bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colonial officers and gentlemen: the British Empire and the globalization of ‘tradition’
Authors: Misra Maria 
Published: July 2008

AbstractThis article asks why simplistic accounts of the British Empire as a modernizing force have been so popular in recent years. It contends that, aside from the obvious ideological appeal of these views to some, academic literature has found it difficult to offer a powerful rebuttal. This article argues that in order to do so we need to think more comparatively about the British Empire as a system, and to restore attention to imperial agency. However, this is not best achieved through a traditional study of high politics, but by bringing cultural historical approaches to the study of Britain’s lower imperial cadre. The second half of the article offers a preliminary analysis of the attitudes of local colonial officers. It argues that, contrary to the arguments of neo-imperialist popular historians, this group was hostile to modernization, and in many cases was determined to maintain or restore what they regarded as a traditional order.
Serfs, slaves, or wage earners? The legal status of labour in Russia from a comparative perspective, from the sixteenth to the nineteenth century
Authors: Stanziani Alessandro 
Published: July 2008

AbstractComparative analyses of labour in Russia and the West often assume a dividing line between free and forced labour that is universally applicable. The first aim of this article is to show that, in Russia, the historical and institutional definition of serfdom poses a problem. I will therefore explore Russian legislation, and how it was applied, from the sixteenth to the nineteenth century. Contrary to generally accepted arguments, serfdom as such was never clearly introduced institutionally in Russia. I will also discuss the presence of slaves in Russia, and the association between certain forms of servitude (especially for debt) and slavery. The presence of chattel slaves in the empire was related to territorial expansion, and to commercial relations with the Caucasus and the Ottoman Empire. Russian forms of bondage are compared to those in other situations, such as indentured service in the West, debt servitude in India, and Islamic slavery. My conclusion is that, not only in Russia but also around the globe, the prevailing forms of labour were not those familiar to us today, which were not introduced until the early twentieth century. Russia constituted an extreme case in a world in which severe constraints were imposed everywhere on labour and its movement, and the legal status of the wage earner and the peasant was lower than that of the master.
In the Russians’ steppes: the introduction of Russian wheat on the Great Plains of the United States of America
Authors: Moon David 
Published: July 2008

AbstractIn the late nineteenth and early twentieth centuries, wheat varieties from the Russian steppes were introduced on the Great Plains of the USA, a region with a similar environment. The introduction was partly a by-product of the migration of German farmers from the steppes to the Great Plains in the 1870s. The US Department of Agriculture, eager to promote American wheat production in a competitive world market for grain in which Russia was in the lead, sought out wheat varieties on the steppes that were suitable for the Great Plains. Russian wheat varieties became mainstays on the Great Plains for the next few decades, while Russian agriculture declined under Soviet power. On the basis of research on both sides of the Atlantic, this article sheds light on an important aspect of the global exchange of peoples and crops that has shaped the agricultural and economic history of societies around the world since the invention of agriculture.
Commoners in the process of Islamization: reassessing their role in the light of evidence from southeastern Tanzania
Authors: Becker Felicitas 
Published: July 2008

AbstractMany societies became Muslim gradually, without conquest by Muslim rulers. Explanations of this process typically focus on Muslim traders, proselytizing ‘holy men’, and the conversion of ruling elites, as the limited sources suggest. Yet it cannot be assumed that Islamization always made sense for elites as a power-enhancing stratagem, or that rulers or holy men were willing or able to shape the religious allegiances of commoners. In fact, studies of contemporary Islamic societies demonstrate the relative autonomy of commoners’ religious observance, and the tendency of elites towards accommodation. Evidence from a recently Islamized region in East Africa shows that, rather than following elite converts, ordinary villagers initiated rural Islamization. They learned from coastal Muslim ritual rather than scripture, and evoked Islam to challenge social hierarchies and assert a more egalitarian social ethos. The possibility of similar processes also exists in other sites of gradual Islamization.
Microbial contributions to climate change through carbon cycle feedbacks
Authors: Bardgett Richard D , Freeman Chris , Ostle Nicholas J 
Published: July 2008

Abstract
There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle–climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land–atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land–atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.
Fluoroscopy-guided percutaneous lung biopsy: a valuable alternative to computed tomography
Authors: Kurban L. A. , Gomersall L. , Weir J. , Wade P. 
Published: July 2008

