bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a Single-Axis Molecular Puller for Measuring Polysaccharide and Protein Mechanics by Atomic Force Microscopy
Authors: Rabbi Mahir , Marszalek Piotr E. 
Published: December 2007

INTRODUCTIONPolysaccharides and proteins are frequently subjected to mechanical forces in vivo. Because these forces affect a wide range of biological activities, it is important to develop methods that directly investigate the mechanical properties of these molecules. Recent progress in techniques that allow the mechanical manipulation of biopolymers at a single-molecule level has revealed the complex nature of the elasticity of proteins and polysaccharides. The atomic force microscope (AFM) is an excellent force spectrometer for probing the mechanical properties (e.g., length and tension) of individual polysaccharides and proteins. The following protocol describes the basic design and construction of an AFM (a single-axis molecular puller) that has four parts: a head, a base, electronics, and software. Those with a background in mechanical engineering, basic knowledge of electronics and data acquisition techniques, and some computer programming skills (e.g., with LabView, Matlab, or Igor) should be able to construct this instrument. It is advisable to inspect commercial AFMs before constructing one from scratch.
Measuring Protein Mechanics by Atomic Force Microscopy: Figure 1.
Authors: Rabbi Mahir , Marszalek Piotr E. 
Published: December 2007

INTRODUCTIONProteins are frequently subjected to mechanical forces in vivo. Because these forces affect a wide range of biological activities, it is important to develop methods that directly investigate the mechanical properties of these molecules. Force spectroscopy of individual proteins (modular or single-domain) allows one to characterize their entropic elasticity under low stretching forces and to determine their persistence length by fitting the worm-like chain (WLC) model to the force-extension curve. At higher stretching forces, it is possible to mechanically unravel these proteins, study their mechanical strength, and examine their unfolding and refolding properties. This provides data on their rates of mechanical unfolding and refolding, as well as on the position of the transition state along the unfolding reaction coordinate, which is defined as the extension of the protein module along the direction of the applied force. Thus, single-protein force spectroscopy may generate a plethora of interesting data that cannot be obtained using traditional biophysical methods. The atomic force microscope (AFM) is an excellent force spectrometer for probing the mechanical properties (e.g., length and tension) of individual proteins. The following protocol describes the use of AFM for measurements of protein mechanics under the constant extension rate regime.
Dot Matrix Pairwise Sequence Comparison
Authors: Mount David W. 
Published: December 2007

INTRODUCTIONA dot matrix analysis is primarily a method for comparing two sequences to look for possible alignment of characters between the sequences. The method is also used for finding direct or inverted repeats in protein and DNA sequences, and for predicting regions in RNA that are self-complementary and that, therefore, have the potential of forming secondary structure through base-pairing.
A field guide to models of sex‐ratio evolution in gynodioecious species
Authors: Bailey Maia F. , Delph Lynda F. 
Published: December 2007

Gynodioecious plant species, species in which individuals are females or hermaphrodites, are ideal systems for studying connections between genetics, ecology, and long‐term evolutionary changes because sex determination can be complex, involving cytoplasmic and/or nuclear genes, and sex ratio is often variable across landscapes. Field data are needed to evaluate the many theories concerning this breeding system. In order to facilitate the gathering of relevant data, this paper introduces the four types of gynodiocy (nuclear, nuclear‐cytoplasmic and stochastic gynodioecy plus subdioecy), describes example species and expected patterns, discusses the various forces that drive the evolution of female frequencies, and gives concrete advice on where to start collecting data for different systems. For species in which females are relatively rare, we recommend reciprocal crosses to determine if sex‐determination is nuclear or nuclear‐cytoplasmic along with a search for correlations between female frequencies and ecological factors. For species in which females are common and sex ratios are highly variable, we recommend looking at female offspring sex ratios to determine if females are primarily produced in ephemeral epidemics.In the course of this discussion, we argue that the majority of natural gynodioecious species will have complex sex determination in which multiple cytoplasmic male sterility (CMS) genes interact with multiple nuclear restorers of fertility. Sex‐ratio evolution in such species will be primarily influenced by fitness differences among hermaphrodites (costs of restoration) and less influenced by fitness differences between the sexes (compensation). Metapopulation dynamics alone may explain population sex ratios of species in which females are associated with marginal environments or hybrid zones; however, we feel that in most cases equilibrium forces within populations and metapopulation dynamics among populations each explain portions of the sex‐ratio pattern.
Control of phytoplankton–bacteria interactions by stoichiometric constraints
Authors: Danger Michael , Leflaive Joséphine , Oumarou Catherine , Ten‐Hage Loïc , Lacroix Gérard 
Published: December 2007

