bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Generalized Composite Commodity Theorem and Food Demand Estimation
Authors: Reed Albert J. , Levedahl J. William , Hallahan Charles 
Published: January 2005

AbstractThis article reports tests of aggregation over consumer food products and estimates of aggregate food demand elasticities. Evidence that food demand variables follow unit root processes leads us to build on and simplify existing tests of the Generalized Composite Commodity Theorem. We compute food demand elasticities using a method of cointegration that is shown to apply to a convenient but nonlinear functional form. Estimates are based on consumer reported expenditure data rather than commercial disappearance data.
A Varying Coefficient Approach to Global Flexibility in Demand Analysis: A Semiparametric Approximation
Authors: Sarmiento Camilo 
Published: January 2005

AbstractTo reduce dimensionality issues, this article derives a globally flexible demand system that can be estimated non‐parametrically with a specially devised temporal kernel. Statistical and economic results from a meat demand application underscores the usefulness of a temporal kernel in globally approximating an integrable demand system.
Share Tenancy, Ownership Structure, and Prevented Planting Claims in Crop Insurance
Authors: Rejesus Roderick M. , Escalante Cesar L. , Lovell Ashley C. 
Published: January 2005

AbstractA conceptual model based on opportunity cost and expected utility principles establishes linkages between the likelihood of prevented planting claims in crop insurance and existing share leasing arrangements/internal farm business structures. Results of heteroskedastic probit estimation procedures indicate that simpler internal business structures and more dominant farmer‐tenant leasing position can increase the probability of submitting a prevented planting claim.
University Life Science Programs and Agricultural Biotechnology
Authors: Xia Yin , Buccola Steven 
Published: January 2005

AbstractWe examine sources of productivity in bioscience research and graduate training in U.S. universities. For this purpose, we first identify the scientific publications cited on agricultural biotechnology patents, and then trace the citations back to the universities producing the cited research. Insight is thus gained into the university investments that demonstrably influence useful technology. Life‐science budget allocations substantially affect both graduate education and technology‐relevant science. Graduate training shows decreasing returns to budget scale, while productive research shows decreasing returns in the short run but increasing returns in the long run. Training is a weak substitute for research, while research is a moderate complement to training.
Slippage in the Conservation Reserve Program or Spurious Correlation? A Comment
Authors: Roberts Michael J. , Bucholtz Shawn 
Published: January 2005

AbstractThe Conservation Reserve Program (CRP) pays farmers about $2 billion per year to retire cropland under ten‐ to fifteen‐year contracts. Recent research by Wu found that slippage—an unintended stimulus of new plantings—offsets some of CRP's environmental benefits. Wu does not account for the endogeneity of CRP enrollments. Furthermore, the data used by Wu cannot be used to estimate slippage arising from a price feedback effect. We replicate Wu's findings, demonstrate the possible presence of spurious correlation, and construct new estimates with corrections for endogeneity and other econometric problems. We find no convincing evidence of slippage.
Slippage Effects of the Conservation Reserve Program: Reply
Authors: Wu JunJie 
Published: January 2005

AbstractGiven that the Conservation Reserve Program (CRP) costs taxpayers $2 billion per year and remains the largest conservation program in U.S. history, Roberts and Bucholtz are to be commended for revisiting the slippage issue. However, their central point that regional variation in CRP acreage is endogenous is inconsistent with CRP implementation rules and data. Thus, it is not surprising that the null hypothesis of exogeneity cannot be rejected by statistical tests.
Two chorismate mutase genes from the root‐knot nematode Meloidogyne incognita
Authors: HUANG GUOZHONG , DONG RUIHUA , ALLEN REX , DAVIS ERIC L. , BAUM THOMAS J. , HUSSEY RICHARD S. 
Published: February 2005

