purpose

Aims to explore the topic of leadership as perceived and practised by public library leaders. Library leaders have a wide‐ranging impact on society but have been largely overlooked as the subject of serious study. The current study seeks to investigate the perspectives of public library leaders beyond national boundaries in order to develop an understanding of the perceptions of current leaders in the field of public librarianship.

Design/methodology/approach

A total of 30 senior public library leaders were selected for in‐depth face‐to‐face interviews in three national jurisdictions – Ireland, the UK, and the USA.

Findings

The study of the perceptions of senior public library leaders, across national boundaries, makes a theoretical contribution not just to leadership in librarianship, but also to the broader literature on organizational leadership. Nine main thematic areas emerged from the findings. One of these themes, the centrality of leadership to librarianship, is the particular focus of this paper.

Practical implications

The findings support the centrality of leadership for optimal strategic and operational practices in the field of public librarianship. The challenge for the public library sector is to identify and consider the leadership skills and personal attributes that are essential to success.

Originality/value

Presents a representative sample of insights, reflections and assessments from participating public library leaders regarding the centrality of leadership to librarianship.
Risking knowledge management
Authors: Jones Heather
Published: July 2005

Purpose

To describe the process of conducting an information audit at the Hobart City Council and to demonstrate how the audit contributed to knowledge management at the Council.

Design/methodology/approach

This paper is a personalised account of a pilot information audit conducted in the area of risk management activities across the organisation. It gives an overview of some relevant knowledge management texts, the methodology of the pilot audit and a summary of the findings and outcomes of the project.

Findings

The Council units have yet to implement all the findings and recommendations of the pilot, but there have already been significant outcomes. Units have used the audit to coordinate risk management initiatives and processes with other areas. This has contributed to breaking down the information silos and to the development of a culture of knowledge sharing.

Research limitations/implications

This paper describes the process used for the Pilot Information Audit – Risk Management project, and what happened as a result.

Practical implications

This paper may provide some useful insights to other librarians in a small special library environment with limited resources who are planning to conduct an information audit.

Originality/value

This is an example of an information audit undertaken in a local government setting.
Designing virtual organizations? Themes and trends in political and organizational discourses
Authors: Thorne Kym
Published: July 2005

Purpose

This paper aims to explore the contemporary fascination with seemingly new, benign and transcendent virtual organizations.

Design/methodology/approach

The paper extends Gerlach and Hamilton's investigations and critique into virtuality within the genres of business restructuring and science fiction.

Findings

The paper unravels a purposeful, enveloping consciousness that masks both neo‐liberal fictions and postmodern fantasies dominating the virtual organization discourse. This paper finds that practical examples of de‐physicalized, technologically transcendent virtual organizations, crucial to this virtual consciousness, do not exist or are fundamentally different from expectations. The paper finds that the presumed new epoch of global capitalism, based on the productivity unleashed by virtual organizations, is illusory. The paper concludes that once virtual consciousness is penetrated not only are the material and ideological aspects of virtual organizations unmasked but it is possible to locate a pragmatic, conjoint, physicalized type of “virtualized” organization that is not new, benign or transcendental. This type of co‐destiny, virtual organization (such as terrorist organizations and organized crime), is more reflective of enduring concerns and contemporary purposes fundamental to what organizations make visible or render invisible.

Originality/value

This paper presents an innovative and critical examination of the collusion between neo‐liberal and postmodern thought and the practicalities, or otherwise, of designing virtual organizations. This paper should also be valuable to those concerned with the “virtuality” of terrorist and criminal organizations and the relationship between the visible and invisible aspects of organization.
RFID tags: commercial applications v. privacy rights
Authors: Kelly Eileen P. , Erickson G. Scott
Published: July 2005

Purpose

This article seeks to examine the use of radio frequency identification (RFID) technology in commercial applications and to discuss whether regulation is needed to balance commercial economic interests versus consumer privacy and libertarian concerns.

Design/methodology/approach

This paper covers discussions and comparative studies of others' work and thinking.

