bluuebunny/crossref_metadata_2025 huggingface dataset:
Adoption and perceptions of shelter-in-place in California's Rancho Santa Fe Fire Protection District
Authors: Paveglio Travis B. , Carroll Matthew S. , Jakes Pamela J.
Published: September 2010

The increasing impact of wildland fire on human settlements in the USA, and a growing recognition that evacuation might not always to the safest option for those in the path of the flames, continue to spur consideration of alternatives to evacuation among the American public and its fire professionals. Alternatives to evacuation typically include the option for residents to remain in fire-hardened structures while the flames pass; however, it appears there is no clear consensus on whether existing Australian alternatives or new variations should be used in American communities, and if any option will reduce risks to residents and firefighters. This study uses structuration theory to analyse adoption of the shelter-in-place policy created by the Rancho Santa Fe Fire Protection District in southern California. We interviewed professionals working in and around the District and the public affected by the policy. Results suggest that professional support and implementation of shelter-in-place are influenced by the breadth of their personal firefighting experience, their agencies’ flexibility and constraints on innovation, and perceived potential liability for damage from adoption of alternatives. Resident knowledge and understanding of shelter-in-place are also lacking. We conclude with recommendations for continued development of alternatives to evacuation.
Building bridges to fight fire: the role of informal social interactions in six Colorado wildland - urban interface communities
Authors: Brenkert-Smith Hannah
Published: September 2010

Property owners in fire-prone communities have been identified as key stakeholders in the wildfire dilemma. Although past research has examined stakeholder characteristics and their behaviours, less is known about how small-scale social processes among stakeholders might shape mitigation decision-making and related actions. This manuscript highlights the role informal social interactions play in building bridges among full-time and part-time residents that facilitate the spread of wildfire information and galvanise small-scale cooperative efforts to reduce wildfire risk. Data from in-depth interviews conducted with residents in six fire-prone Colorado communities indicate that these interactions create bridging capital that links those who are not likely to be the direct recipients of wildfire outreach efforts to those who are.
Global assessment of the temporal reporting accuracy and precision of the MODIS burned area product
Authors: Boschetti Luigi , Roy David P. , Justice Christopher O. , Giglio Louis
Published: September 2010

A method for the systematic evaluation of the temporal reporting accuracy and precision of burned area products conducted using active fire detections as the reference dataset is described. The method is applied globally to 6 years of Moderate Resolution Imaging Spectroradiometer (MODIS) burned area and active fire product data. The distribution of the time difference between active fire and burned area detections that occur within 90 days is analysed and summary statistics extracted globally. The median time difference in reporting between the MODIS burned area and the active fire product detections is 1 day and the majority of MODIS burned area product detections occur temporally close to an active fire detection: 50% within a single day and 75% within 4 days. Users of the MODIS burned area product with temporal reporting requirements should be aware of these findings if using the approximate day of burning information provided in the burned area product.
Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation
Authors: Dethlefsen Les , Relman David A.
Published: September 2010

The indigenous human microbiota is essential to the health of the host. Although the microbiota can be affected by many features of modern life, we know little about its responses to disturbance, especially repeated disturbances, and how these changes compare with baseline temporal variation. We examined the distal gut microbiota of three individuals over 10 mo that spanned two courses of the antibiotic ciprofloxacin, analyzing more than 1.7 million bacterial 16S rRNA hypervariable region sequences from 52 to 56 samples per subject. Interindividual variation was the major source of variability between samples. Day-to-day temporal variability was evident but constrained around an average community composition that was stable over several months in the absence of deliberate perturbation. The effect of ciprofloxacin on the gut microbiota was profound and rapid, with a loss of diversity and a shift in community composition occurring within 3–4 d of drug initiation. By 1 wk after the end of each course, communities began to return to their initial state, but the return was often incomplete. Although broadly similar, community changes after ciprofloxacin varied among subjects and between the two courses within subjects. In all subjects, the composition of the gut microbiota stabilized by the end of the experiment but was altered from its initial state. As with other ecosystems, the human distal gut microbiome at baseline is a dynamic regimen with a stable average state. Antibiotic perturbation may cause a shift to an alternative stable state, the full consequences of which remain unknown.
Bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria
Authors: Watt Ian N. , Montgomery Martin G. , Runswick Michael J. , Leslie Andrew G. W. , Walker John E.
Published: September 2010