In aquatic ecosystems, phytoplanktonic organisms are the major primary producers and bacteria the major decomposers. The interactions between phytoplankton and bacteria may be dependent on nutrient resources. Anthropogenic inputs, by modifying nutrient status and stoichiometry of lakes, might induce changes in these interactions, and thus, could have many consequences on some ecological processes such as primary production or importance of microbial recycling activity.To test this hypothesis, we grew an axenic strain of a green alga, Scenedesmus obliquus, in a range of stoichiometric situations, in absence and in presence of a natural bacterial community. Here, we show that different phytoplankton limiting factors can generate between algae and bacteria either competition for nutrients in phosphorus‐limited conditions, commensalism in nitrogen‐limited conditions, or mutualism in eutrophic nutrient‐unlimited conditions. Causes of these different interaction types are discussed, in particular the hypothesis that in very eutrophic systems with high primary production, mutualism between algae and bacteria could be due to CO2 supply by heterotrophic respiration to inorganic carbon limited algae. Some probable consequences for aquatic ecosystems functioning are proposed.
The role of model selection in describing stochastic ecological processes
Authors: Kuparinen Anna , Snäll Tord , Vänskä Simopekka , O'Hara Robert B. 
Published: December 2007

A great deal of variation in ecological processes can be generated through variation in environmental conditions. Models describing the underlying processes should be able to account for this variation. However, models may not be flexible enough, so that different realizations of a process may be better described by different models. This may lead to uncertainty in model selection.Here we examine the question of whether two empirical models can provide consistent fits to different realizations of a process affected by environmental variation. We further examine the sensitivity of the model predictions to the amount of data available and the selection of the model. To study this, we simulated pollen dispersal patterns under varying wind conditions and then investigated whether the datasets consistently supported the same model. The role of the model selection and the impact of the spatial range over which the dispersal distances were observed were assessed by comparing model predictions at long dispersal distances.There was no consistent pattern of one model providing a better fit than the other across simulations. The model providing better fit varied depending on the range of distances over which the dispersal patterns were observed, and on the amount of long‐distance dispersal. The model predictions were found to be very sensitive to the selection of the model.The variation between datasets produced with the same underlying mechanisms cannot be easily described using one model, which also limits our ability to reliably predict the underlying process. Therefore, the amount of information about a model choice provided by an individual field study may be rather limited. If we are to understand processes that are affected by environmental variation then we have to observe the range of possible outcomes of the processes under varying spatio‐temporal conditions.
Making Haste Slowly: the evolution of a unified qualifications framework in Scotland
Authors: RAFFE DAVID 
Published: December 2007

AbstractThe Scottish Credit and Qualifications Framework is often claimed to be a success and an example to other countries. However, if other countries wish to learn from this example they should not only study the current framework; they should also examine the sequence of policy reforms, over a quarter of a century, through which it developed. The article traces the history of these reforms and shows how they incrementally created the conditions for a successful comprehensive qualifications framework. It argues that the main drivers for change have been internal to the education system, rather than external economic, social or ideological pressures, and the main barriers have been institutional and political rather than epistemological. There were specific reasons why it took such a long time to develop the Scottish framework, but in any country it takes many years to establish the conditions for a successful comprehensive framework.
VISION AS REVISION: RANKE AND THE BEGINNING OF MODERN HISTORY
Authors: BRAW J. D. 
Published: December 2007

