bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying Vasculature: New Measures Applied to Arterial Trees in the Quail Chorioallantoic Membrane
Authors: Lubkin Sharon R. , Funk Sarah E. , Sage E. Helene
Published: December 2005

A wide variety of measures is currently in use in the morphometry of vascular systems. We introduce two additional classes of measures based on erosions and dilations of the image. Each measure has a clear biological interpretation in terms of the measured structures and their function. The measures are illustrated on images of the arterial tree of the quail chorioallantoic membrane (CAM). The new measures are correlated with widely‐used measures, such as fractal dimension, but allow a clearer biological interpretation. To distinguish one CAM arterial tree from another, we propose reporting just three independent, uncorrelated numbers: (i) the fraction of tissue which is vascular (VF0, a pure ratio), (ii) a measure of the typical distance of the vascularized tissue to its vessels (CL, a length), and (iii) the flow capacity of the tissue (P, an area). An unusually large CL would indicate the presence of large avascular areas, a characteristic feature of tumor tissue. CL is inversely highly correlated with fractal dimension of the skeletonized image, but has a more direct biological interpretation.
The Oldest Extant Undergraduate Essay in Economics?
Authors: Waterman A. M. C.
Published: December 2005

The manuscript collection of the National Library of Scotland contains two undergraduate essays in “political economy” written for the Rev. Thomas Chalmers while he was Professor of Moral Philosophy at St Andrews University from 1823 to 1828. The first is signed “Pat. J. Stirling.” The second is unsigned, but is in the same hand. The Library attributes both manuscripts to Patrick James Stirling (1809–1891). The essays are marked with deletions and insertions, most of which appear to be by Stirling himself, and the summary appraisal at the end of each in Chalmers's own hand is signed “Thomas Chalmers.” In the transcription of the shorter essay printed in section VI below, [bracketed] words are those which have been deleted. Underlined words are those inserted by Stirling or possibly Chalmers. Stirling's erratic capitalization and hyphenation, and the indentation of his first paragraph, have been preserved.
The Greek “Society for the Freedoms of Trade” (1865–67): Rise, Activities, Decline
Authors: Psalidopoulos Michalis
Published: December 2005

The 150th celebration of the repeal of the Corn Laws in 1846 was a major stimulus for new publications on the issue of free trade versus protection, a question that dominated economic policy agendas all over Europe in the nineteenth century. Original texts dating from that period were again made public (Kadish 1996, Schonhardt-Bailey 1997), the works of Richard Cobden became available (Cain 1995), and Douglas A. Irwin's book (1996) and Anthony Howe's treatise (1997) can be seen as the “cosmopolitan” answers to older (Semmel 1970) and contemporary (Magnusson 1994 and Wendler 1996) defenses of a “national” economic policy. This literature, however, as well as conferences on the reception of free trade (Marrison 1998), concentrated on the commercial policy of the most economically advanced nations, leaving completely out of scope discussions, debates and economic policy dilemmas related to international trade in other, less-developed countries.
Emigré Economists and American Neoclassical Economics, 1933–1945
Authors: Mongiovi Gary
Published: December 2005

The rise of European fascism in the 1920s and '30s triggered the greatest migration of intellectual capital the world has ever known. This paper is concerned with the German-speaking economists who formed the core of the original Graduate Faculty of the New School for Social Research. Among émigré economists of the interwar period, those who found refuge at the New School exerted a distinctive influence on American economics, partly owing to their concentration at a single institution, and partly by virtue of the character and quality of their work. The paper has three aims: to provide an overview of the contributions of these economists, to assess their impact on American economics, and to account for the apparent evaporation of their legacy after the onset of the Cold War.
Richard A. Musgrave and Ludwig von Mises: Two Cases of Emigrè Economists in America
Authors: Moss Laurence S.
Published: December 2005