Background: Computed tomography (CT) fluoroscopy nowadays is the most preferred method of guidance to perform percutaneous lung biopsy of pulmonary masses. Conventional fluoroscopy is an increasingly forgotten technique that still can be used to perform lung biopsies, with many advantages. Purpose: To compare the accuracy, safety, and effective dose (ED) of conventional fluoroscopy-guided needle lung biopsy (FNLB) with CT-guided needle lung biopsy procedures (CTNLB) reported in the literature. Material and Methods: 100 consecutive patients who underwent FNLB were reviewed retrospectively. Using the final histological diagnoses and the clinical and radiological course of the disease as references, the accuracy and sensitivity of FNLB were calculated. The complication rates of FNLB were assessed. Using computer software (XDOSE), the ED was calculated. The accuracy, complication rates, and the ED of FNLB were compared with CTNLB reported in the literature. Results: The overall accuracy rate and sensitivity of FNLB were both 87%, which are comparable to the range of accuracies reported in the literature for CTNLB (74–97%). The complication rates of FNLB were also comparable to the complication rates reported for CTNLB. The commonest complication was pneumothorax, at a rate of 25%. The ED of FNLB was small, significantly lower than reported in the literature for CT-guided procedures. The mean ED of FNLB was 0.029 mSv, which is approximately equivalent to one chest X-ray. Conclusion: Conventional fluoroscopy is an accurate, safe, and low-dose alternative modality to CT to obtain an image-guided histological diagnosis of pulmonary lesions.
Quantitative renal cortical perfusion in human subjects with magnetic resonance imaging using iron-oxide nanoparticles: influence of t1 shortening
Authors: Morell A. , Ahlstrom H. , Schoenberg S. O. , Abildgaard A. , Bock M. , Bjørnerud A. 
Published: July 2008

Background: Using conventional contrast agents, the technique of quantitative perfusion by observing the transport of a bolus with magnetic resonance imaging (MRI) is limited to the brain due to extravascular leakage. Purpose: To perform quantitative perfusion measurements in humans with an intravascular contrast agent, and to estimate the influence of the T1 relaxivity of the contrast agent on the first-pass response. Material and Methods: Renal cortical perfusion was measured quantitatively in six patients with unilateral renal artery stenosis using a rapid gradient double-echo sequence in combination with an intravenous bolus injection of NC100150 Injection, an intravascular contrast agent based on iron-oxide nanoparticles. The influence of T1 relaxivity was measured by comparing perfusion results based on single- and double-echo data. Results: The mean values of cortical blood flow, cortical blood volume, and mean transit time in the normal kidneys were measured to 339±60 ml/min/100 g, 41±8 ml/100 g, and 7.3±1.0 s, respectively, based on double-echo data. The corresponding results based on single-echo data, which are not compensated for the T1 relaxivity, were 254±47 ml/min/100 g, 27±3 ml/100 g, and 6±1.2 s, respectively. Conclusion: The use of a double-echo sequence enabled elimination of confounding T1 effects and consequent systematic underestimation of the perfusion.
Differential diagnosis between osteomyelitis and bone tumors
Authors: Shimose S. , Sugita T. , Kubo T. , Matsuo T. , Nobuto H. , Ochi M. 
Published: July 2008

Background: Hematogenous osteomyelitis is often difficult to distinguish from a bone tumor because clinical findings are noncontributory and radiological features can mimic a bone tumor. Recently, the penumbra sign, a higher signal intensity feature of the thin layer of granulation tissue which lines the abscess cavity on T1-weighted magnetic resonance (MR) images, has been reported to be helpful for discriminating subacute osteomyelitis. Purpose: To determine helpful findings for distinguishing osteomyelitis from bone tumors. Material and Methods: The laboratory and imaging findings of a consecutive series of 244 patients referred to our institution with a suspected bone tumor were reviewed. There were 15 cases of osteomyelitis, 160 bone tumors, and 69 tumor-like lesions. Results: In osteomyelitis, the C-reactive protein (CRP) level increased in nine patients and the penumbra sign was seen in 11 patients. In bone tumors and tumor-like lesions, a high CRP level was observed in 21 patients and the penumbra sign was seen in two patients. The sensitivity of the penumbra sign for osteomyelitis was 73.3%, with a specificity of 99.1%. Conclusion: The penumbra sign and a high CRP level support the diagnosis of osteomyelitis and may help to exclude the presence of a tumor.
Rapid Antibacterial Activity of 2 Novel Hand Soaps: Evaluation of the Risk of Development of Bacterial Resistance to the Antibacterial Agents
Authors: Geraldo Ingrid M. , Gilman Allan , Shintre Milind S. , Modak Shanta M. 
Published: July 2008