The catalytic domain of the F-ATPase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. Energy for the synthesis of ATP from ADP and phosphate is provided by the transmembrane proton-motive-force across the inner membrane, generated by respiration. The proton-motive force is coupled mechanically to ATP synthesis by the rotation at about 100 times per second of the central stalk and an attached ring of c-subunits in the membrane domain. Each c-subunit carries a glutamate exposed around the midpoint of the membrane on the external surface of the ring. The rotation is generated by protonation and deprotonation successively of each glutamate. Each 360° rotation produces three ATP molecules, and requires the translocation of one proton per glutamate by each c-subunit in the ring. In fungi, eubacteria, and plant chloroplasts, ring sizes of c
10
–c
15
subunits have been observed, implying that these enzymes need 3.3–5 protons to make each ATP, but until now no higher eukaryote has been examined. As shown here in the structure of the bovine F
1
-c-ring complex, the c-ring has eight c-subunits. As the sequences of c-subunits are identical throughout almost all vertebrates and are highly conserved in invertebrates, their F-ATPases probably contain c
8
-rings also. Therefore, in about 50,000 vertebrate species, and probably in many or all of the two million invertebrate species, 2.7 protons are required by the F-ATPase to make each ATP molecule.
On the relevance of the mathematics curriculum to young people
Authors: Sealey Paula , Noyes Andrew
Published: September 2010

In this article we draw upon focus group data from a large study of learner trajectories through 14–19 mathematics education to think about the notion of relevance in the mathematics curriculum. Drawing on data from three socially distanced sites we explore how different emphases on what might be termed practical, process and/or professional forms of relevance affect the experiences and aspirations of learners of mathematics. We consider whether an emphasis on practical relevance in schools serving relatively disadvantaged communities might aid the reproduction of students' social position. This leads us to suggest that a fourth category of curriculum relevance – political relevance – is largely missing from classrooms.
Politics and pedagogy: discursive constructions in the IB Theory of knowledge – Guide
Authors: Smith Nigel V. , Morgan Mandy
Published: September 2010

The International Baccalaureate (IB) curriculum is increasingly popular in both national and international secondary education settings. The Theory of knowledge (TOK) course is cast as the prime example of the international globalised values the IB Diploma represents. This article argues that such a positioning is contested within the TOK curriculum document, leading to confusion and tension in the positioning of teachers, students and learning. Two constructions of TOK are identified through discourse analysis, each of which positions teachers, students and learning differently. One construction serves primarily political goals, while the other serves pedagogical purposes. The tension between these positions may cause confusion for teachers and students, although techniques of tension reduction are identified. Further, this article argues that, in practice, both the pedagogical and political purposes of TOK may be achieved despite the tension in the curriculum document, if the personal pedagogical ideology of the teacher coincides with the political positioning of TOK.
Communicative‐based curriculum innovations between theory and practice: implications for EFL curriculum development and student cognitive and affective change
Authors: Shawer Saad
Published: September 2010

This qualitative study examines the influence of teacher conceptualisations of communicative language teaching on their actual classroom practice and student cognitive and affective change. The qualitative paradigm underpinned this research at the levels of ontology (multiple teacher realities), epistemology (interaction with, rather than detachment from, the respondents), and methodology through using an idiographic strategy (qualitative case study), instruments (qualitative interviews, participant observation and questionnaires), and data analysis technique (explanation‐building). The results indicated that teachers who understood CLT and managed to materialise its principles into action significantly improved student language learning (cognitive change) and motivation (affective change). Moreover, traditional, structural and didactic teaching as well as communicative knowledge that was not translated into practice had almost a typical negative impact on student learning and motivation. Recommendations for curriculum development, teacher development, teacher training and future research are made.
Response to a Review and Update on Developing Literacy in Second-language Learners: Report of the National Literacy Panel on Language Minority Children and Youth
Authors: August Diane , Shanahan Timothy
Published: September 2010

The purpose of this article is to respond to a review of the report Developing Literacy in Second-language Learners: Report of the National Literacy Panel on Language Minority Children and Youth, written by our respected colleague Kathy Escamilla, which appeared in a recent edition of the Journal of Literacy Research. This will also give us the opportunity to offer a brief update of the research on effective reading and writing instruction for English-language learners that has appeared since 2002, the cut-off year for the inclusion of studies in the original panel report.
Assessing contamination levels of amprolium and tylosin using the embryo toxicity assay and three biomarkers
Authors: Hu Jun , Liang Yong , Chen Minjie , Wang Xiaorong
Published: September 2010

This study was conducted to examine the adverse biological effects of two veterinary pharmaceuticals (Amprolium and tylosin) on aquatic organisms. The zebrafish embryo toxicity assays were performed in combination with three biomarkers, including superoxide dismutase (SOD), lipid peroxidation (LPO) and heat shock protein 70(Hsp70). The LPO extent was expressed by malondialdehyde (MDA) in this paper. Logit Loglinear analysis was used to study the effect of exposure concentration and time on survival rate and percent hatched in embryo toxicity tests. The data on SOD, MDA and Hsp70 were analyzed by one-way ANOVA followed by Dunnett's test. The results showed that both pharmaceuticals had no effect on Hsp70 levels in zebrafish. Amprolium and tylosin had significant effect on the survival rate, the percent hatched, SOD and MDA in the range of the experimental concentrations. Furthermore, there was a sharp increase, followed by a decrease in the survival rate, as the exposure concentrations of amprolium or tylosin increased; while SOD and MDA indicated a sharp decrease followed by an increase in survival rates. These results indicated that both pharmaceuticals can be useful to the embryos at low concentrations, while causing acute toxicity at high concentrations. However, two pharmaceuticals cause an acute toxicity effect at concentrations several orders of magnitude higher than detected in the aquatic environments. Both do not result in acute toxicity to zebrafish, but it is recommended that the proper strategy and approach be found to perform chronic low-dose exposure studies.
Turtle captures in shrimp trawl nets in Bahrain
Authors: Abdulqader Ebrahim A. A.
Published: September 2010