Findings

RFID technology provides enormous economic benefits for both business and consumers, while simultaneously potentially constituting one of the most invasive surveillance technologies threatening consumer privacy.

Practical implications

The use of RFID technology has profound consumer privacy, civil liberty and security implications.

Originality/value

RFID technology is at an embryonic stage. Like many new technologies, it poses both potential benefit and harm to society. The article recommends that legislation is needed to tip the balance enough to provide adequate privacy protection without unduly harming economic efficiency.
The evolution of SAP implementation environments
Authors: Gulledge Thomas , Simon Georg
Published: July 2005

Purpose

This paper seeks to describe the evolution of SAP implementation methodologies and tools, in particular, Value SAP, with a focus on the Accelerated SAP (ASAP) implementation methodology and its evolution as a part of SAP's new Solution Manager tool.

Design/methodology/approach

The general approach is more focused on monitoring and managing an ongoing SAP implementation project using an enterprise solution architecture. Three options are explored.

Findings

Finds that one option supports end‐to‐end business process management – other options can be managed, but with cost and risk.

Originality/value

This paper has reviewed the latest developments in SAP implementation methodologies from a management orientation. The issues in this paper are often taken for granted by researchers, so it is hoped that the focus on these issues will elevate interests in pursuing some of the unanswered questions.
Non‐enforceable implementation of enterprise mobilization
Authors: Luarn Pin , Lin Tom M.Y. , Lo Peter K.Y.
Published: July 2005

Purpose

Enterprise mobilization refers to the provision by an enterprise of the means for its employees to update information at any time and any place through the use of a wireless network system and related equipment. The implementation of enterprise mobilization can be separated into two main methods, non‐enforceable and enforceable. Non‐enforceable implementation refers to those situations where, although an enterprise encourages its employees to use a mobilized system, it does not enforce such use, whereas the reverse is true in the case of enforceable methods. Aims to examine this situation.

Design/methodology/approach

Since this is a relatively new research topic with very little previous research having been undertaken in this area, this paper employs a triangulation. This method enables integration of both quantitative and qualitative data, to investigate the critical success factors (CSFs) for the implementation of non‐enforceable mobilization by enterprises. The data were collected by means of in‐depth interviews with corporate managers and specialists from 29 enterprises and comprise 126 samples of employees currently using mobilization systems.

Findings

The study reveals a total of six CSFs for the implementation of non‐enforceable mobilization by enterprises, comprising: cooperation with a good solution “value added reseller”; appropriate planning and the support of senior management; user participation and minimization of any resistance to the installation of the system; open communication channels; enhancement of the understanding of mobilization itself and of employee requirements; and effective mobilization equipment.

Originality/value

This paper will be of interest to organizations looking to implement a wireless network system. The results provided can be used as references for industry and businesses in general, to support their decision‐making processes concerning the introduction of mobilization.
Collaborative supply‐chain partnerships built upon trust and electronically mediated exchange
Authors: Myhr Niklas , Spekman Robert E.
Published: July 2005

Purpose

To investigate how supply‐chain partners can achieve collaboration under varying circumstances (transactional types) by developing trust‐based social foundations and by utilizing electronically mediated exchange.

Design/methodology/approach

A conceptual framework illustrates the roles of trust and electronically mediated exchange in achieving collaboration and its hypotheses are tested with a sample of 157 supply‐chain relationships of international subsidiaries of Nordic multinational corporations (MNCs).

Findings

Finds that collaborative partnerships can be achieved both via trust and through electronically mediated exchange. Results also indicate that electronically mediated exchange more readily enhances collaboration in exchange relationships involving standardized products, while trust plays a larger role when customized products are being exchanged.

Research limitations/implications

The transactional type involved impacts the relative effectiveness of trust and electronically mediated exchange in achieving collaboration. This finding might stimulate research of the impact of other contextual factors. Limitations include that only managers on one side of inter‐organizational dyads were surveyed.