The expulsion of the academicians from Germany, Austria, and other central European countries is for the history of social science as traumatic and significant an event as the bombing of Pearl Harbor was for the United States' naval fleet in the South Pacific. The Restoration of the Civil Service Act occurred on April 7, 1933, shortly after the National Socialists came to power. It ordered “disagreeable” persons to leave the Universities and was the harbinger of other “cleansing” that followed the German war machine into Austria, the Czech Republic, and so on. The start of this intellectual exodus occurred a whole eight years before the United States entered the war on December 7, 1941. The destruction of the American naval fleet by the Japanese air force in 1941 required a massive State-sponsored mobilization as the United States prepared for and entered the war in the Pacific. The destruction of social science in the German-speaking Universities started on April 7, 1933, and continued as the German armies moved eastward, resulting in no less than 328 dislocated economists who emigrated out of central and eastern Europe to rebuild their lives and academic reputations in other places, especially in the United States. As Hagemann has demonstrated, the United States “was the direct or indirect destination for some two-thirds of the German-speaking emigré economists” (Hagemann 2005). This “rebuilding” of lives, families, and scientific reputations is amazing in its magnitude and complexity and is also itself a topic for serious study and understanding within the sociology of the social sciences. Hagemann has made major contributions to the telling of this story (Hagemann 1997).
Rapid, Diffusional Shuttling of Poly(A) RNA between Nuclear Speckles and the Nucleoplasm
Authors: Politz Joan C. Ritland , Tuft Richard A. , Prasanth Kannanganattu V. , Baudendistel Nina , Fogarty Kevin E. , Lifshitz Larry M. , Langowski Jörg , Spector David L. , Pederson Thoru
Published: December 2005

Speckles are nuclear bodies that contain pre-mRNA splicing factors and polyadenylated RNA. Because nuclear poly(A) RNA consists of both mRNA transcripts and nucleus-restricted RNAs, we tested whether poly(A) RNA in speckles is dynamic or rather an immobile, perhaps structural, component. Fluorescein-labeled oligo(dT) was introduced into HeLa cells stably expressing a red fluorescent protein chimera of the splicing factor SC35 and allowed to hybridize. Fluorescence correlation spectroscopy (FCS) showed that the mobility of the tagged poly(A) RNA was virtually identical in both speckles and at random nucleoplasmic sites. This same result was observed in photoactivation-tracking studies in which caged fluorescein-labeled oligo(dT) was used as hybridization probe, and the rate of movement away from either a speckle or nucleoplasmic site was monitored using digital imaging microscopy after photoactivation. Furthermore, the tagged poly(A) RNA was observed to rapidly distribute throughout the entire nucleoplasm and other speckles, regardless of whether the tracking observations were initiated in a speckle or the nucleoplasm. Finally, in both FCS and photoactivation-tracking studies, a temperature reduction from 37 to 22°C had no discernible effect on the behavior of poly(A) RNA in either speckles or the nucleoplasm, strongly suggesting that its movement in and out of speckles does not require metabolic energy.
BioContrasts: extracting and exploiting protein–protein contrastive relations from biomedical literature
Authors: Kim Jung-jae , Zhang Zhuo , Park Jong C. , Ng See-Kiong
Published: December 2005

Motivation: Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation.

Results: Our BioContrasts system extracts protein–protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as ‘A but not B’. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways.

Availability: BioContrasts can be accessed at . It is also mirrored at

Supplementary information: Supplementary materials are available at Bioinformatics online.

Contact:  skng@i2r.a-star.edu.sg; park@cs.kaist.ac.kr
Bayesian sparse hidden components analysis for transcription regulation networks
Authors: Sabatti Chiara , James Gareth M.
Published: December 2005

Motivation: In systems like Escherichia Coli, the abundance of sequence information, gene expression array studies and small scale experiments allows one to reconstruct the regulatory network and to quantify the effects of transcription factors on gene expression. However, this goal can only be achieved if all information sources are used in concert.