Based on fishermen logbooks, this study assessed turtle captures in Bahrain's shrimp trawl fishery for five fishing seasons during 1998–2003. Estimated total turtle captures were 298 ±184, 264 ±171, 433 ± 243, 394 ± 227, and 234 ± 177 cases which were caught during 39,147 ± 1,269, 35,761 ± 12,400, 42,747 ± 13,637, 37,071 ± 11,781, 43,923 ± 11,994 fishing days, respectively. It is likely that the green turtle was the species involved for most of these turtle captures. Fishing effort mean values were significantly different between seasons and fishing areas; while turtle capture rate mean values were not significantly different between seasons, months and areas. This suggests that turtles are randomly appearing in the shrimp fishing areas irrespective of the month, season, or fishing ground. These turtles are likely foraging in parts of the shrimp fishing ground or passing through the area during their migrations. Shrimp fishing grounds have previously been identified as a foraging habitat for sea turtles. Conservation actions are required to minimize the threat of shrimp trawl nets on green turtles. An immediate action should be to deliver a fishermen's awareness program that would improve their handling of live marine turtles once caught in the nets. Furthermore, fishermen should be required to adopt gear modifications and the government should enforce regulations that minimize the impact of shrimp trawls on Bahrain's green turtle population. These requirements are not only a national necessity, but contribute to the achievement of global conservation objectives.
Effects of a small planktivore (Pseudorasbora parva: Cyprinidae) on eutrophication of a shallow eutrophic lake in central China
Authors: Chen Yushun , Li Zhongjie , Lin Lian-Shin
Published: September 2010

An enclosure experiment was performed in Lake Yuehu, central China, to assess the effects of a gradient of Pseudorasbora parva biomass on eutrophication state parameters, from May 15 to June 14, 2004. Experimental enclosures were placed into the lake and four treatments were conducted: Control (no fish), low fish (16.5 g m– 3), medium fish (55 g m– 3), and high fish (110 g m– 3). The experimental fish were an average total length of 78 ± 7 mm (mean ± standard deviation) and an average weight of 5.5 ± 1.5 g (mean ± standard deviation). In general, fish increased Secchi disk transparency (SD) and reduced chlorophyll a and total phytoplankton cells, especially in the medium and high fish treatments. No significant effect of fish on total nitrogen (TN) and total phosphorus (TP) was observed. Relatively higher SD, and lower TN and TP were observed in the medium fish treatment as compared to other fish treatments. Effects of fish biomass on chlorophyll a and total phytoplankton cells were not significantly different between the medium and the high fish treatments. Based on the observed eutrophication parameters and fish mortality, the current experiments suggest that maintaining a 55 g m– 3 biomass of P. parva may be helpful for controlling eutrophic state in the studied lake. Further studies are needed to extrapolate the current results to the whole-lake management decisions.
Abundance and composition of solid waste materials on the western part of the Turkish Black Sea seabed
Authors: Topçu Eda N. , Öztürk Bayram
Published: September 2010

Accumulation of marine litter is a worldwide growing problem of pollution in seas. Although it is recognized as one of the major pollution types for the Black Sea, very few studies can provide quantitative data and there are no data at all on solid wastes of the Black Sea seabed. This study was therefore aimed at investigating the abundance and composition of solid wastes in the southwestern Black Sea. Litter items were collected by trawling in October 2007, and in February and April 2008, at depths ranging from 25 m to 100 m. The solid waste concentration on the seabed showed a large variability (with zones ranging from 128–1320 items km– 2 and 8–217 kg km-2). Marine litter concentrations were higher than in the Mediterranean Sea, consisting mainly of plastic materials. Most items were fragmented, which indicated that they had spent a long time at sea, and this made their identification difficult. Only 8 items had legible labels, 2 of them being Turkish and 6 foreign. This suggested that marine litter is a trans-boundary problem, not only in the oceans, but also for enclosed seas like the Black Sea. The situation needs to be monitored all over the basin using standardised methods in order to develop regionally valid and effective solutions.
Overview of the Zambezi River System: Its history, fish fauna, fisheries, and conservation
Authors: Tweddle Denis
Published: September 2010