Practical implications

Practicing managers need to prioritize the time and effort they spend developing partnerships. While both trust and electronically mediated exchange play pivotal roles in fostering collaboration, managers involved in the exchange of standardized products can place a relative emphasis on electronically mediated exchange, while trust is of higher importance when customized products are being exchanged.

Originality/value

This paper examines the complex interplay of trust and electronically mediated exchange in achieving collaborative supply‐chain partnerships and offers guidance to practicing managers as well as implications of theoretical interest to academics.
Cooperative adoption of complex systems: a comprehensive model within and across networks
Authors: Hausman Angela , Johnston Wesley J. , Oyedele Adesegun
Published: July 2005

Purpose

The purpose of this study was to develop a better understanding of cooperation among members of network firms.

Design/methodology/approach

An extensive literature review of industrial cooperation/adaptation was conducted, especially research pertaining to industrial adoption of communication technology across partner firms. This review was combined with elements of population ecology, as it has been applied to business networks, and other sociological aspects of inter‐firm relationships to develop a set of propositions related to cooperative adoption.

Findings

This is a conceptual paper, so there were no quantifiable results. Instead, the paper contains a number of propositions related to the relational, structural, and influential aspects that affect adoption and sustained use of innovative products in a network context.

Research limitations/implications

The lack of empirical support for hypothesized relationships is the major limitation. However, the study provides guidance toward empirical testing and suggests a number of managerial implications resulting from the understandings provided by the proposed relationship.

Originality/value

This study helps extend earlier models developed to understand intra‐organizational adoption to reflect the more common situation where adoption occurs within and affects a network of related firms.
The impact of supply‐chain management capabilities on business performance
Authors: Tracey Michael , Lim Jeen‐Su , Vonderembse Mark A.
Published: July 2005

Purpose

The purpose of this article is to empirically test the impact of supply‐chain management (SCM) capabilities on business performance so as to determine to what degree customer‐oriented SCM issues influence competitive position and organizational performance.

Design/methodology/approach

A rigorous methodology is employed to generate a reliable and valid measurement instrument. Responses from 474 manufacturing managers are then utilized to test a causal model using LISREL®.

Findings

The results indicate significant positive relationships exist among three types of SCM capabilities (outside‐in, inside‐out, and spanning) and business performance (perceived customer value, customer loyalty, market performance, and financial performance).

Practical implications

The article demonstrates that strategically developing SCM capabilities such as efficient inbound and outbound transportation, warehousing, and inventory control, production support, packaging, purchasing, order processing, and information dissemination enable a manufacturing firm to identify and take advantage of opportunities in the global marketplace.

Research limitations/implications

The sample was drawn from manufacturing firms in the USA across four SIC codes. Future studies could collect more extensive data to confirm, refine, and expand upon the model presented and the associated construct measures utilizing confirmatory factor analysis. Extending the research to include additional industries and firms from outside of the USA would enhance the generalizability and usefulness of the findings.

Originality/value

The paper statistically validates that managers should regard the cultivation of SCM capabilities as a proprietary resource that facilitates competitive advantage. It also contributes a concise instrument that may be used by academics interested in the areas of supply‐chain management processes and firm performance.
Building an activity‐based costing hospital model using quality function deployment and benchmarking
Authors: González Marvin E. , Quesada Gioconda , Mack Rhonda , Urrutia Ignacio
Published: July 2005

Purpose

To use quality function deployment (QFD)/benchmarking for building an optimal activity‐based costing (ABC) model using baseline information from five different Spanish hospitals.

Design/methodology/approach

The customer satisfaction benchmarking process in QFD is discussed along with the benefits of hierarchical benchmarks in specifying areas of strategic competition and the logically ensuing product/service strategic decision‐making requirements. A case study is presented to illustrate the use of two methodological approaches: benchmarking and QFD to obtain the final product of the paper: an optimal ABC.

Findings

The resulting outcome from the QFD/benchmarking analysis is an ABC model, which has the customer expectations and the requirements that hospitals are looking for.

Research limitations/implications

Future research can benefit from this research by expanding the scope from hospitals to other types of industries in order to comparatively analyze the applicability of the proposed tools, and applying the same methodology to other hospitals for developing a model for a standardized costing system in health care industry.