Results: Our method integrates literature information, DNA sequences and expression arrays. A set of relevant transcription factors is defined on the basis of literature. Sequence data are used to identify potential target genes and the results are used to define a prior distribution on the topology of the regulatory network. A Bayesian hidden component model for the expression array data allows us to identify which of the potential binding sites are actually used by the regulatory proteins in the studied cell conditions, the strength of their control, and their activation profile in a series of experiments. We apply our methodology to 35 expression studies in E.Coli with convincing results.

Availability:  

Supplementary information: The supplementary material are available at Bioinformatics online.

Contact:  csabatti@mednet.ucla.edu
The Completely Opacified Frontal or Sphenoid Sinus: A Marker of More Severe Disease in Chronic Rhinosinusitis?
Authors: Bhattacharyya Neil
Published: December 2005

Objective: Determine whether complete opacification of the sphenoid or frontal sinus is associated with increased clinical severity of chronic rhinosinusitis (CRS).

Methods: Adult patients undergoing evaluation for CRS prospectively completed the rhinosinusitis symptom inventory (RSI) and underwent computed tomography of the paranasal sinuses. A cohort with at least one completely opacified frontal sinus was identified. To each patient in this opacified cohort, a control patient without complete frontal sinus opacification was matched with corresponding Lund score. Symptom scores for headache, facial pressure, RSI symptom domains, and medical resource consumption were statistically compared. Similar analysis was conducted for patients with complete sphenoid sinus opacification.

Results: Fifty‐four patients with at least one completely opacified frontal sinus were matched for Lund score to the control group (mean Lund score 17.1). There was no statistically significant difference in headache (2.1 vs. 2.8) or pressure scores (2.0 vs. 2.3) or in the RSI symptom domains between those patients with completely opacified frontal sinuses and controls, respectively. Although completely opacified patients received more antibiotic treatment and missed more workdays, only the increased numbers of physicians visits (4.0 vs. 2.1, P = .02) was significant. Thirty‐four of 35 completely opacified sphenoid patients were matched to control patients (mean Lund score 16.7). Again, differences in symptom scores for headache (2.5 vs. 2.5), facial pressure (2.3 vs. 2.3), and RSI symptom domains were not statistically significant. Increased use of antibiotics (9.6 vs. 3.9, P = .036) and physician visits (5.8 vs. 1.8, P = .024) for sphenoid opacification patients was statistically significant.

Conclusions: Patients with a completely opacified sphenoid or frontal sinus do not necessarily manifest more severe clinical symptoms of CRS. Thus, a higher radiographic stage should not be automatically assigned to patients with a completely opacified sphenoid of frontal sinus in CRS.
Magnetohelioseismology
Authors: Thompson Michael J
Published: December 2005

The helioseismic investigation of the solar interior to elucidate the behaviour of the Sun's magnetic field and the interior's role in the solar interior is considered. Such study may be called magnetohelioseismology (from the Greek roots
magnetis, helios
and
seismos
).
Recent progress in prominence seismology
Authors: Ballester José Luis
Published: December 2005

Prominence seismology is a rapidly developing topic which seeks to infer the internal structure and properties of solar prominences from the study of their oscillations. An extense observational background about oscillations in quiescent solar prominences has been gathered during the last 70 years. These observations point out the existence of two different types of oscillations: flare-induced oscillations (winking filaments) which affect the whole prominence and are of large amplitude and small amplitude oscillations which seem to be of local nature. From the theoretical point of view, few models have been set up to explain the phenomenon of winking filaments while, on the contrary, for small amplitude oscillations a large number of models trying to explain the observed features have been proposed. Here, recent theoretical and observational developments on both types of oscillations are reviewed, and suggestions about future research topics which should provide us with a more in-depth knowledge of solar prominences are made.
Multiplexed profiling of candidate genes for CpG island methylation status using a flexible PCR/LDR/Universal Array assay
Authors: Cheng Yu-Wei , Shawber Carrie , Notterman Dan , Paty Philip , Barany Francis
Published: December 2005