ABSTRACTIt is widely agreed that a new conception of history was developed in the early nineteenth century: the past came to be seen in a new light, as did the way of studying the past. This article discusses the nature of this collective revision, focusing on one of its first and most important manifestations: Ranke's 1824 Geschichten der romanischen und germanischen Völker. It argues that, in Ranke's case, the driving force of the revision was religious, and that, subsequently, an understanding of the nature of Ranke's religious attitude is vital to any interpretation of his historical revision. Being aesthetic‐experiential rather than conceptual or “positive,” this religious element is reflected throughout Ranke's enterprise, in source criticism and in historical representation no less than in the conception of cause and effect in the historical process. These three levels or aspects of the historical enterprise correspond to the experience of the past, and are connected by the essence of the experience: visual perception. The highly individual character of the enterprise, its foundation in sentiments and experiences of little persuasive force that only with difficulty can be brought into language at all, explains the paradoxical nature of the Rankean heritage. On the one hand, Ranke had a great and lasting impact; on the other hand, his approach was never re‐utilized as a whole, only in its constituent parts—which, when not in the relationship Ranke had envisioned, took on a new and different character. This also suggests the difference between Ranke's revision and a new paradigm: whereas the latter is an exemplary solution providing binding regulations, the former is unrepeatable.
THE “INS” AND “OUTS” OF HISTORY: REVISION AS NON‐PLACE
Authors: HUGHES‐WARRINGTON MARNIE 
Published: December 2007

ABSTRACTRevision in history is conventionally characterized as a linear sequence of changes over time. Drawing together the contributions of those engaged in historiographical debates that are often associated with the term “revision,” however, we find our attention directed to the spaces rather than the sequences of history. Contributions to historical debates are characterized by the marked use of spatial imagery and spatialized language. These used to suggest both the demarcation of the “space of history” and the erasure of existing historiographies from that space. Bearing these features in mind, the essay argues that traditional, temporally oriented explanations for revision in history, such as Thomas S. Kuhn's Structure of Scientific Revolutions, miss the mark, and that a more promising line of explanation arises from the combined use of Michel Foucault's idea of “heterotopias” and Marc Augé's idea of “non‐places.” Revision in history is to be found where writers use imagery to move readers away from rival historiographies and to control their movement in the space of history toward their desired vision. Revision is thus associated more with control than with liberation.
REVISIONISM IN SOVIET HISTORY
Authors: FITZPATRICK SHEILA 
Published: December 2007

ABSTRACTThis essay is an account of the “revisionism” movement of the 1970s and 1980s in Soviet history, analyzing its challenge to the totalitarian model in terms of Kuhnian paradigm shift. The focus is on revisionism of the Stalin period, an area that was particularly highly charged by the passions of the Cold War. These passions tended to obscure the fact that one of the main issues at stake was not ideological but purely disciplinary, namely a challenge by social historians to the dominance of political history. A similar challenge, this time against the dominance of social history on behalf of cultural history, was issued in the 1990s by “post‐revisionists.” Although I was a participant in the battles of the 1970s, the essay is less a personal account than a case‐based analysis of the way disciplinary orthodoxies in the social sciences and humanities are established and challenged, and why this happens when it does. In the case of Soviet history, I argue that new data and external events played a surprisingly small role, and generational change a large one.
Tfm‐AR modulates the effects of ApoE4 on cognition
Authors: Rizk‐Jackson Angela , Robertson Jennifer , Raber Jacob 
Published: December 2007