Practical implications

With the outcomes produced by the methodology applied in this paper, hospital strategic decision makers can now have specifics on which to base decisions regarding the most appropriate allocation of time, human and capital resources.

Originality/value

The paper presents a new approach for developing an optimal ABC for healthcare by applying two important methodologies: benchmarking and QFD. The use and modification of these methodologies in healthcare are new to research for achieving a final ABC model that will easily identify any performance improvements.
Embedding sustainable development at Cambridge University Engineering Department
Authors: Fenner Richard A. , Ainger Charles M. , Cruickshank Heather J. , Guthrie Peter M.
Published: July 2005

Purpose

The paper seeks to examine the latest stage in a process of change aimed at introducing concepts of sustainable development into the activities of the Department of Engineering at Cambridge University, UK.

Design/methodology/approach

The rationale behind defining the skills which future engineers require is discussed and vehicles for change at both undergraduate and postgraduate level are described. Reflections on the paradigms and pedagogy of teaching sustainable development issues to engineers are offered, as well as notes on barriers to progress which have been encountered.

Findings

The paper observes that the ability to effectively initiate a change process is a vital skill which must be formally developed in those engineers wishing to seek sustainable solutions from within the organisations for which they will work. Lessons are drawn about managing a change process within a large academic department, so that concepts of sustainable development can be effectively introduced across all areas of the engineering curriculum.

Practical implications

A new pedagogy for dealing with changes from the quantitative to the qualitative is required, as the paper questions where the education balance should lie between providing access to technological knowledge which can be applied to designing hard solutions, and training engineers to rethink their fundamental attitudes towards a broader, multiple perspective approach in which problem formulation and context setting play a vital role in reaching consensual solutions.

Originality/value

The paper reviews previously recognised key themes for engineering education for sustainable development, and proposes three further essential ingredients relating to an engineer's ability to engage in problem definition, manage change in organisations, and understand the nature of technical and business innovations.
Design of enhanced agonists through the use of a new virtual screening method: Application to peptides that bind class I major histocompatibility complex (MHC) molecules
Authors: Madurga Sergio , Belda Ignasi , Llorà Xavier , Giralt Ernest
Published: July 2005

A new screening procedure is described that uses docking calculations to design enhanced agonist peptides that bind to major histocompatibility complex (MHC) class I receptors. The screening process proceeds via single mutations of one amino acid at the positions that directly interact with the MHC receptor. The energetic and structural effects of these mutations have been studied using fragments of the original ligand that vary in length. The results of these docking studies indicate that the mutant affinity ranking of long peptides can be practically reproduced with a screening approach performed using fragments of six residues. Fragments of four and five residues could mimic, in some cases, the structural arrangement of the side chains of the full‐length peptide. We have compared the structural and energetic results of the docking calculations with experimental data using three unrelated ligand peptides that differ greatly in their affinity for the MHC complex. Analysis of the affinity of the fragments led to the identification of three important parameters in the construction of fragments that mimic the structural and energetic properties of the full‐length ligand: the length of the fragment; its intermolecular energy; and the number and localization, internal or terminal, of the anchor residues. The results of this new peptide‐design methodology have been applied to suggest new peptides derived from the MUC1–8 peptide that could be used as murine vaccines that trigger the immune response through the MHC class I protein H‐2Kb.
Crystal structure of Yersinia enterocolitica type III secretion chaperone SycT
Authors: Büttner Carina R. , Cornelis Guy R. , Heinz Dirk W. , Niemann Hartmut H.
Published: July 2005