SUMMARYParasitism genes encoding secretory proteins expressed in the oesophageal glands of phytoparasitic nematodes play critical roles in nematode invasion of host plants, establishment of feeding sites and suppression of host defences. Two chorismate mutase (CM) genes potentially having a role in one or more of these processes were identified from a Meloidogyne incognita oesophageal gland‐cell subtractive cDNA library. These M. incognita enzymes (designated as MI‐CM‐1 and MI‐CM‐2) with amino‐terminal signal peptides, were significantly similar to chorismate mutases in M. javanica and bacteria. The complementation of an Escherichia coli CM‐deficient mutant by the expression of Mi‐cm‐1 or Mi‐cm‐2 confirmed their CM activity. In‐situ mRNA hybridization showed that the transcripts of Mi‐cm‐1 and Mi‐cm‐2 accumulated specifically in the two subventral oesophageal gland cells of M. incognita. RT‐PCR analysis confirmed that their transcript abundances were high in the early parasitic juvenile stages, and low (Mi‐cm‐1) or undetectable (Mi‐cm‐2) in later parasitic stages of the nematode. Southern blot analysis revealed that these CM genes were members of a small multigene family in Meloidogyne species. The widespread presence of CMs in the specialized sedentary endoparasitic nematode species suggests that this multifunctional enzyme may be a key factor in modulating plant parasitism.
Beet poleroviruses: close friends or distant relatives?
Authors: STEVENS MARK , FREEMAN BENJAMIN , LIU HSING‐YEH , HERRBACH ETIENNE , LEMAIRE OLIVIER 
Published: February 2005

SUMMARYTaxonomy:  There are three members of the genus Polerovirus (family Luteoviridae) that induce yellowing of sugar beet: Beet mild yellowing virus (BMYV), Beet chlorosis virus (BChV) and Beet western yellows virus‐USA (BWYV‐USA, Fig. 1). Non‐beet‐infecting isolates of BWYV found particularly within Europe have now been re‐named Turnip yellows virus (TuYV). Species‐specific antibodies are unavailable, but the viruses can be distinguished by RT‐PCR using primers specifically designed to the 5′ end of their respective genomes.Taxonomy and genome organization of members of the Luteoviridae family as adopted by ICTV (Mayo, 2002). The term ‘Beet Polerovirus’ indicates virus species (in bold type) that induce yellowing of sugar beet. Schematic diagrams of genome organization of the three Luteoviridae genera are shown.imagePhysical properties:  The isometric virus particles are approximately 26 nm in diameter and the genome consists of a single strand of positive sense RNA that utilizes almost all known plant virus gene expression strategies (initiation bypass, translational frameshifting and readthrough, synthesis of subgenomic RNA and proteolytic processing).Host range:   Many members of the Chenopodiaceae are susceptible, including commercial crops of sugar beet (Beta vulgaris), red beet and spinach. Experimental hosts include Montia perfoliata, Nicotiana benthamiana and Arabidopsis thaliana.Symptoms:  Sugar beet infected with beet poleroviruses show patches of chlorosis on the older leaves 4–6 weeks post‐infection; these areas expand until the whole leaf becomes yellow and older leaves then tend to thicken and become brittle.Transmission:  Beet poleroviruses are transmitted in a persistent (circulative, non‐propagative) manner by several different aphid species, Myzus persicae being the most important vector.
Lysosomal storage disorders
Authors: Vellodi Ashok 
Published: February 2005

SummaryAlthough the first description of a lysosomal storage disorder was that of Tay‐Sachs disease in 1881, the lysosome was not discovered until 1955, by Christian De Duve. The first demonstration by Hers in 1963 of a link between an enzyme deficiency and a storage disorder (Pompe's disease) paved the way for a series of seminal discoveries about the intracellular biology of these enzymes and their substrates, culminating in the successful treatment of Gaucher's disease with β‐glucosidase in the early 1990s. It is now recognized that these disorders are not simply a consequence of pure storage, but result from perturbation of complex cell signalling mechanisms. These in turn give rise to secondary structural and biochemical changes, which have important implications for therapy. Significant challenges remain, particularly the treatment of central nervous system disease. It is hoped that recent advances in our understanding of lysosomal biology will enable successful therapies to be developed.
Induction of CCAAT/enhancer binding protein‐δ by cytokinins, but not by retinoic acid, during granulocytic differentiation of human myeloid leukaemia cells
Authors: Ishii Yuki , Kasukabe Takashi , Honma Yoshio 
Published: February 2005

SummaryCytokinins, purine derivatives that act as hormones to control many processes in plants, are very effective at inducing the granulocytic differentiation of human myeloid leukaemia cells. Isopentenyladenine (IPA), a potent cytokinin, significantly induced the expression of CCAAT/enhancer‐binding protein (C/EBP)δ, but not C/EBPα protein, whereas all‐trans retinoic acid, a well‐known inducer of granulocytic differentiation, induced C/EBPα but not C/EBPδ protein. Antisense oligonucleotide for C/EBPδ, but not C/EBPα or C/EBPβ, effectively suppressed IPA‐induced differentiation, suggesting that the expression of C/EBPδ protein is necessary for cytokinin‐induced differentiation. Although C/EBPα is known to be crucial for granulocytic differentiation, the function of C/EBPδ has not been well documented in the regulation of haematopoiesis. The role of C/EBPδ in the granulocytic differentiation of myeloid leukaemia cells is discussed.
Differential control of G0 programme in chronic lymphocytic leukaemia: a novel prognostic factor
Authors: Danilov Alexey V. , Klein Andreas K. , Lee Henry J. , Baez Diana Velez , Huber Brigitte T. 
Published: February 2005