DNA methylation in CpG islands is associated with transcriptional silencing. Accurate determination of cytosine methylation status in promoter CpG dinucleotides may provide diagnostic and prognostic value for human cancers. We have developed a quantitative PCR/LDR/Universal Array assay that allows parallel evaluation of methylation status of 75 CpG dinucleotides in the promoter regions of 15 tumor suppressor genes (CDKN2B, CDKN2A, CDKN2D, CDKN1A, CDKN1B, TP53, BRCA1, TIMP3, APC, RASSF1, CDH1, MGMT, DAPK1, GSTP1, and RARB). When compared with an independent pyrosequencing method at a single promoter, the two approaches gave good correlation. In a study using 15 promoter regions and seven blinded tumor cell lines, our technology was capable of distinguishing methylation profiles that identified cancer cell lines derived from the same origins. Preliminary studies using 96 colorectal tumor samples and 73 matched normal tissues indicated CpG methylation is a gene-specific and nonrandom event in colon cancer. This new approach is suitable for clinical applications where sample quantity and purity can be limiting factors.
The prion protein gene in humans revisited: Lessons from a worldwide resequencing study
Authors: Soldevila Marta , Andrés Aida M. , Ramírez-Soriano Anna , Marquès-Bonet Tomàs , Calafell Francesc , Navarro Arcadi , Bertranpetit Jaume
Published: December 2005

Ample evidence has accumulated showing that different coding variants of the PRNP gene confer differential susceptibility for prion diseases. Here we evaluate the patterns of nucleotide variation in PRNP exon 2, which includes all the protein-coding sequence, by resequencing a worldwide sample of 174 humans for 2378 bp. In line with previous studies, we found two main haplotypes differentiated by nonsynonymous substitution in codon 129. Our analyses reveal the worldwide pattern of variation at the PRNP gene to be inconsistent with neutral expectations, indicating instead an excess of low-frequency variants, a footprint of the action of either positive or purifying selection. A comparison of neutrality test statistics for PRNP with other human genes indicates that the signal of positive selection on PRNP is stronger than expected from a possible confounding genome-wide background signal of population expansion. Two main conclusions arise from our analysis. First, the existence of an ancient, stable, balanced polymorphism that has been claimed in a previous study and related to cannibalism can be rejected and is shown to be due to ascertainment bias. Second, our results are consistent with a complex history of selection including mainly positive selection, even if short local periods of balancing selection (Kuru-like episodes), or even a weak purifying selection model, are consistent with our data.
Identification by full-coverage array CGH of human DNA copy number increases relative to chimpanzee and gorilla
Authors: Wilson Gary M. , Flibotte Stephane , Missirlis Perseus I. , Marra Marco A. , Jones Steven , Thornton Kevin , Clark Andrew G. , Holt Robert A.
Published: December 2005

Duplication of chromosomal segments and associated genes is thought to be a primary mechanism for generating evolutionary novelty. By comparative genome hybridization using a full-coverage (tiling) human BAC array with 79-kb resolution, we have identified 63 chromosomal segments, ranging in size from 0.65 to 1.3 Mb, that have inferred copy number increases in human relative to chimpanzee. These segments span 192 Ensembl genes, including 82 gene duplicates (41 reciprocal best BLAST matches). Synonymous and nonsynonymous substitution rates across these pairs provide evidence for general conservation of the amino acid sequence, consistent with the maintenance of function of both copies, and one case of putative positive selection for an uncharacterized gene. Surprisingly, the core histone genes H2A, H2B, H3, and H4 have been duplicated in the human lineage since our split with chimpanzee. The observation of increased copy number of a human cluster of core histone genes suggests that altered dosage, even of highly constrained genes, may be an important evolutionary mechanism.
GeoDa: An Introduction to Spatial Data Analysis
Authors: Anselin Luc , Syabri Ibnu , Kho Youngihn
Published: December 2005