Pathogenic Yersinia species use a type III secretion (TTS) system to deliver a number of cytotoxic effector proteins directly into the mammalian host cell. To ensure effective translocation, several such effector proteins transiently bind to specific chaperones in the bacterial cytoplasm. Correspondingly, SycT is the chaperone of YopT, a cysteine protease that cleaves the membrane‐anchor of Rho‐GTPases in the host. We have analyzed the complex between YopT and SycT and determined the structure of SycT in three crystal forms. Biochemical studies indicate a stoichometric effector/chaperone ratio of 1:2 and the chaperone‐binding site contains at least residues 52–103 of YopT. The crystal structures reveal a SycT homodimer with an overall fold similar to that of other TTS effector chaperones. In contrast to the canonical five‐stranded anti‐parallel β‐sheet flanked by three α‐helices, SycT lacks the dimerization α‐helix and has an additional β‐strand capable of undergoing a conformational change. The dimer interface consists of two β‐strands and the connecting loops. Two hydrophobic patches involved in effector binding in other TTS effector chaperones are also found in SycT. The structural similarity of SycT to other chaperones and the spatial conservation of effector‐binding sites support the idea that TTS effector chaperones form a single functional and structural group.
Focus‐Pocus? Thinking Critically about Whether Aid Organizations Should Do Fewer Things in Fewer Countries
Authors: Munro Lauchlan T.
Published: July 2005

The OECD Development Assistance Committee and G7 Finance Ministers have suggested that many bilateral and multilateral aid organizations are too dispersed, pursuing too many objectives in too many countries and too many sectors with too many partners. These organizations are accused of lacking critical mass, failing to follow their comparative advantage, failing to find and exploit a niche, and having high transactions costs and low effectiveness. Such aid organizations are being told to ‘focus’, ‘concentrate’, or be more ‘selective’ in order to become more effective. This article analyses the arguments in favour of greater focus by aid organizations and suggests that, while some of these arguments are valid, some are not and others need to be more nuanced. There are many possible dimensions along which an aid organization could focus and the link — if any — between focus and aid effectiveness is complex along each of those dimensions. The debate so far has also ignored the possibility that less focus may promote more effective aid. There is no clear, simple link between focus and aid effectiveness, but this finding should not be interpreted as carte blanche for spreading aid programmes indiscriminately. Dispersion, like focus, needs careful thought and justification.
Combined small‐cell carcinoma of the stomach: p53 and K‐ras gene mutational analysis supports a monoclonal origin of three histological components
Authors: Han Bo , Mori Ichiro , Wang Xiaojuan , Nakamura Misa , Nakamura Yasushi , Kakudo Kennichi
Published: July 2005

Primary small‐cell carcinoma (SmCC) is extremely rare in stomach. We reported an autopsy case of combined gastric SmCC with p53 and K‐ras mutational analysis. Histologically, the tumour was composed of well‐differentiated adenocarcinoma surrounding the central dominant SmCC component with scattered nests of squamous cell carcinoma. Immunohistochemically, all the neoplastic components revealed strong expression for p53 protein. Based on these findings, we hypothesized that these histologically different components originated from a same progenitor cell that possessed p53 mutation. Using Laser‐capture microdissection technique and mutational analysis, we identified the same point mutations of p53 gene (A→G transversion in codon 239) and K‐ras gene (G→A transversion in codon 13) in all the neoplastic components, but not in the adjacent normal gastric epithelium. Our results strongly support a hypothesis that the combined SmCC of stomach in this case was of monoclonal origin.
Radiation sensitivities of 31 human oesophageal squamous cell carcinoma cell lines
Authors: Ban Sadayuki , Michikawa Yuichi , Ishikawa Ken‐ichi , Sagara Masashi , Watanabe Koji , Shimada Yutaka , Inazawa Johji , Imai Takashi
Published: July 2005

The purpose of this study was to determine the radiosensitivities of 31 human oesophageal squamous cell carcinoma cell lines with a colony‐formation assay. A large variation in radiosensitivity existed among 31 cell lines. Such a large variation may partly explain the poor result of radiotherapy for this cancer. One cell line (KYSE190) demonstrated an unusual radiosensitivity. Ataxia‐telangiectasia‐mutated (ATM) gene in these cells had five missense mutations, and ATM protein was truncated or degraded. Inability to phosphorylate Chk2 in the irradiated KYSE190 cells suggests that the ATM protein in these cells had lost its function. The dysfunctional ATM protein may be a main cause of unusual radiosensitivity of KYSE190 cells. Because the donor of these cells was not diagnosed with ataxia telangiectasia, mutations in ATM gene might have occurred during the initiation and progression of cancer. Radiosensitive cancer developed in non‐hereditary diseased patients must be a good target for radiotherapy.
Dendritic cells in viral pathogenesis: protective or defective?
Authors: Pollara Gabriele , Kwan Antonia , Newton Philippa J. , Handley Matthew E. , Chain Benjamin M. , Katz David R.
Published: July 2005