SummaryChronic lymphocytic leukaemia (CLL) is a unique malignancy where quiescent B cells accumulate in the peripheral blood. Since clinical outcomes in CLL are very heterogeneous, it is of utmost importance to correctly assess the disease prognosis in each individual case. Recently, it has been shown that high ZAP‐70 [Zeta‐chain (T‐cell receptor) associated protein kinase (70 kDa)] expression level strongly correlates with lack of IgVH mutations and poor prognosis in B‐CLL. As CLL malignant cells are arrested in G0, we investigated whether Dipeptidyl Peptidase 2 (DPP2), a serine protease that plays a key role in keeping cells in the quiescent state, is involved in cell‐cycle control in CLL. We have previously shown that specific inhibition of DPP2 results in apoptosis of normal lymphocytes. In this study, cell apoptosis experiments were conducted in 38 patients with B‐CLL. Two distinct subsets of B‐CLL were identified, susceptible and resistant to DPP2‐inhibition‐induced apoptosis. If resistant to apoptosis (42·1%), the CLL cells have higher expression of ZAP‐70 and exhibit a worse prognosis, such as shorter treatment‐free time period. Thus, resistance vs. susceptibility to DPP2‐inhibiton induced apoptosis can be employed as a novel prognostic factor in CLL.
Accuracy of platelet counting haematology analysers in severe thrombocytopenia and potential impact on platelet transfusion
Authors: Segal H. C. , Briggs C. , Kunka S. , Casbard A. , Harrison P. , Machin S. J. , Murphy M. F. 
Published: February 2005

SummaryAlthough haematology analysers provide reliable full blood counts, they are known to be inaccurate at enumerating platelets in severe thrombocytopenia. If the thresholds for platelet transfusion, currently set at 10 × 109/l, are to be further reduced, it is vital that the limitations of current analysers are fully understood. The aim of this large multicentre study was to determine the accuracy of haematology analysers in current routine practice for platelet counts below 20 × 109/l. Platelet counts estimated by analysers using optical, impedance and immunological methods were compared with the International Reference Method for platelet counting. The results demonstrated variation in platelet counting between different analysers and even the same type of analyser at different sites. Optical methods for platelet counting on the XE 2100, Advia 120, Cell‐Dyn 4000 and H3* were not superior to impedance methods on the XE 2100, LH750 and Pentra analysers. All analysers except one overestimated the platelet count, which would result in under transfusion of platelets. This study highlights the inaccuracies of haematology analysers in platelet counting in severe thrombocytopenia. It re‐emphasizes the need for external quality control to improve analyser calibration for samples with low platelet counts, and suggests that the optimal thresholds for prophylactic platelet transfusions should be re‐evaluated.
Global change effects on a mechanistic decomposer food web model
Authors: Kuijper Lothar D. J. , Berg Matty P. , Morriën Elly , Kooi Bob W. , Verhoef Herman A. 
Published: February 2005

AbstractGlobal change may affect the structure and functioning of decomposer food webs through qualitative changes in freshly fallen litter. We analyzed the predicted effects of a changing environment on a dynamic model of a donor‐controlled natural decomposer ecosystem near Wekerom, the Netherlands. This system consists of fungi, bacteria, fungivores, bacterivores and omnivores feeding on microbiota and litter as well. The model concentrates on carbon and nitrogen flows through the trophic niches that define this decomposer system, and is designed to predict litter masses and abundances of soil biota. For modeling purposes, the quality of freshly fallen leaf litter is defined in terms of nitrogenous and non‐nitrogenous components, of which refractory and labile forms are present. The environmental impacts of elevated CO2, enhanced UV‐B and eutrophication, each with their own influence on leaf litter quality, are studied. The model predicts steady‐state dynamics exclusively, for all three scenarios. Environmental changes impact most demonstratively on the highest trophic niches, and affect microbiotic abundances and litter decomposition rates to a lesser extent. We conclude that the absence of trophic cascade effects may be attributed to weak trophic links, and that non‐equilibrium dynamics occurring in the system are generally because of encounter rates based on fractional substrate densities in the litter. We set out a number of experimentally testable hypotheses that may improve understanding of ecosystem dynamics.
Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl‐homoserine lactones
Authors: Collins Cynthia H. , Arnold Frances H. , Leadbetter Jared R. 
Published: January 2005

