bluuebunny/crossref_metadata_2025_split huggingface dataset:
The sensitivity of Fanconi anaemia group C cells to apoptosis induced by mitomycin C is due to oxygen radical generation, not DNA crosslinking
Authors: CLARKE A. A. , PHILPOTT N. J. , GORDON‐SMITH E. C. , RUTHERFORD T. R. 
Published: January 2005

Fanconi's anaemia (FA) is characterized by increased spontaneous and induced chromosome fragility. This has been widely regarded to be due to a defect in DNA crosslink repair, because of the sensitivity of cells to known DNA crosslinking agents such as mitomycin C (MMC) and diepoxybutane (DEB). Although Fanconi cells are also sensitive to molecular oxygen, and may be protected by antioxidants, this has generally been considered to be a secondary phenomenon. However, it has recently been demonstrated that the FAC protein, coded for by the Fanconi anaemia gene for complementation group C, is strictly cytoplasmic and does not enter the nucleus even after DNA damage, which seems inconsistent with a role in DNA repair.We have studied the effects of MMC and oxygen on apoptotic cell death in FA group C (FA‐C) and normal lymphoblastoid cell lines. Hyperoxia alone failed to induce apoptosis in either FA‐C or normal cells. At ambient oxygen, MMC is known to generate oxygen free radicals, whereas decreased oxygen tension facilitates the metabolic activation of MMC for DNA crosslinking. We therefore studied the effects of MMC at 20% and 5% oxygen to favour oxygen radical generation or DNA crosslinking respectively. FA‐C cells showed increased sensitivity compared to normal cells for the induction of apoptosis by MMC at 20% oxygen. When cells were treated with MMC at 5% oxygen we found no increased sensitivity of Fanconi cells to MMC when compared to normal cells. These results imply a role for oxygen free radicals, but not for DNA crosslinking, in the sensitivity of FA cells to MMC.
On Food Companies Liability for Obesity
Authors: Coestier Bénédicte , Gozlan Estelle , Marette Stéphan 
Published: January 2005

AbstractThe U.S. food industry faces tobacco‐style lawsuits for providing misleading information about health risks linked to the consumption of fatty products. This article investigates the link between alternative liability rules and the incentive for disclosing health information to consumers. We show that if the expected damage is relatively low, the absence of intervention is socially optimal. If the expected damage is not too high, mandatory labeling is socially optimal. Liability rules are only welfare‐enhancing for high levels of risk and/or when consumers misperceive health warnings.
The Harvesting Decisions When a Standing Forest with Multiple Age‐Classes Has Value
Authors: Uusivuori Jussi , Kuuluvainen Jari 
Published: January 2005

AbstractA solution is demonstrated to an infinite‐horizon, discrete‐time utility model describing the consumption and cutting behavior of a nonindustrial private landowner who is managing a multiple age‐class forest and who values both consumption derived from harvesting the trees and amenity derived from the standing trees. A policy rule is derived to attain a normal forest from any initial age‐class distribution. It is demonstrated that a noncyclical forest allowing a constant periodic harvest is typically not a normal forest. Therefore, an even‐flow timber harvesting is not tied to the existence of a normal forest structure.
Modeling Discrete Choice with Uncertain Data: An Augmented MNL Estimator
Authors: Hellerstein Daniel 
Published: January 2005

AbstractThis article introduces a multinomial logit model that uses ancillary information to control for uncertainty in both the observed choices made by respondents, and in the attributes of a respondent's choice set. Simulated data are used to compare the performance of this estimator versus simpler models, under several different kinds of uncertainty.
Retail Price Fixity as a Facilitating Mechanism
Authors: Richards Timothy J. , Patterson Paul M. 
Published: January 2005

AbstractPrevious theoretical explanations for retail price fixity show that fixed retail prices can be consistent with either competitive or imperfectly competitive behavior. We develop a conceptual model of retail pricing wherein fixed price points are facilitating mechanisms for tacit collusion. A non‐cooperative equilibrium in fixed retail prices is supported through credible threats to revert to Nash pricing if cheating is suspected. We test the implications of this model using a two‐stage, ordered probit approach in weekly supermarket pricing data. The results show that price fixity does support collusive equilibria among retailers, but other factors may also explain retail price behavior.
The Persistence of Profitability among Firms in the Food Economy
Authors: Schumacher Sara K. , Boland Michael A. 
Published: January 2005

AbstractThe persistence of industry, firm‐specific, and corporate‐parent effects on firm profitability in the food economy are calculated and further analyzed within its four major sectors: food processing, wholesale grocery, retail supermarket, and restaurant. Profits are more persistent within an industry than within a corporation. The retail supermarket sector has had stable profits as has individual retail supermarket firms relative to the other three sectors.
Technological Change and Economies of Scale in U.S. Poultry Processing
Authors: Ollinger Michael , MacDonald James M. , Madison Milton 
Published: January 2005