Dendritic cells (DC) are potent antigen‐presenting cells that are critical in the initiation of immune responses to control and/or eliminate viral infections. Recent studies have investigated the effects of virus infection on the biology of DC. This review summarizes these changes, focusing on both the DC parameters affected and the viral factors involved. In addition, the central role of DC biology in the pathogenesis of several viral families, including herpesviruses, paramyxoviruses and retroviruses, is explored. The field of pathogen recognition by DC is addressed, focusing on its role in protecting the host from viral infection, as well as the ability of viruses to exploit such host receptor ligation and signalling to their replicative advantage. The hypothesis is proposed that virus and host have evolved a symbiotic relationship to ensure both viral transmission and host survival.
Do dams and levees impact nitrogen cycling? Simulating the effects of flood alterations on floodplain denitrification
Authors: Gergel Sarah E. , Carpenter Stephen R. , Stanley Emily H.
Published: July 2005

A fundamental challenge in understanding the global nitrogen cycle is the quantification of denitrification on large heterogeneous landscapes. Because floodplains are important sites for denitrification and nitrogen retention, we developed a generalized floodplain biogeochemical model to determine whether dams and flood‐control levees affect floodplain denitrification by altering floodplain inundation. We combined a statistical model of floodplain topography with a model of hydrology and nitrogen biogeochemistry to simulate floods of different magnitude. The model predicted substantial decreases in NO3‐N processing on floodplains whose overbank floods have been altered by levees and upstream dams. Our simulations suggest that dams may reduce nitrate processing more than setback levees. Levees increased areal floodplain denitrification rates, but this effect was offset by a reduction in the area inundated. Scenarios that involved a levee also resulted in more variability in N processing among replicate floodplains.

Nitrate loss occurred rapidly and completely in our model floodplains. As a consequence, total flood volume and the initial mass of nitrate reaching a floodplain may provide reasonable estimates of total N processing on floodplains during floods. This finding suggests that quantifying the impact of dams and levees on floodplain denitrification may be possible using recent advances in remote sensing of floodplain topography and flood stage. Furthermore, when considering flooding over the long‐term, the cumulative N processed by frequent smaller floods was estimated to be quite large relative to that processed by larger, less frequent floods. Our results suggest that floodplain denitrification may be greatly influenced by the pervasive anthropogenic flood‐control measures that currently exist on most majors river floodplains throughout the world, and may have the potential to be impacted by future changes in flood probabilities that will likely occur as a result of climate shifts.
Tree photosynthesis modulates soil respiration on a diurnal time scale
Authors: Tang Jianwu , Baldocchi Dennis D. , Xu Liukang
Published: July 2005

To estimate how tree photosynthesis modulates soil respiration, we simultaneously and continuously measured soil respiration and canopy photosynthesis over an oak‐grass savanna during the summer, when the annual grass between trees was dead. Soil respiration measured under a tree crown reflected the sum of rhizosphere respiration and heterotrophic respiration; soil respiration measured in an open area represented heterotrophic respiration. Soil respiration was measured using solid‐state CO2 sensors buried in soils and the flux‐gradient method. Canopy photosynthesis was obtained from overstory and understory flux measurements using the eddy covariance method. We found that the diurnal pattern of soil respiration in the open was driven by soil temperature, while soil respiration under the tree was decoupled with soil temperature. Although soil moisture controlled the seasonal pattern of soil respiration, it did not influence the diurnal pattern of soil respiration. Soil respiration under the tree controlled by the root component was strongly correlated with tree photosynthesis, but with a time lag of 7–12 h. These results indicate that photosynthesis drives soil respiration in addition to soil temperature and moisture.
Growth of Eastern Cottonwoods (Populus deltoides) in elevated [CO2] stimulates stand‐level respiration and rhizodeposition of carbohydrates, accelerates soil nutrient depletion, yet stimulates above‐ and belowground biomass production
Authors: Barron‐Gafford Greg , Martens Dean , Grieve Katie , Biel Karl , Kudeyarov Valery , McLain Jean E. T. , Lipson David , Murthy Ramesh
Published: July 2005