SummaryLuxR‐type  transcriptional  regulators  play  key  roles in quorum‐sensing systems that employ acyl‐homoserine lactones (acyl‐HSLs) as signal molecules. These proteins mediate quorum control by changing their interactions with RNA polymerase and DNA in response to binding their cognate acyl‐HSL. The evolutionarily related LuxR‐type proteins exhibit considerable diversity in primary sequence and in their response to acyl‐HSLs having acyl groups of differing length and composition. Little is known about which residues determine acyl‐HSL specificity, and less about the evolutionary time scales required to forge new ones. To begin to examine such issues, we have focused on the LuxR protein from Vibrio fischeri, which activates gene transcription in response to binding its cognate quorum signal, 3‐oxohexanoyl‐homoserine lactone (3OC6HSL). Libraries of luxR mutants were screened for variants exhibiting increased gene activation in response to octanoyl‐HSL (C8HSL), with which wild‐type LuxR interacts only weakly. Eight LuxR variants were identified that showed a 100‐fold increase in sensitivity to C8HSL; these variants also displayed increased sensitivities to pentanoyl‐HSL and tetradecanoyl‐HSL, while maintaining a wild‐type or greater response to 3OC6HSL. The most sensitive variants activated gene transcription as strongly with C8HSL as the wild type did with 3OC6HSL. With one exception, the amino acid residues involved were restricted to the N‐terminal, ‘signal‐binding’ domain of LuxR. These residue positions differed from critical positions previously identified via ‘loss‐of‐function’ mutagenesis. We have demonstrated that acyl‐HSL‐dependent quorum‐sensing systems can evolve rapidly to respond to new acyl‐HSLs, suggesting that there may be an evolutionary advantage to maintaining such plasticity.
Mutations in the amino‐terminal domain of λ‐integrase have differential effects on integrative and excisive recombination
Authors: Warren David , Lee Sang Yeol , Landy Arthur 
Published: February 2005

SummaryLambda integrase (Int) forms higher‐order protein–DNA complexes necessary for site‐specific recombination. The carboxy‐terminal domain of Int (75–356) is responsible for catalysis at specific core‐type binding sites whereas the amino‐terminal domain (1–70) is responsible for cooperative arm‐type DNA binding. Alanine scanning mutagenesis of residues 64–70, within full‐length integrase, has revealed differential effects on cooperative arm binding interactions that are required for integrative and excisive recombination. Interestingly, while these residues are required for cooperative arm‐type binding on both P′1,2 and P′2,3 substrates, cooperative binding at the arm‐type sites P′2,3 was more severely compromised than binding at arm‐type sites P′1,2 for L64A. Concomitantly, L64A had a much stronger effect on integrative than on excisive recombination. The arm‐binding properties of Int appear to be intrinsic to the amino‐terminal domain because the phenotype of L64A was the same in an amino‐terminal fragment (Int 1–75) as it was in the full‐length protein.
Genetic determinants of biofilm development of opaque and translucent Vibrio parahaemolyticus
Authors: Enos‐Berlage Jodi L. , Guvener Zehra T. , Keenan Carrie E. , McCarter Linda L. 
Published: February 2005

Summary Vibrio parahaemolyticus isolates display variation in colony morphology, alternating between opaque (OP) and translucent (TR) cell types. Phase variation is the consequence of genetic alterations in the locus encoding the quorum sensing output regulator OpaR. Here, we show that both cell types form stable, but distinguishable biofilms that differ with respect to attachment and detachment profiles to polystyrene, pellicle formation and stability at the air/medium interface, and submerged biofilm architecture and dispersion at a solid/liquid interface. The pellicle, which is a cohesive mat of cells, was exploited to identify mutants having altered or defective biofilm formation. Transposon insertion mutants were obtained with defects in genes affecting multiple cell surface characteristics, including extracellular polysaccharide, mannose‐sensitive haemagglutinin type 4 pili and polar (but not lateral) flagella. Other insertions disrupted genes coding for potential secreted proteins or transporters of secreted proteins, specifically haemolysin co‐regulated protein and an RTX toxin‐like membrane fusion transporter, as well as potential modifiers of cell surface molecules (nagAC operon). The pellicle screen also identified mutants with lesions in regulatory genes encoding H‐NS, a CsgD‐like repressor and an AraC‐like protein. This work initiates the characterization of V. parahaemolyticus biofilm formation in the OP and TR cell types and identifies a diverse repertoire of cell surface elements that participate in determining multicellular architecture.
TUP1 disruption reveals biological differences between MATa and MATα strains of Cryptococcus neoformans
Authors: Lee Hyeseung , Chang Yun C. , Kwon‐Chung K. J. 
Published: February 2005