AbstractFemale mice are more susceptible to apolipoprotein E (apoE4)‐induced cognitive deficits than male mice. These deficits can be antagonized by stimulating androgen receptors (ARs). To determine the role of AR in the cognitive effects of apoE4, we backcrossed mutant mice with a naturally occurring defect in the AR [testicular feminization mutant (tfm)] onto the Apoe−/− background to eliminate mouse apoE gene resulting in non‐functional AR, and crossed the tfm/Apoe−/− female mice with apoE4 transgenic male mice. We behaviorally compared Apoe−/−, apoE4, tfm, and tfm/apoE4 male mice. Apoe−/−, apoE4, and tfm mice showed hippocampus‐dependent novel location recognition but tfm/apoE4 mice did not. In contrast, all groups showed hippocampus‐independent novel object recognition. Hippocampus‐dependent learning and memory were also assessed in the water maze. In the water maze probe trial following the second day of hidden platform training, Apoe−/− and apoE4 mice showed spatial memory retention, but tfm and tfm/ApoE4 mice did not. In the water maze, probe trial following the third day of hidden platform training, Apoe−/−, apoE4, and tfm/Apoe−/− mice showed spatial memory retention, but tfm mice did not. These data support an important role for AR in protecting against the detrimental effects of apoE4 on hippocampus‐dependent learning and memory.
The Use of Linear Instrumental Variables Methods in Health Services Research and Health Economics: A Cautionary Note
Authors: Terza Joseph V. , Bradford W. David , Dismuke Clara E. 
Published: December 2007

Objective.To investigate potential bias in the use of the conventional linear instrumental variables (IV) method for the estimation of causal effects in inherently nonlinear regression settings.Data Sources.Smoking Supplement to the 1979 National Health Interview Survey, National Longitudinal Alcohol Epidemiologic Survey, and simulated data.Study Design.Potential bias from the use of the linear IV method in nonlinear models is assessed via simulation studies and real world data analyses in two commonly encountered regression setting: (1) models with a nonnegative outcome (e.g., a count) and a continuous endogenous regressor; and (2) models with a binary outcome and a binary endogenous regressor.Principle Findings.The simulation analyses show that substantial bias in the estimation of causal effects can result from applying the conventional IV method in inherently nonlinear regression settings. Moreover, the bias is not attenuated as the sample size increases. This point is further illustrated in the survey data analyses in which IV‐based estimates of the relevant causal effects diverge substantially from those obtained with appropriate nonlinear estimation methods.Conclusions.We offer this research as a cautionary note to those who would opt for the use of linear specifications in inherently nonlinear settings involving endogeneity.
Visual prognosis and vitreous cytokine levels after arteriovenous sheathotomy in branch retinal vein occlusion associated with macular oedema
Authors: Shimura Masahiko , Nakazawa Toru , Yasuda Kanako , Kunikata Hiroshi , Shiono Takashi , Nishida Kohji 
Published: December 2007

Abstract.Purpose:  To investigate the relationship between vitreous levels of cytokines, including interleukin‐6 (IL‐6) and vascular endothelial growth factor (VEGF), and visual prognosis after pars plana vitrectomy (PPV) with arteriovenous sheathotomy in patients with branch retinal vein occlusion (BRVO) associated with macular oedema.Methods:  We studied 60 patients with logMAR visual acuity (VA) scores of < 0.3 and visual impairment secondary to BRVO‐associated macular oedema. All patients underwent PPV with arteriovenous sheathotomy. At the time of PPV, vitreous samples were collected from the operated eye and vitreous levels of VEGF and IL‐6 were measured. Best corrected VA (BCVA) (using a logMAR chart) and foveal thickness (FT) (using optical coherence tomography) were monitored for up to 6 months after PPV.Results:  Both BCVA and FT significantly improved after PPV. According to multiple regression analysis, both the improvement in BCVA and decrease in FT were closely related to the vitreous level of IL‐6 but not to that of VEGF. The vitreous level of VEGF was strongly correlated with duration of BRVO.Conclusions:  Both improvement in BCVA and decrease in FT were observed after PPV in BRVO patients with macular oedema. Interestingly, these visual prognoses strongly correlate with the vitreous level of IL‐6, whereas the duration of BRVO strongly correlates with the vitreous level of VEGF.
Titus Andronicus: A Violent Change of Fortunes
Authors: Kingsley‐Smith Jane 
Published: December 2007