This article presents an overview of GeoDa™, a free software program intended to serve as a user‐friendly and graphical introduction to spatial analysis for non‐geographic information systems (GIS) specialists. It includes functionality ranging from simple mapping to exploratory data analysis, the visualization of global and local spatial autocorrelation, and spatial regression. A key feature of GeoDa is an interactive environment that combines maps with statistical graphics, using the technology of dynamically linked windows. A brief review of the software design is given, as well as some illustrative examples that highlight distinctive features of the program in applications dealing with public health, economic development, real estate analysis, and criminology.
The Influence of Ethnicity and Generational Status on Parent and Family Relations Among Chinese and Filipino Adolescents
Authors: Willgerodt Mayumi Anne , Thompson Elaine Adams
Published: December 2005

Abstract 
Objective:
The purpose of this study was to explore the influence of ethnic and generational differences on perceptions about parent and family relationships in a nationally representative sample of Chinese and Filipino adolescents living in the United States. Design: This was a cross‐sectional descriptive study, utilizing data from the National Longitudinal Study on Adolescent Health. Sample: The sample was weighted to produce a nationally representative sample, based on 216 self‐identified Chinese and 387 self‐identified Filipino adolescents. Results: Results indicated that generational status plays a role in predicting how adolescents perceive the parent–adolescent relationship. Conclusions: Findings provide a basis by which community health nurses can begin to understand the uniqueness of Asian subgroups, as well as generations of immigrant youth.
Predicting Smoking Status in a College‐Age Population
Authors: Ridner S. Lee
Published: December 2005

Abstract 
Objective:
The purpose of this study was to determine the factors that predict smoking group membership in a college‐age population. Design: A nonexperimental cross‐sectional design was used to examine factors that distinguished among four groups: never established (n = 591), former (n = 41), nondaily (n = 80), and daily (n = 76) cigarette smokers. Sample: A pencil and paper questionnaire was returned by 788 randomly selected college students, 18–24 years of age. Results: Significant differences were found among the groups on their mothers', fathers', siblings', and peers' smoking behaviors and attitudes toward smoking. The nondaily and daily smoking groups reported a greater number of risk behaviors than the never established and former smoking groups. The two groups of current smokers also were more likely to report an increased level of depressive symptoms compared with the nonsmoking groups. The number of high school and college friends who smoke and self‐reported high‐risk alcohol and drug behaviors predicted smoking group membership in a polytomous logistic regression. Conclusions: Strategies to alter the social environment and decrease the exposure of nonsmoking students to others who model smoking behaviors may help decrease smoking initiation and prevent relapse on college campuses.
Re‐Evaluating Current Public Health Policy: Alternative Public Health Nursing Approaches to Sexually Transmitted Infection Testing for Teens and Males who Have Sex with Males
Authors: O'Byrne Patrick , Holmes Dave
Published: December 2005

Abstract 
Objective:
Due to a recent increase in the rates of reportable sexually transmitted infections (STI) across Canada, and the movement of public health nursing initiatives to a health promotion/illness prevention model, this paper proposes alternative strategies to current public health initiatives to encourage individuals who are labelled as at‐risk by public health discourses, such as teens and males who have sex with males (MSM), to undertake preventative screening. Theoretical Design: To undertake this task, we approached Health Canada's (2002) determinants of health utilizing Lupton's (1995) post‐structuralist work on public health to suggest that for some members of these groups, health is not an imperative. Conclusions: As such, we propose that increasing anonymous testing and its advertisement would provide one means of providing population‐sensitive care and could thus increase the screening rates of individuals within groups who reject the public health “healthy” disquisition.
Health‐Risk Behaviors in a Sample of First‐Time Pregnant Adolescents
Authors: Kaiser Margaret M. , Hays Bevely J.
Published: December 2005