Summary Cryptococcus neoformans exists in two mating types MATa and MATα. Although the morphology, growth characteristics and genetic segregation patterns among MATa and MATα strains are indistinguishable in the laboratory, the predominance of MATα strains in nature suggests that MATα strains are better suited for survival in nature. We disrupted the TUP1 gene, a global repressor, to find the possible biological differences in congenic MATα and MATa cells of C. neoformans. Disruption of TUP1 affected neither the yeast nor the hyphal cell morphology but resulted in a similar reduction of mating frequencies in both MATα and MATa cells. Disruption of TUP1, however, functionally manifested itself in several mating type‐dependent phenotypes: (i) MATα cells became more sensitive to 0.8 M KCl while MATa cells showed no change in sensitivity, (ii) a temperature‐dependent growth reduction was exhibited at both 30°C and 25°C in MATa but a similar growth reduction was not observed in MATα cells until the temperature was lowered to 25°C and (iii) the transcriptional level of genes in several different biological pathways was markedly altered in a mating type‐dependent manner. This work is the first case in which non‐mating‐related biological differences are observed between two congenic mating partners in yeast.
Retinal biosynthesis in Eubacteria: in vitro characterization of a novel carotenoid oxygenase from Synechocystis sp. PCC 6803
Authors: Ruch Sandra , Beyer Peter , Ernst Hansgeorg , Al‐Babili Salim 
Published: February 2005

SummaryRetinal and its derivatives represent essential compounds in many biological systems. In animals, they are synthesized through a symmetrical cleavage of β‐carotene catalysed by a monooxygenase. Here, we demonstrate that the open reading frame sll1541 from the cyanobacterium Synechocystis sp. PCC 6803 encodes the first eubacterial, retinal synthesizing enzyme (Diox1) thus far reported. In contrast to enzymes from animals, Diox1 converts β‐apo‐carotenals instead of β‐carotene into retinal in vitro. The identity of the enzymatic product was proven by HPLC, GC‐MS and in a biological test. Investigations, of the stereospecifity showed that Diox1 cleaved only the all‐trans form of β‐apo‐8′‐carotenal, yielding all‐trans‐retinal. However, Diox1 exhibited wide substrate specificity with respect to chain‐lengths and functional end‐groups. Although with divergent Km and Vmax values, the enzyme converted β‐apo‐carotenals, (3R)‐3‐OH‐β‐apo‐carotenals as well as apo‐lycopenals into retinal, (3R)‐3‐hydroxy‐retinal and acycloretinal respectively. In addition, the alcohols of these substrates were cleaved to yield the corresponding retinal derivatives.
Telomere length control and transcriptional regulation of subtelomeric adhesins in Candida glabrata
Authors: Castaño Irene , Pan Shih‐Jung , Zupancic Margaret , Hennequin Christophe , Dujon Bernard , Cormack Brendan P. 
Published: February 2005

SummaryThe pathogenic yeast Candida glabrata is able to bind in vitro to human epithelial cells. This interaction depends on expression of the adhesin Epa1p. The genome contains a number of EPA1 paralogues which localize to the subtelomeric regions of the C. glabrata. We have identified three hyperadherent mutants of C. glabrata. The first has an insertion adjacent to EPA7, an EPA1‐related adhesin. The others disrupt the SIR3 and RIF1 genes of C. glabrata. We show that SIR3 and RIF1 are required for subtelomeric silencing in C. glabrata and that RIF1 regulates telomere length in C. glabrata. We show that the hyperadherent phenotype of the sir3Δ and rif1Δ deletion strains depends primarily on derepression of two novel members of the EPA gene family –EPA6 and EPA7. The sir3Δ and rif1Δ mutants show increased colonization of the kidney in a murine model of disseminated infection and this hypercolonization depends, at least in part, on derepression of EPA6 and EPA7. The analysis here is the first evidence that multiple EPA genes encode adhesins and demonstrates that transcription of at least two of these adhesins is regulated by subtelomeric silencing.