The Zambezi River has a catchment area of 1.32 million km2, including parts of eight countries. Three divisions of the river are recognised: the Upper Zambezi separated from the Middle Zambezi by Victoria Falls, and the Lower Zambezi below Cahora Bassa gorge. The Okavango River is also linked to the Upper Zambezi system in wet years in an area of complex geomorphological history. Habitats include forested headwater streams, extensive floodplains, deep gorges, two large man-made lakes and an extensive delta. On floodplains, subsistence fisheries exploit the natural seasonal cycles, while the man-made lakes have commercial-scale fisheries for introduced kapenta, Limnothrissa miodon. Aquaculture is on a small scale, though with larger commercial cage culture enterprises on Lake Kariba. This paper summarises current knowledge on the fish faunas and their origins, the status of the different fisheries and their management, and the conservation status of the river's resources.
Fish species diversity and relative abundance in Lake Albert—Uganda
Authors: Wandera Sylvester Bwaku , Balirwa John Stephen
Published: September 2010

Lake Albert is located towards the tip of the western arm of the African Great Rift Valley, between Uganda and the Democratic Republic of Congo. Despite the presence of several predatory fishes, including the Nile perch (Lates niloticus), Lake Albert supports the most diverse commercial fisheries in Uganda with at least 55 species that vary markedly in size. The lake contributes at least 30% of the national fish production. Increased human activity around and within Lake Albert, especially oil and gas exploration, may pose threats to the well being of the lake, its diverse fish communities and its fishery. During 2007, fishery surveys were undertaken using gill-nets and seines in the Uganda part of the lake to identify existing fish species and their critical habitats and provide management recommendations for sustaining the fisheries. Six main habitat types for fishes were identified: shallow river-associated waters; open sandy shorelines; lagoons; large bays; rocky escarpments; and, open-water habitats. Together, these habitats harboured 40 fish species belonging to 12 families. Lagoons, large bays and rocky shores had higher numbers of fish species. Some species rare in most parts of the lake were recovered from the rocky habitats. The shoreline waters contained mostly juvenile fishes. These habitats were considered as natural refugia to fishes in the lake and effort should be made to protect them in order to sustain species diversity in the lake.
The fall of Native Fishes and the rise of Non-native Fishes in the Great Lakes Basin
Authors: Mandrak Nicholas E. , Cudmore B.
Published: September 2010

Over the last 200 years, the fish fauna of the Great Lakes has changed significantly as a result of declines in native species and the deliberate and inadvertent stocking of non-native fishes. These changes have resulted in the global extinction of three taxa and the extirpation of 18 species lowering the number of currently extant native species in the Great Lakes basin from 169 to 148 species. A further 82 species have declined to the point of endangerment in at least one jurisdiction in the basin. The causes of these declines are primarily habitat alterations, aquatic invasive species, and overexploitation. Some significant changes in the fish fauna of the Great Lakes basin have also been the result of the successful introduction and establishment of 35 non-native species. In addition, 34 non-native species have been found in the basin, but have not, or are not thought to have, established reproducing populations. These species have been introduced through a variety of pathways including commercial shipping, dispersal, live trade, recreational boating and angling, and stocking. Many of these species have substantially impacted the Great Lakes ecosystem directly through predation and competition or indirectly through trophic disruption and disease transmission. The relative importance of pathways as a source of new introductions has changed over time, and can be expected to continue to change as a result of evolving regulations and trade patterns. The fish fauna of the Great Lakes basin will continue to change as the result of continuing threats to native species and ongoing introductions of non-native species, and such change will undoubtedly be influenced by climate change and human population growth.
Reptile: representative tiling for short read error correction
Authors: Yang Xiao , Dorman Karin S. , Aluru Srinivas
Published: September 2010

Motivation: Error correction is critical to the success of next-generation sequencing applications, such as resequencing and de novo genome sequencing. It is especially important for high-throughput short-read sequencing, where reads are much shorter and more abundant, and errors more frequent than in traditional Sanger sequencing. Processing massive numbers of short reads with existing error correction methods is both compute and memory intensive, yet the results are far from satisfactory when applied to real datasets.

Results: We present a novel approach, termed Reptile, for error correction in short-read data from next-generation sequencing. Reptile works with the spectrum of k-mers from the input reads, and corrects errors by simultaneously examining: (i) Hamming distance-based correction possibilities for potentially erroneous k-mers; and (ii) neighboring k-mers from the same read for correct contextual information. By not needing to store input data, Reptile has the favorable property that it can handle data that does not fit in main memory. In addition to sequence data, Reptile can make use of available quality score information. Our experiments show that Reptile outperforms previous methods in the percentage of errors removed from the data and the accuracy in true base assignment. In addition, a significant reduction in run time and memory usage have been achieved compared with previous methods, making it more practical for short-read error correction when sampling larger genomes.