AbstractThis article uses a unique data set provided by the Census Bureau and a translog cost function to empirically examine technological change in the U.S. poultry industry. Results reveal substantial scale economies that show no evidence of diminishing with plant size and that are much greater than those realized in cattle and hog slaughter. Findings suggest that consolidation is likely to continue, particularly if demand growth diminishes, and that controlling for plant product mix is critical to accurate cost estimates.
Economic Adjustments to Groundwater Depletion in the High Plains: Do Water‐Saving Irrigation Systems Save Water?
Authors: Peterson Jeffrey M. , Ding Ya 
Published: January 2005

AbstractA common policy prescription for conserving irrigation water is to promote more efficient or “water‐saving” irrigation technologies. We develop a risk‐programing model to quantify the effect of irrigation efficiency on irrigation water use in the High Plains, taking account of irrigation timing and well capacity limits. We find that optimal irrigation does not respond monotonically to changes in efficiency, although intermediate and high‐efficiency systems both result in less water use than an inefficient flood system.
Farm Household Production Efficiency: Evidence from The Gambia
Authors: Chavas Jean‐Paul , Petrie Ragan , Roth Michael 
Published: January 2005

AbstractThis article investigates the economic efficiency of farm households, with an application to The Gambia. The efficiency analysis is conducted not at the farm level but at the household level, thus capturing the importance of off‐farm activities. Output‐based measures of technical, allocative, and scale efficiency are generated using nonparametric measurements. An econometric analysis of factors affecting the efficiency indexes is then conducted using a Tobit model. Technical efficiency is fairly high indicating that access to technology is not a severe constraint for most farm households. The cost of scale inefficiency is modest. Allocative inefficiency by contrast is found to be important for the majority of farm households. On the basis of the Tobit results, imperfections in markets for financial capital and nonfarm employment contribute to significant allocative inefficiency.
Credit Risk Models and Agricultural Lending
Authors: Katchova Ani L. , Barry Peter J. 
Published: January 2005

AbstractCredit risk models are developed and used to estimate capital requirements for agricultural lenders under the New Basel Capital Accord. The study uses credit value‐at‐risk methods to calculate probability of default, loss given default, and expected and unexpected losses. Two applied models, CreditMetrics and Moody's KMV, are estimated using farm financial data. The results show that the necessary capital for agricultural lenders under the New Basel Accord varies substantially depending on the riskiness and granularity of the portfolio.
Collective Reputation and Quality
Authors: Winfree Jason A. , McCluskey Jill J. 
Published: January 2005

AbstractFirms who sell regional or specialty products often share a collective reputation based on aggregate quality. Collective reputation can be approached as a dynamic common property resource problem. We show that for an experience good without firm traceability, individual firms have the incentive to choose quality levels that are sub‐optimal for the group. These results support minimum quality standards. Trigger strategies are analyzed as an alternative solution to this problem. Finally, the implications of these results are discussed as they relate to the case study of Washington apples.
Milk by Any Other Name … Consumer Benefits from Labeled Milk
Authors: Dhar Tirtha , Foltz Jeremy D. 
Published: January 2005

AbstractThis article uses revealed preferences of consumers to study the consumer benefits from rBST‐free and organic labeled milk. The article specifies and estimates a quadratic AIDS demand system model for different milk types using U.S. supermarket scanner data. The introduction of rBST‐free and organic milk is used to estimate consumer benefits that are decomposed into two components, competitive and variety effects. Results show significant consumer benefits from organic milk and to a lesser extent from rBST‐free milk. Based on the findings, we explore implications for present U.S. labeling standards.
Abstracts of the 23rd Annual Meeting of the Willi Hennig Society. “Phylogenetics and Evolutionary Biology”
Authors: Grandcolas Philippe 
Published: January 2005