We took advantage of the distinctive system‐level measurement capabilities of the Biosphere 2 Laboratory (B2L) to examine the effects of prolonged exposure to elevated [CO2] on carbon flux dynamics, above‐ and belowground biomass changes, and soil carbon and nutrient capital in plantation forest stands over 4 years. Annually coppiced stands of eastern cottonwoods (Populus deltoides) were grown under ambient (400 ppm) and two levels of elevated (800 and 1200 ppm) atmospheric [CO2] in carbon and N‐replete soils of the Intensive Forestry Mesocosm in the B2L. The large semiclosed space of B2L uniquely enabled precise CO2 exchange measurements at the near ecosystem scale. Highly controllable climatic conditions within B2L also allowed for reproducible examination of CO2 exchange under different scales in space and time. Elevated [CO2] significantly stimulated whole‐system maximum net CO2 influx by an average of 21% and 83% in years 3 and 4 of the experiment. Over the 4‐year experiment, cumulative belowground, foliar, and total aboveground biomass increased in both elevated [CO2] treatments. After 2 years of growth at elevated [CO2], early season stand respiration was decoupled from CO2 influx aboveground, presumably because of accelerated fine root production from stored carbohydrates in the coppiced system prior to canopy development and to the increased soil carbohydrate status under elevated [CO2] treatments. Soil respiration was stimulated by elevated [CO2] whether measured at the system level in the undisturbed soil block, by soil collars in situ, or by substrate‐induced respiration in vitro. Elevated [CO2] accelerated depletion of soil nutrients, phosphorus, calcium and potassium, after 3 years of growth, litter removal, and coppicing, especially in the upper soil profile, although total N showed no change. Enhancement of above‐ and belowground biomass production by elevated [CO2] accelerated carbon cycling through the coppiced system and did not sequester additional carbon in the soil.
Remote sensing of heterogeneity in photosynthetic efficiency, electron transport and dissipation of excess light in Populus deltoides stands under ambient and elevated CO2 concentrations, and in a tropical forest canopy, using a new laser‐induced fluorescence transient device
Authors: Ananyev Gennady , Kolber Zbigniew S. , Klimov Dennis , Falkowski Paul G. , Berry Joseph A. , Rascher Uwe , Martin Robin , Osmond Barry
Published: July 2005

Determining the spatial and temporal diversity of photosynthetic processes in forest canopies presents a challenge to the evaluation of biological feedbacks needed for improvement of carbon and climate models. Limited access with portable instrumentation, especially in the outer canopy, makes remote sensing of these processes a priority in experimental ecosystem and climate change research. Here, we describe the application of a new, active, chlorophyll fluorescence measurement system for remote sensing of light use efficiency, based on analysis of laser‐induced fluorescence transients (LIFT). We used mature stands of Populus grown at ambient (380 ppm) and elevated CO2 (1220 ppm) in the enclosed agriforests of the Biosphere 2 Laboratory (B2L) to compare parameters of photosynthetic efficiency, photosynthetic electron transport, and dissipation of excess light measured by LIFT and by standard on‐the‐leaf saturating flash methods using a commercially available pulse‐modulated chlorophyll fluorescence instrument (Mini‐PAM). We also used LIFT to observe the diel courses of these parameters in leaves of two tropical forest dominants, Inga and Pterocarpus, growing in the enclosed model tropical forest of B2L. Midcanopy leaves of both trees showed the expected relationships among chlorophyll fluorescence‐derived photosynthetic parameters in response to sun exposure, but, unusually, both displayed an afternoon increase in nonphotochemical quenching in the shade, which was ascribed to reversible inhibition of photosynthesis at high leaf temperatures in the enclosed canopy. Inga generally showed higher rates of photosynthetic electron transport, but greater afternoon reduction in photosynthetic efficiency. The potential for estimation of the contribution of outer canopy photosynthesis to forest CO2 assimilation, and assessment of its response to environmental stress using remote sensing devices such as LIFT, is briefly discussed.
The effect of elevated CO2 on diel leaf growth cycle, leaf carbohydrate content and canopy growth performance of Populus deltoides
Authors: Walter Achim , Christ Maja M. , Barron‐gafford Greg A. , Grieve Katie A. , Murthy Ramesh , Rascher Uwe
Published: July 2005