Availability: Reptile is implemented in C++ and is available through the link: http://aluru-sun.ece.iastate.edu/doku.php?id=software

Contact:  aluru@iastate.edu
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes
Authors: Koestler Devin C. , Marsit Carmen J. , Christensen Brock C. , Karagas Margaret R. , Bueno Raphael , Sugarbaker David J. , Kelsey Karl T. , Houseman E. Andres
Published: September 2010

Motivation: Patients with identical cancer diagnoses often progress differently. The disparity we see in disease progression and treatment response can be attributed to the idea that two histologically similar cancers may be completely different diseases on the molecular level. Methods for identifying cancer subtypes associated with patient survival have the capacity to be powerful instruments for understanding the biochemical processes that underlie disease progression as well as providing an initial step toward more personalized therapy for cancer patients. We propose a method called semi-supervised recursively partitioned mixture models (SS-RPMM) that utilizes array-based genetic and patient-level clinical data for finding cancer subtypes that are associated with patient survival.

Results: In the proposed SS-RPMM, cancer subtypes are identified using a selected subset of genes that are associated with survival time. Since survival information is used in the gene selection step, this method is semi-supervised. Unlike other semi-supervised clustering classification methods, SS-RPMM does not require specification of the number of cancer subtypes, which is often unknown. In a simulation study, our proposed method compared favorably with other competing semi-supervised methods, including: semi-supervised clustering and supervised principal components analysis. Furthermore, an analysis of mesothelioma cancer data using SS-RPMM, revealed at least two distinct methylation profiles that are informative for survival.

Availability: The analyses implemented in this article were carried out using R (http://www.r.project.org/).

Contact:  devin_koestler@brown.edu; e_andres_houseman@brown.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Ruffus: a lightweight Python library for computational pipelines
Authors: Goodstadt Leo
Published: September 2010

Summary: Computational pipelines are common place in scientific research. However, most of the resources for constructing pipelines are heavyweight systems with graphical user interfaces. Ruffus is a library for the creation of computational pipelines. Its lightweight and unobtrusive design recommends it for use even for the most trivial of analyses. At the same time, it is powerful enough to have been used for complex workflows involving more than 50 interdependent stages.

Availability and implementation: Ruffus is written in python. Source code, a short tutorial, examples and a comprehensive user manual are freely available at http://www.ruffus.org.uk. The example program is available at http://www.ruffus.org.uk/examples/bioinformatics

Contact:  ruffus@llew.org.uk
Spatial quantification and classification of skin response following perturbation using organotypic skin cultures
Authors: Pommerencke Thora , Westphal Kathi , Ernst Claudia , Safferling Kai , Dickhaus Hartmut , Steinberg Thorsten , Tomakidi Pascal , Grabe Niels
Published: September 2010

Motivation: For a mechanistic understanding of skin and its response to an induced perturbation, systems biology is gaining increasing attention. Unfortunately, quantitative and spatial expression data for skin, like for most other tissues, are almost not available.

Results: Integrating organotypic skin cultures, whole-slide scanning and subsequent image processing provides bioinformatics with a novel source of spatial expression data. We here used this approach to quantitatively describe the effect of treating organotypic skin cultures with sodium dodecyl sulphate in a non-corrosive concentration. We first measured the differentiation-related spatial expression gradient of Heat-Shock-Protein 27 in a time series of up to 24 h. Secondly, a multi-dimensional tissue classifier for predicting skin irritation was developed based on abstract features of these profiles. We obtained a high specificity of 0.94 and a sensitivity of 0.92 compared with manual classification. Our results demonstrate that the integration of tissue cultures, whole-slide scanning and image processing is well suited for both the standardized data acquisition for systems biological tissue models and a highly robust classification of tissue responses.

Contact:  niels.grabe@bioquant.uni-heidelberg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Validation of the Chlamydia trachomatis genital challenge pig model for testing recombinant protein vaccines
Authors: Schautteet Katelijn , Stuyven Edith , Cox Eric , Vanrompay Daisy
Published: September 2010

Chlamydia trachomatis is a Gram-negative obligate intracellular bacterial pathogen that is the leading cause of bacterial sexually transmitted disease in humans in developing countries. A vaccination programme is considered to be the best approach to reduce the prevalence of C. trachomatis infections. However, there are still no commercial C. trachomatis vaccines. In order to develop effective C. trachomatis vaccines, it is important to identify those antigens that elicit a protective immune response, and to develop new and adequate methods and adjuvants for effective vaccine delivery, as conventional methods have failed to induce protective immunity. In order to test different vaccine candidates, animal models are needed. Former studies have used non-primate monkeys, mice or guinea pig infection models. The present study used a pig model for testing recombinant protein vaccines. Two recombinant proteins, polymorphic membrane protein G (PmpG), and secretion and cellular translocation protein C (SctC), were tested for their ability to create protection in a pig C. trachomatis challenge model. The vaccines were administered subcutaneously with GNE adjuvant. Six weeks later, animals were challenged intravaginally with C. trachomatis serovar E. After a further 4 weeks, the pigs were euthanized. PmpG-immunized pigs were better protected than pigs immunized with the less promising SctC candidate vaccine antigen. Interestingly, significant protection was apparently not correlated with a strong humoral immune response upon subcutaneous immunization. In conclusion, the pig model is useful for studying the efficacy of vaccine candidates against genital human C. trachomatis infection.
Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase
Authors: Gu Xiaogang , Lee Sung G. , Bar-Peled Maor
Published: September 2010