Abstract Titus Andronicus has often been judged to be less than the sum of its parts – perhaps because those parts are so sensational. Yet, in the late twentieth and early twenty‐first centuries, the play has experienced a striking reversal in its critical and theatrical fortunes. This reversal has been based on a perception of the play's integrity, discovered not just in the links between stage properties and language, nor between its violent set‐pieces and its overall structure, but in the play's claim to moral and aesthetic unity. This essay focuses on the critical fortunes of Titus Andronicus in the last fifty years, with particular reference to Julie Taymor's film, Titus (USA, 1999). It engages with issues of violence, language and the body, gender and racial difference, and genre.
Florida nurse practitioners’ attitudes and practices regarding oral cancer prevention and early detection
Authors: Meng Xiaoxian , Duncan R. Paul , Porter Colleen K. , Li Qing , Tomar Scott L. 
Published: December 2007

AbstractPurpose: To examine Florida nurse practitioners’ (NPs’) attitudes and practices regarding oral cancer prevention and early detection.Data source: A statewide mail survey was conducted among Florida NPs who provided primary care. The questionnaire was adapted from an existing survey instrument used to measure NPs’ knowledge, attitudes, and practices about oral cancer prevention and early detection. A total of 448 Florida NPs (33% response rate) completed the survey.Conclusions: Florida NPs reportedly were not well prepared for oral cancer prevention and early detection. Although most NPs realized the importance of annual oral cancer screening for high‐risk populations and held positive attitudes toward the benefit of early detection, only 39.3% of respondents thought his or her knowledge about oral cancer was current and more than half had never provided oral cancer examinations.Implications for practice: Florida has among the nation’s highest oral cancer rates, but persons at highest risk are among those least likely to see a dentist. Therefore, a multidisciplinary approach involving all relevant healthcare providers, including NPs, may be more effective than relying only on dentists’ efforts in improving survival rates for oral cancer. Strategies are needed to increase the involvement of Florida’s NPs in oral cancer detection.
Making the Perfect Queen: The Cultural Production of Identities in Beauty Pageants
Authors: King‐O’Riain Rebecca Chiyoko 
Published: December 2007

AbstractBeauty queens are symbolic representations of collective cultural indentities and beauty pageants are fields of active ‘cultural production’. This article surveys the growing literature on beauty pageants to better understand how culture is produced within the contexts of pageants. To do so, the article examines how beauty pageants operate as sites of commodification and consumption in a world increasingly influenced by global markets and media institutions. It also illustrates how culture is produced in beauty pageants by examining beauty pageants as sites of oppression, sites to articulate cultural agency, and sites of ethnic, gender, cultural, and sexual identity production.
Covert Racism in the USA and Globally
Authors: Coates Rodney D. 
Published: December 2007

AbstractCovert racism, born out of imperialist needs to maximize profit at the expense of racialized others, stands shielded by institutions, culture, stereotypical assumptions, and tradition. Whereas overt racism assumed blatant and insidious forms, covert racism hides behind the façade of ‘politeness’, political correctness and expediency. Racially coded words and calls for racial blindness obfuscate the reality of this subtle, subversive, and often hidden form of racism. Covert racism, just like its twin overt racism, is neither innocent nor harmless. The scars of covert racism, often seen in terms of increased levels of disease, negative sanctions, inadequate information, and lost opportunities – serve to continually victimize racial nonelites.
Democracy, Nationalism and Culture: A Social Critique of Liberal Monoculturalism
Authors: Conversi Daniele 
Published: December 2007

AbstractDoes liberal democracy provide an ideal framework for solving nationalist disputes? Or is rather democracy more conductive to nationalism and conflict? No definitive answer can be given to this broadly formulated question. However, the trend in the scholarly literature has recently pointed towards the latter direction. This article first introduces the ‘demo‐skeptical turn’, which has emerged across disciplines in the study of democratic transitions. It then relates this to an understudied area – cultural homogenization. A social history of cultural homogenization remains yet to be written, but its historical impact is so overwhelming that its key features need to be studies on its own. This is, in turn, related to mainstream concepts of majoritarian liberal democracy.