Image sequence processing methods were applied to study the effect of elevated CO2 on the diel leaf growth cycle for the first time in a dicot plant. Growing leaves of Populus deltoides, in stands maintained under ambient and elevated CO2 for up to 4 years, showed a high degree of heterogeneity and pronounced diel variations of their relative growth rate (RGR) with maxima at dusk. At the beginning of the season, leaf growth did not differ between treatments. At the end of the season, final individual leaf area and total leaf biomass of the canopy was increased in elevated CO2. Increased final leaf area at elevated CO2 was achieved via a prolonged phase of leaf expansion activity and not via larger leaf size upon emergence. The fraction of leaves growing at 30–40% day−1 was increased by a factor of two in the elevated CO2 treatment. A transient minimum of leaf expansion developed during the late afternoon in leaves grown under elevated CO2 as the growing season progressed. During this minimum, leaves grown under elevated CO2 decreased their RGR to 50% of the ambient value. The transient growth minimum in the afternoon was correlated with a transient depletion of glucose (less than 50%) in the growing leaf in elevated CO2, suggesting diversion of glucose to starch or other carbohydrates, making this substrate temporarily unavailable for growth. Increased leaf growth was observed at the end of the night in elevated CO2. Net CO2 exchange and starch concentration of growing leaves was higher in elevated CO2. The extent to which the transient reduction in diel leaf growth might dampen the overall growth response of these trees to elevated CO2 is discussed.
The impact of recent increases in atmospheric CO2 on biomass production and vegetative retention of Cheatgrass (Bromus tectorum): implications for fire disturbance
Authors: Ziska L. H. , Reeves J. B. , Blank B.
Published: July 2005

Cheatgrass (Bromus tectorum) is a recognized, invasive annual weed of the western United States that reduces fire return times from decades to less than 5 years. To determine the interaction between rising carbon dioxide concentration ([CO2]) and fuel load, we characterized potential changes in biomass accumulation, C : N ratio and digestibility of three cheatgrass populations from different elevations to recent and near‐term projections in atmospheric [CO2]. The experimental CO2 values (270, 320, 370, 420 μmol mol−1) corresponded roughly to the CO2 concentrations that existed at the beginning of the 19th century, that during the 1960s, the current [CO2], and the near‐term [CO2] projection for 2020, respectively. From 25 until 87 days after sowing (DAS), aboveground biomass for these different populations increased 1.5–2.7 g per plant for every 10 μmol mol−1 increase above the 270 μmol mol−1 preindustrial baseline. CO2 sensitivity among populations varied with elevational origin with populations from the lowest elevation showing the greatest productivity. Among all populations, the undigestible portion of aboveground plant material (acid detergent fiber ADF, mostly cellulose and lignin) increased with increasing [CO2]. In addition, the ratio of C : N increased with leaf age, with [CO2] and was highest for the lower elevational population. These CO2‐induced qualitative changes could, in turn, result in potential decreases in herbivory and decomposition with subsequent effects on the aboveground retention of cheatgrass biomass. Overall, these data suggest that increasing atmospheric [CO2] above preambient levels may have contributed significantly to cheatgrass productivity and fuel load with subsequent effects on fire frequency and intensity.