Sinorhizobium meliloti is a soil bacterium that fixes nitrogen after being established inside nodules that can form on the roots of several legumes, including Medicago truncatula. A mutation in an S. meliloti gene (lpsB) required for lipopolysaccharide synthesis has been reported to result in defective nodulation and an increase in the synthesis of a xylose-containing glycan. Glycans containing xylose as well as arabinose are also formed by other rhizobial species, but little is known about their structures and the biosynthetic pathways leading to their formation. To gain insight into the biosynthesis of these glycans and their biological roles, we report the identification of an operon in S. meliloti 1021 that contains two genes encoding activities not previously described in bacteria. One gene encodes a UDP-xylose synthase (Uxs) that converts UDP-glucuronic acid to UDP-xylose, and the second encodes a UDP-xylose 4-epimerase (Uxe) that interconverts UDP-xylose and UDP-arabinose. Similar genes were also identified in other rhizobial species, including Rhizobium leguminosarum, suggesting that they have important roles in the life cycle of this agronomically important class of bacteria. Functional studies established that recombinant SmUxs1 is likely to be active as a dimer and is inhibited by NADH and UDP-arabinose. SmUxe is inhibited by UDP-galactose, even though this nucleotide sugar is not a substrate for the 4-epimerase. Unambiguous evidence for the conversions of UDP-glucuronic acid to UDP-α-d-xylose and then to UDP-β-l-arabinose (UDP-arabinopyranose) was obtained using real-time 1H-NMR spectroscopy. Our results provide new information about the ability of rhizobia to form UDP-xylose and UDP-arabinose, which are then used for the synthesis of xylose- and arabinose-containing glycans.
Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri
Authors: MacKenzie Donald A. , Jeffers Faye , Parker Mary L. , Vibert-Vallet Amandine , Bongaerts Roy J. , Roos Stefan , Walter Jens , Juge Nathalie
Published: September 2010

Mucus-binding proteins (MUBs) have been revealed as one of the effector molecules involved in mechanisms of the adherence of lactobacilli to the host; mub, or mub-like, genes are found in all of the six genomes of Lactobacillus reuteri that are available. We recently reported the crystal structure of a Mub repeat from L. reuteri ATCC 53608 (also designated strain 1063), revealing an unexpected recognition of immunoglobulins. In the current study, we explored the diversity of the ATCC 53608 mub gene, and MUB expression levels in a large collection of L. reuteri strains isolated from a range of vertebrate hosts. This analysis revealed that the MUB was only detectable on the cell surface of two highly related isolates when using antibodies that were raised against the protein. There was considerable variation in quantitative mucus adhesion in vitro among L. reuteri strains, and mucus binding showed excellent correlation with the presence of cell-surface ATCC 53608 MUB. ATCC 53608 MUB presence was further highly associated with the autoaggregation of L. reuteri strains in washed cell suspensions, suggesting a novel role of this surface protein in cell aggregation. We also characterized MUB expression in representative L. reuteri strains. This analysis revealed that one derivative of strain 1063 was a spontaneous mutant that expressed a C-terminally truncated version of MUB. This frameshift mutation was caused by the insertion of a duplicated 13 nt sequence at position 4867 nt in the mub gene, producing a truncated MUB also lacking the C-terminal LPxTG region, and thus unable to anchor to the cell wall. This mutant, designated 1063N (mub-4867i), displayed low mucus-binding and aggregation capacities, further providing evidence for the contribution of cell-wall-anchored MUB to such phenotypes. In conclusion, this study provided novel information on the functional attributes of MUB in L. reuteri, and further demonstrated that MUB and MUB-like proteins, although present in many L. reuteri isolates, show a high genetic heterogeneity among strains.
Like a River: The Million Man March and the Black Nationalist Tradition in the United States
Authors: West Michael O.
Published: September 2010

This article examines the Million Man March in the wider context of black nationalism, a persistent, though inconsistent, factor in African American life, enjoying wider currency at some historical junctures than others. Those periods when black nationalism resonated strongly among African Americans are called black nationalist moments, four of which are identified here. The Million Man March, with its heavy inflection of patriarchy and black capitalism, is seen as the iconic event of the fourth moment. The subsequent Million Woman March is pivoted as a more radical and activist rejoinder to the Million Man March, a response continued by the even more recent Black Radical Congress.
“The World’s Against Me As A Black Man”: Charles Mingus and Segregated America
Authors: King Desmond
Published: September 2010