Objective.To evaluate the antimicrobial efficacy of and risk of organisms developing resistance to 2 novel hand soaps: (1) a soap containing triclosan, polyhexamethylene biguanide, and benzethonium chloride added to a soap base (TPB soap); and (2) a soap containing farnesol, polyhexamethylene biguanide, and benzethonium chloride added to a soap base (FPB soap). Tests also included soaps containing only triclosan.Design.The risk of emergence of resistant bacterial mutants was investigated by determining the susceptibility changes after repeated exposure of bacteria to the drugs and soaps in vitro. The effectiveness of the soaps was evaluated using an in vitro tube dilution method, a volunteer method (the ASTM standard), and 2 pig skin methods.Results.The minimum inhibitory concentration and minimum bactericidal concentration of triclosan against Staphylococcus, aureus increased 8- to 62.5-fold, whereas those of TPB and FPB (both alone and in soap) were unchanged. In vitro, TPB and FPB soaps produced higher log10 reductions in colony-forming units of all tested organisms (4.95-8.58) than did soaps containing triclosan alone (0.29-4.86). In the test using the pig skin and volunteer methods, TPB soap produced a higher log10 reduction in colony-forming units (3.1-3.3) than did the soap containing triclosan alone (2.6-2.8).Conclusion.The results indicate that TPB and FPB soaps may provide superior rapid and broad-spectrum efficacy with a lower risk of organisms developing resistance than do soaps containing triclosan alone. Pig skin methods may be used to predict the efficacy of antibacterial soaps in the rapid disinfection of contaminated hands. Hand washing with TPB and FPB soaps by healthcare workers and the general population may reduce the transmission of pathogens, with a lower risk of promoting the emergence of resistant organisms.
Synchronous versus asynchronous modeling of gene regulatory networks
Authors: Garg Abhishek , Di Cara Alessandro , Xenarios Ioannis , Mendoza Luis , De Micheli Giovanni 
Published: July 2008

Abstract
Motivation: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, protein–protein and gene–protein interactions. The two dynamical properties that are often experimentally testable are perturbations and stable steady states. Although a lot of work has been done on the identification of steady states, not much work has been reported on in silico modeling of cellular differentiation processes.
Results: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks. Algorithms for synchronous and asynchronous transition models have been proposed and their corresponding computational properties have been analyzed. These algorithms allow users to compute cyclic attractors of large networks that are currently not feasible using existing software.
Hereby we provide a framework to analyze the effect of multiple gene perturbation protocols, and their effect on cell differentiation processes. These algorithms were validated on the T-helper model showing the correct steady state identification and Th1–Th2 cellular differentiation process.
Availability: The software binaries for Windows and Linux platforms can be downloaded from http://si2.epfl.ch/~garg/genysis.html.
Contact: abhishek.garg@epfl.ch
Yale Image Finder (YIF): a new search engine for retrieving biomedical images
Authors: Xu Songhua , McCusker Jamie , Krauthammer Michael 
Published: July 2008

Abstract
Summary: Yale Image Finder (YIF) is a publicly accessible search engine featuring a new way of retrieving biomedical images and associated papers based on the text carried inside the images. Image queries can also be issued against the image caption, as well as words in the associated paper abstract and title. A typical search scenario using YIF is as follows: a user provides few search keywords and the most relevant images are returned and presented in the form of thumbnails. Users can click on the image of interest to retrieve the high resolution image. In addition, the search engine will provide two types of related images: those that appear in the same paper, and those from other papers with similar image content. Retrieved images link back to their source papers, allowing users to find related papers starting with an image of interest. Currently, YIF has indexed over 140 000 images from over 34 000 open access biomedical journal papers.
Availability: http://krauthammerlab.med.yale.edu/imagefinder/
Contact: michael.krauthammer@yale.edu
Dynamical modeling and multi-experiment fitting with PottersWheel
Authors: Maiwald Thomas , Timmer Jens 
Published: July 2008

Abstract
Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization.
Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian- and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator–optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox.
Availability: PottersWheel is freely available for academic usage at http://www.PottersWheel.de/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes.
Contact: maiwald@fdm.uni-freiburg.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Immunolocalization of Solanaceous SUT1 Proteins in Companion Cells and Xylem Parenchyma: New Perspectives for Phloem Loading and Transport
Authors: Schmitt Bianca , Stadler Ruth , Sauer Norbert 
Published: July 2008