The 23rd annual meeting of the Willi Hennig Society took place in Paris with the support of Muséum national d'Histoire naturelle and CNRS (Centre National de la recherche Scientifique), from the 18th to the 23rd of July 2004. Ninety four participants from 16 countries presented 67 talks and 11 posters. The symposia comprised both methodological contributions and strong analyses of case studies, focusing on hot topics in systematics, methodological advances in phylogenetic analysis, epistemology, phylogenetic analysis of behavioral and ecological traits, phylogeny and coevolution of microbial symbioses, taxon and character sampling, biogeography, and the evolution of arthropods. The student participation was very high with 30 student talks (45%) distributed among all symposia, showing the same healthy trend seen in previous meetings. The present abstracts show how much systematics and phylogenetics are scientifically growing and contribute significantly to all research fields of evolutionary biology in the framework of comparative biology.The Student Awards Committee (Cyrille D'Haese, Diana Lipscomb, John Wenzel) nominated the following winners: Johannes Bergsten, the Hennig Prize ($1000) for “Antagonistic coevolution between the sexes in diving‐beetles (Coleoptera: Dytiscidae); phylogeny and experiments in reciprocal illumination”, Mahé Ben Hamed, the Brundin Prize ($500) for “Reconstructing the history of Chinese through lexicon. Cladistics, distances and trees” and Lara Lopardo, the Rosen Prize ($250) for the poster “Chilean Anapids and Their Webs, a Phylogenetic Approach (Araneae, Anapidae)”.© The Willi Hennig Society 2004.
Mapping characters on a tree with or without the outgroups
Authors: Grandcolas Philippe , Guilbert Eric , Robillard Tony , D'Haese Cyrille A. , Murienne Jérôme , Legendre Frédéric 
Published: January 2005

AbstractA character of special interest in evolutionary studies is usually optimized on a phylogenetic tree, with or without the outgroups employed in that analysis. Both practices are never justified and look like arbitrary choices. Focusing on one example, we draw the conclusion that authors retain or remove outgroups depending on the way these outgroups sample the diversity of states of the character(s) of special interest. The topology without outgroups is often used by authors when different outgroup taxa non‐exhaustively sample the different states of the character of interest outside of the ingroup. This can make the analysis incoherent, because its different steps are not based on the same data matrix (outgroups are removed in the last step). It can provide several incoherent and possibly different patterns for a same character of interest, one issuing from the first step of phylogeny construction and the other resulting from the a posteriori optimization on the truncated topology. Phylogenetic analyses should be designed to minimize this problem, selecting outgroup and ingroup taxa whose diversity of character states is needed for reconstructing the evolutionary history of the character of interest. © The Willi Hennig Society 2004.
Mitochondrial genome data alone are not enough to unambiguously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)
Authors: Cameron Stephen L. , Miller Kelly B. , D'Haese Cyrille A. , Whiting Michael F. , Barker Stephen C. 
Published: January 2005

AbstractAn analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13 mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola's relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological grounds.© The Willi Hennig Society 2004.
The phylogenetic position of the comb jellies (Ctenophora) and the importance of taxonomic sampling
Authors: Wallberg Andreas , Thollesson Mikael , Farris James S. , Jondelius Ulf 
Published: January 2005

AbstractThe transition to a vermiform body shape is one of the most important events in animal evolution, having led to the impressive radiation of Bilateria. However, the sister group of Bilateria has remained obscure. Cladistic analyses of morphology indicate that Ctenophora is the sister group of Bilateria. Previous analyses of SSU rRNA sequences have yielded conflicting results; in many studies Ctenophora forms the sister group of Cnidaria + Bilateria, but in others the ctenophores group with poriferans. Here we re‐examine the SSU sequence by analyzing a dataset with 528 metazoan + outgroup sequences, including almost 120 poriferan and diploblast sequences. We use parsimony ratchet and jackknife methods, as well as Bayesian methods, to analyze the data. The results indicate strong phylogenetic signals for a cnidarian + bilaterian group and for the comb jellies to have branched off early within a group uniting all epithelial animals [(Ct,(Cn,Bi))]. We demonstrate the importance of inclusive taxonomic coverage of ribosomal sequences for resolving this problematic part of the metazoan tree: topological stability increases dramatically with the addition of taxa, and the jackknife frequencies of the internal nodes uniting the lineages [(Cn,Bi) and ((Ct,(Cn,Bi))] also increase. We consider the reconstructed topology to represent the current best hypothesis of the interrelationships of these old lineages. Some morphological features supporting alternative hypotheses are discussed in the light of this result.© The Willi Hennig Society 2004.
Demonstration of differential virulence gene promoter activation in vivo in Bordetella pertussis using RIVET
Authors: Veal‐Carr Wendy L. , Stibitz Scott 
Published: January 2005