This paper examines how the artistic output of Charles Mingus was influenced by the question of race in U.S. politics. Employing material from the liner notes of Mingus’s albums, his autobiography, and interviews for his oral history, I argue that issues of race and their political manifestation were forced upon Mingus by the circumstances of American politics. Mingus’s experience as an African American vehemently opposed to segregated race relations and alert, throughout his life, to racism, is part of his compositional presence.
From White to Western: “Racial Decline” and the Idea of the West in Britain, 1890–1930
Authors: BONNETT ALASTAIR
Published: September 2010

Abstract Drawing on British works of imperial and social commentary, this article shows how a literature of white crisis emerged between 1890–1930. It was a literature that, whilst claiming to defend and affirm white identity, in fact exposed the limits of whiteness as a form of social solidarity. It is shown how these studies drew together a variety of challenges deemed to be facing the white race and, more specifically, how they exhibited a contradictory desire to defend white racial community whilst attacking “the masses”. The idea of the West, developing alongside, within and in the wake of this crisis literature, provided a less racially reductive but not necessarily less socially exclusive identity.
Cheap Talk and Investment Rivalry in the Pulp and Paper Industry
Authors: Christensen Laurits Rolf , Caves Richard E.
Published: September 2010

Determinants of the abandonment of previously announced capacity expansions are analyzed in eleven industries within the North American pulp and paper sector. Given the investor's initial confidence, extent of precommitment of resources, and post‐announcement fresh news, abandonment's likelihood increases with unanticipated projects subsequently announced by rivals. The process suggests a continual auction with the winning projects and firms having certain systematic properties. Unexpected announcements by rivals promote abandonment only in less concentrated industries; elsewhere completion is actually encouraged. Short‐run price competition is found highly sensitive to capacity utilization, and the market's geographic scope is tested.
On the Consistency of Merger Policy
Authors: Nilssen Tore
Published: September 2010

This paper presents a way to get around the information problem facing outside analysts who want to scrutinize competition authorities' decisions. A formal model of how decisions are taken is applied to infer information that is available to the authorities but not to the outside analyst. If the information thus inferred from several decisions is incompatible, it is claimed that the policy executed by the competition authorities is inconsistent. A case study is presented of two recent decisions by the Norwegian Competition Authority on proposed mergers in the Norwegian insurance industry, indicating they most likely were mutually inconsistent.
Corporate Growth and Profitability
Authors: Geroski Paul A. , Machin Stephen J. , Walters Christopher F.
Published: September 2010

This paper argues that current period corporate growth rates reflect changes in current expectations about the long run profitability of a firm. This means that growth rates are likely to vary randomly over time. Using data from 271 large, quoted UK firms over the period 1976–1982, we report the existence of a positive, statistically significant and robust correlation between current period growth rates and a natural measure of changes in current expectations about long run profitability, namely changes in the stock market valuation of the firm. Nevertheless, we find that variations in corporate growth rates are difficult to predict.
Sequential Auctions of Interdependent Objects: Israeli Cable Television Licenses
Authors: Gandal Neil
Published: September 2010

In Israel, area cable television (CATV) licenses were auctioned sequentially. This paper provides evidence that (i) there were interdependencies among many of the franchises and that (ii) subscriber fees for the interdependent franchises decreased over time in this auction.
The Restructuring and Privatisation of Britain's CEGB—Was It Worth It?
Authors: Newbery David M. , Pollitt Michael G.
Published: September 2010

We report a social cost‐benefit analysis of the privatisation and restructuring of the Central Electricity Generating Board which generated and transmitted all public electricity in England and Wales until 1990. The main benefits came from generator efficiency gains, switching from nuclear power, and lower emissions. The main costs came from higher prices for imported French electricity, the cost of restructuring and premature investment in the gas‐fired generating plant. Our central estimate is a permanent cost reduction of 5% per year, equivalent to an extra 40% return on assets. Consumers and government lose, and producers gain more than the cost reduction.
Utilization of R&D Results in the Home and Foreign Plants of Multinationals
Authors: Fors Gunnar
Published: September 2010

This paper analyzes the utilization of R&D results in the home and foreign plants of Swedish multinational enterprises (MNEs). The findings indicate that firms' R&D undertaken in the home country is used as an input in both the home and foreign plants of the MNEs. This suggests that technology is transferred to the foreign plants. Around four‐fifths of the gain in value‐added attributed to home R&D was realized in the MNEs' home plants, while the remaining fifth benefitted the foreign plants. R&D in foreign affiliates does not appear to be used as an input in home plants.
The Nature of Diversified Business Groups: A Research Design and Two Case Studies
Authors: Ghemawat Pankaj , Khanna Tarun
Published: September 2010