Abstract 
Objective:
The purpose of this study was to assess the frequency of prenatal health‐risk behaviors (substance use, sexual risk taking, and prenatal class attendance) among a nonrandom sample of first‐time pregnant adolescents. Design: The design is descriptive. Sample: 145 ethnically diverse first‐time pregnant adolescents aged 15–18 years. Measurement: Health behavior questions modified from the Center for Disease Control's Youth Risk Behavior Surveillance System. Results: The health‐risk behavior most modified during pregnancy was alcohol use (64/145 drank but quit and 1/145 did not quit). Of the 52/145 who used street drugs, nine continued despite pregnancy. Of the 75/145 who smoked early in pregnancy, 39 continued. The majority did not use a condom at last sexual intercourse. Approximately half attended a prenatal class and half attended a teen parenting class. Conclusion: Health‐risk behaviors captured by birth certificate data are thought to be underreported for all age groups, and the prevalence of health‐risk behaviors in this sample of pregnant teens was often greater than the most recent national trend data available. The magnitude of the effects of health‐risk behaviors on pregnancy outcomes necessitates improved data gathering to enhance planning and evaluation of research and interventions at community, system, and individual/family levels.
A hepatocarcinogenic tryptophan–pyrolyzate component, Trp‐P‐1, decreases serum total testosterone level and induces hepatic Cyp1a2 in male mice
Authors: Degawa Masakuni , Hanaki Koji , Sekimoto Masashi
Published: December 2005

Male (BALB/c × DBA/2) F1 mice were given 3‐amino‐1,4‐dimethyl‐5H‐pyrido [4,3‐b] indole acetate (Trp‐P‐1; 20 mg/kg body weight) by gavage at 24‐h intervals for 1 or 2 weeks, and the effects of Trp‐P‐1 on the levels of serum total testosterone and hepatic cytochrome P4501a2 (Cyp1a2) were examined. A significant decrease in serum total testosterone level was observed after treatment with Trp‐P‐1 for 2 weeks, but not for 1 week. Likewise, gene expression levels of testicular androgenic enzymes, including cholesterol side chain cleavage cytochrome P450, 3β‐hydroxysteroid dehydrogenase and steroid 17α‐hydroxylase/C17‐20 lyase, decreased only in the mice treated with Trp‐P‐1 for 2 weeks. In contrast, levels of the mRNA and apoprotein of hepatic Cyp1a2 and its enzyme activity for O‐demethylation of methoxyresorufin significantly increased in the mice treated with Trp‐P‐1 for 2 weeks, but only a small increase was observed in mice treated for 1 week. In the present study, we demonstrate for the first time that treatment of male mice with Trp‐P‐1 results in a decrease in serum total testosterone level through suppression of the gene expression of testicular enzymes responsible for androgen biosynthesis, and this then leads to induction of hepatic Cyp1a2. (Cancer Sci 2006; 97: 32–37)
SUCI02 inhibits the erbB‐2 tyrosine kinase receptor signaling pathway and arrests the cell cycle in G1 phase in breast cancer cells
Authors: Zhu Xiao‐Feng , Wang Jing‐Song , Cai Li‐Ling , Zeng Yi‐Xin , Yang Dajun
Published: December 2005