Summary Bordetella pertussis, the etiologic agent of whooping cough, causes disease by employing an array of virulence factors controlled by the BvgA–BvgS two‐component signal transduction system. Regulation by this system has been extensively characterized in vitro, where bvg‐activated genes are repressed in a process known as phenotypic modulation. Differential regulation of these genes by the response regulator BvgA results in promoters that are activated early, middle, or late after being released from modulation. However, the in vivo environmental signal and regulation pattern has not been described. In order to investigate BvgAS‐mediated regulation of B. pertussis virulence factors in vivo using the mouse aerosol challenge model, we have adapted the recombinase‐based in vivo technology (RIVET) system for use in B. pertussis. We have demonstrated that these strains show resolution during in vitro growth under non‐modulating conditions. In addition, we have demonstrated that modulating strains by growth on media containing MgSO4 does not affect virulence in the mouse aerosol challenge model. We have therefore used the RIVET system to reveal the time‐course of gene expression in vivo for selected B. pertussis virulence factors (cya, fha, prn and ptx). Our data indicate that this method can be effectively used to monitor and compare in vivo and in vitro gene expression in B. pertussis, and that temporal regulation patterns previously observed in vitro are mirrored in vivo.
Population density‐dependent regulation of exopolysaccharide formation in the hyperthermophilic bacterium Thermotoga maritima
Authors: Johnson Matthew R. , Montero Clemente I. , Conners Shannon B. , Shockley Keith R. , Bridger Stephanie L. , Kelly Robert M. 
Published: January 2005

SummaryCo‐cultivation of the hyperthermophiles Thermotoga maritima and Methanococcus jannaschii resulted in fivefold higher T. maritima cell densities when compared with monoculture as well as concomitant formation of exopolysaccharide and flocculation of heterotroph‐methanogen cellular aggregates. Transcriptional analysis of T. maritima cells from these aggregates using a whole genome cDNA microarray revealed the induction of a putative exopolysaccharide synthesis pathway, regulated by intracellular levels of cyclic diguanosine 3′,5′‐(cyclic)phosphate (cyclic di‐GMP) and mediated by the action of several GGDEF proteins, including a putative diguanylate cyclase (TM1163) and a putative phosphodiesterase (TM1184). Transcriptional analysis also showed that TM0504, which encodes a polypeptide containing a motif common to known peptide‐signalling molecules in mesophilic bacteria, was strongly upregulated in the co‐culture. Indeed, when a synthetically produced peptide based on TM0504 was dosed into the culture at ecologically relevant levels, the production of exopolysaccharide was induced at significantly lower cell densities than was observed in cultures lacking added peptide. In addition to identifying a pathway for polysaccharide formation in T. maritima, these results point to the existence of peptide‐based quorum sensing in hyperthermophilic bacteria and indicate that cellular communication should be considered as a component of the microbial ecology within hydrothermal habitats.
Recruitment of penicillin‐binding protein PBP2 to the division site of Staphylococcus aureus is dependent on its transpeptidation substrates
Authors: Pinho Mariana G. , Errington Jeff 
Published: January 2005

Summary Staphylococcus aureus penicillin‐binding protein PBP2 is an enzyme involved in the last stages of peptidoglycan assembly and is an important player in the mechanism of methicillin resistance of this pathogen. PBP2 localized to the division site but its recruitment to the forming division septum was prevented after acylation by oxacillin. The presence of the antibiotic did not affect FtsZ ring maintenance nor the localization of externalized peptidoglycan precursors. Delocalization of PBP2 was also observed when its pentapeptide substrate was eliminated by addition of d‐cycloserine or blocked by addition of vancomycin. Taken together these observations suggest that PBP2 is recruited to the division site by binding to its substrate, which is localized at that place. In methicillin‐resistant S. aureus, addition of oxacillin does not result in delocalization of PBP2 indicating that acylated PBP2 can be maintained in place by functional PBP2A, the central element of this resistance mechanism.
Neisseria meningitidis NadA is a new invasin which promotes bacterial adhesion to and penetration into human epithelial cells
Authors: Capecchi Barbara , Adu‐Bobie Jeannette , Di Marcello Federica , Ciucchi Laura , Masignani Vega , Taddei Annarita , Rappuoli Rino , Pizza Mariagrazia , Aricò Beatrice 
Published: January 2005

Summary Neisseria  meningitidis  is  a  human  pathogen,  which is a major cause of sepsis and meningitis. The bacterium colonizes the upper respiratory tract of approximately 10% of humans where it lives as a commensal. On rare occasions, it crosses the epithelium and reaches the bloodstream causing sepsis. From the bloodstream it translocates the blood–brain barrier, causing meningitis. Although all strains have the potential to cause disease, a subset of them, which belongs to hypervirulent lineages, causes disease more frequently than others. Recently, we described NadA, a novel antigen of N. meningitidis, present in three of the four known hypervirulent lineages. Here we show that NadA is a novel bacterial invasin which, when expressed on the surface of Escherichia coli, promotes adhesion to and invasion into Chang epithelial cells. Deletion of the N‐terminal globular domain of recombinant NadA or pronase treatment of human cells abrogated the adhesive phenotype. A hypervirulent strain of N. meningitidis where the nad A gene was inactivated had a reduced ability to adhere to and invade into epithelial cells in vitro. NadA is likely to improve the fitness of N. meningitidis contributing to the increased virulence of strains that belong to the hypervirulent lineages.