Diversified business groups dominate the private sectors of most of the world’s economies. Several of these economies have undergone sudden policy changes that significantly increase domestic competitive intensity. We demonstrate how the changes in corporate scope that accompany such “competitive shocks” can be used to weigh the importance of different explanations for the existence of diversified business groups. We illustrate our reasoning by studying the restructuring of two of India’s largest business groups following a comprehensive post‐1991 package of policy reforms. The case studies also elucidate aspects of the restructuring process that should inform larger‐sample empirical analyses.
The Investment Behaviour of Firms in an Oligopolistic Setting
Authors: Hay Donald A. , Liu Guy S.
Published: September 2010

Industrial organization theory has identified strategic investment in capacity as an important element in competition in oligopolistic markets. In the paper we specify a model of oligopolistic investment behaviour, and test it with panel data for 114 firms in 15 narrowly defined UK manufacturing industries in the 1970s and 1980s. The industries are distinguished according to their market characteristics as fragmented, dominant firm and dominant group sectors. The results indicate behaviour which is noncooperative in fragmented sectors, cooperative in dominant group sectors and competitive in dominant firm sectors.
Japanese Research Consortia: A Microeconometric Analysis of Industrial Policy
Authors: Branstetter Lee , Sakakibara Mariko
Published: September 2010

Despite the existence of much theoretical research analyzing the potential benefits and costs of R&D consortia, there has been little corresponding empirical work on their efficacy. In this paper, we undertake a large‐sample econometric study of Japanese government‐sponsored research consortia. We find evidence that frequent participation in these consortia has a positive impact on research expenditure and research productivity. These results hold after controlling for the potential endogeneity of intensity of participation in consortia to participating firms’ research productivity. Furthermore, we find evidence that part of this impact arises from the increased knowledge spillovers that take place within these consortia.
Sunk Costs, Accommodation, and the Welfare Effects of Entry
Authors: Nachbar John H. , Petersen Bruce C. , Hwang Inhak
Published: September 2010

Although economists usually support the unrestricted entry of firms into an industry, entry may lower social welfare if there are setup costs or if entrants have a cost disadvantage. We consider the welfare effects of entry within a standard Cournot model where some of an incumbent firm’s costs are sunk. We find that the range of parameter values over which entry can harm welfare declines monotonically in the fraction of cost that are sunk. Furthermore, the presence of even a small fraction of sunk costs often reverses an assessment that entry harms welfare.
A Theory of Economic Obsolescence
Authors: Lee In Ho , Lee Jonghwa
Published: September 2010

A new generation of durable goods makes an old generation economically, even if not physically, obsolete. Economic obsolescence due to technological innovation requires the durable goods monopolist to implement price discrimination in two dimensions, both between consumers with different valuations and between consumers with different purchase histories. Equilibrium in the game between the durable goods monopolist and consumers depends on the extent of economic obsolescence and the relative sizes of the consumer groups. Underinvestment in innovation may take place. This contrasts with the standard literature on planned obsolescence where the durable goods monopolist overinvests in durability reducing technology.
Social Status, Entry and Predation: The Case of British Shipping Cartels 1879–1929
Authors: Podolny Joel M. , Scott Morton Fiona M.
Published: September 2010

The authors incorporate social status and regional affiliation—two variables of central sociological interest—into an economic analysis of entry and predation. They build on Scott Morton’s [1997] examination of entry and predation in the merchant shipping industry and examine whether the social status of an entrant owner impacts on the predation behavior of the incumbent cartels. They find that high social status entrants are significantly less likely (40%) to be preyed upon than the low social status entrants. They discuss several interpretations of this result. Subsequent analysis supports the hypothesis that cartel members use social status as an indicator of an entrant’s propensity to be a cooperative cartel participant.
Adoptions and Orphans in the Early Microcomputer Market
Authors: Gandal Neil , Greenstein Shane , Salant David
Published: September 2010

In this paper we examine the development of the microcomputer market in the early 1980s. CP/M, a widely‐adopted operating system, was orphaned by the user and the development communities. A new operating system, DOS, and a new hardware platform, the IBM PC, became the predominant industry standard. We examine the statistical relationship between data that reflects hardware and software sales for the competing platforms. We conclude that the economic processes underlying the development of DOS differed from those underlying CP/M and that many of these differences related to the role of software development.
Heredity or Environment: Why is Automobile Longevity Increasing?
Authors: Hamilton Bruce W. , Macauley Molly K.
Published: September 2010

Over the past 25 years the longevity of automobiles has increased dramatically. We disentangle the rise in longevity into an embodied or inherent‐durability effect and a disembodied effect (driven by the external environment, such as reduced accident rates or reductions in the prices of auto repair parts) and estimate these effects by year from 1950 through 1991. We find that the entire rise in auto longevity is due to some force disembodied from the cars themselves and offer some speculation about the nature of this external environment.