Abstract
Leaf sucrose (Suc) transporters are essential for phloem loading and long-distance partitioning of assimilates in plants that load their phloem from the apoplast. Suc loading into the phloem is indispensable for the generation of the osmotic potential difference that drives phloem bulk flow and is central for the long-distance movement of phloem sap compounds, including hormones and signaling molecules. In previous analyses, solanaceous SUT1 Suc transporters from tobacco (Nicotiana tabacum), potato (Solanum tuberosum), and tomato (Solanum lycopersicum) were immunolocalized in plasma membranes of enucleate sieve elements. Here, we present data that identify solanaceous SUT1 proteins with high specificity in phloem companion cells. Moreover, comparisons of SUT1 localization in the abaxial and adaxial phloem revealed higher levels of SUT1 protein in the abaxial phloem of all three solanaceous species, suggesting different physiological roles for these two types of phloem. Finally, SUT1 proteins were identified in files of xylem parenchyma cells, mainly in the bicollateral veins. Together, our data provide new insight into the role of SUT1 proteins in solanaceous species.
A Novel Type of Thioredoxin Dedicated to Symbiosis in Legumes
Authors: Alkhalfioui Fatima , Renard Michelle , Frendo Pierre , Keichinger Corinne , Meyer Yves , Gelhaye Eric , Hirasawa Masakazu , Knaff David B. , Ritzenthaler Christophe , Montrichard Françoise 
Published: July 2008

Abstract
Thioredoxins (Trxs) constitute a family of small proteins in plants. This family has been extensively characterized in Arabidopsis (Arabidopsis thaliana), which contains six different Trx types: f, m, x, and y in chloroplasts, o in mitochondria, and h mainly in cytosol. A detailed study of this family in the model legume Medicago truncatula, realized here, has established the existence of two isoforms that do not belong to any of the types previously described. As no possible orthologs were further found in either rice (Oryza sativa) or poplar (Populus spp.), these novel isoforms may be specific for legumes. Nevertheless, on the basis of protein sequence and gene structure, they are both related to Trxs m and probably have evolved from Trxs m after the divergence of the higher plant families. They have redox potential values similar to those of the classical Trxs, and one of them can act as a substrate for the M. truncatula NADP-Trx reductase A. However, they differ from classical Trxs in that they possess an atypical putative catalytic site and lack disulfide reductase activity with insulin. Another important feature is the presence in both proteins of an N-terminal extension containing a putative signal peptide that targets them to the endoplasmic reticulum, as demonstrated by their transient expression in fusion with the green fluorescent protein in M. truncatula or Nicotiana benthamiana leaves. According to their pattern of expression, these novel isoforms function specifically in symbiotic interactions in legumes. They were therefore given the name of Trxs s, s for symbiosis.
Enhanced Tolerance to Oxidative Stress in Transgenic Arabidopsis Plants Expressing Proteins of Unknown Function
Authors: Luhua Song , Ciftci-Yilmaz Sultan , Harper Jeffery , Cushman John , Mittler Ron 
Published: July 2008

Abstract
Over one-quarter of all plant genes encode proteins of unknown function that can be further classified as proteins with obscure features (POFs), which lack currently defined motifs or domains, or proteins with defined features, which contain at least one previously defined domain or motif. Although empirical data in the form of transcriptome and proteome profiling suggest that many of these proteins play important roles in plants, their functional characterization remains one of the main challenges in modern biology. To begin the functional annotation of proteins with unknown function, which are involved in the oxidative stress response of Arabidopsis (Arabidopsis thaliana), we generated transgenic Arabidopsis plants that constitutively expressed 23 different POFs (four of which were specific to Arabidopsis) and 18 different proteins with defined features. All were previously found to be expressed in response to oxidative stress in Arabidopsis. Transgenic plants were tested for their tolerance to oxidative stress imposed by paraquat or t-butyl hydroperoxide, or were subjected to osmotic, salinity, cold, and heat stresses. More than 70% of all expressed proteins conferred tolerance to oxidative stress. In contrast, &gt;90% of the expressed proteins did not confer enhanced tolerance to the other abiotic stresses tested, and approximately 50% rendered plants more susceptible to osmotic or salinity stress. Two Arabidopsis-specific POFs, and an Arabidopsis and Brassica-specific protein of unknown function, conferred enhanced tolerance to oxidative stress. Our findings suggest that tolerance to oxidative stress involves mechanisms and pathways that are unknown at present, including some that are specific to Arabidopsis or the Brassicaceae.