The erbB‐2 gene encodes tyrosine kinase receptor p185neu. Overexpression of erbB‐2 plays a key role in tumorigenesis and the progression of tumors such as breast cancer and ovarian cancer. Our investigation suggests that the anti‐inflammatory agent N‐(4‐ethoxyphenol)‐2‐hydroxy‐acid amide (SUCI02) reversibly represses tyrosine phosphorylation of erbB‐2 in a dose‐dependent manner, with half maximal inhibition occurring at a concentration of 21.05 µmol/L without reduced erbB‐2 receptor expression. Activation of mitogen‐activated protein kinase and protein kinase B, downstream molecules of the erbB‐2‐mediated signal transduction pathway, was inhibited following exposure to SUCI02. In contrast, tyrosine phosphorylation of epidermal growth factor receptor (EGFR) was relatively unaffected by SUCI02. Proliferation of erbB‐2‐overexpressing BT474 cells was inhibited to a greater extent than proliferation of EGFR‐overexpressing A431 cells following exposure to SUCI02. SUCI02 induced cell cycle arrest in G1 phase with upregulation of p27 and downregulation of pRb phosphorylation. Systemic administration of SUCI02 in nude mice resulted in inhibition of erbB‐2 tyrosine kinase phosphorylation of subcutaneous human breast cancer BT474 xenografts. We conclude that SUCI02 inhibits erbB‐2 tyrosine kinase phosphorylation in vitro and in vivo, shuts down the erbB‐2 downstream pathway and induces cell cycle arrest in G1 phase. These results suggest that SUCI02 is a potential novel anticancer agent that deserves further investigation. (Cancer Sci 2006; 97: 84–89)
Poor correlation of supratherapeutic international normalised ratio and vitamin K‐dependent procoagulant factor levels during warfarin therapy
Authors: Sarode Ravindra , Rawal Ajay , Lee Ray , Shen Yu‐Min , Frenkel Eugene P
Published: December 2005

Patients with a supratherapeutic international normalised ratio (ST‐INR) are at risk for bleeding. ST‐INR is corrected by withholding warfarin therapy and often by supplementing vitamin K or providing vitamin K‐dependent factors; the exact therapeutic decision is based on the extent of the prolonged INR. Currently, ST‐INRs are frequently observed in clinical practice due to the use of sensitive recombinant tissue thromboplastin reagents and automation. However, there are scant data correlating an ST‐INR with various vitamin K‐dependent factors. This prospective cohort study, set in a large tertiary care teaching hospital for the University of Texas Southwestern Medical Center at Dallas, defined the relationship between ST‐INR (>5·0) and measured vitamin K‐dependent procoagulant factors. Prothrombin time, INR and vitamin K‐dependent factors II, VII, IX and X were measured in 78 patients with an INR > 5·0 (ST‐INR) who were on warfarin therapy for more than 2 months. There was no significant relationship between the ST‐INR and levels of important vitamin K‐dependent factors II and X. These data support the recent guidelines that the management of an INR > 5·0 should be driven by the clinical determinants rather than specific INR values per se.
Glatiramer acetate reduces lymphocyte proliferation and enhances IL-5 and IL-13 production through modulation of monocyte-derived dendritic cells in multiple sclerosis
Authors: Sanna A , Fois M L , Arru G , Huang Y-M , Link H , Pugliatti M , Rosati G , Sotgiu S
Published: December 2005

Dendritic cells (DC), as the most effective antigen presenting cells, are protagonists of the complex immune network involved in multiple sclerosis (MS) lesion formation. Glatiramer acetate (GA), a synthetic random copolymer, is thought to exert its therapeutical effect in MS by favouring both Th2 cell development and IL-10 production from peripheral lymphocytes as well as by systemically affecting the antigen presenting cells. In the present study we further analysed the mechanisms of action of GA by using an autologous DC-lymphocytes (Ly) coculture system from 11 MS patients and 12 matched healthy controls (HC). We found that, in MS patients, pretreatment with GA significantly decreases the in vitro proliferative effect of DC on lymphocytes as compared to HC and to unpulsed or myelin basic protein (MBP)-pulsed DC from MS patients (P < 0·05). In addition, GA-treated DC from both MS patients and HC significantly increase the lymphocyte production of IL-5 and IL-13 as compared to MBP-treated DC (P < 0·05). In conclusion our in vitro study may provide new therapeutical mechanisms of GA on lymphocytes, antiproliferative and Th2-favouring effects, which are mediated by monocyte-derived DC.
Effects of hexachlorocyclohexane on rhizosphere fungal propagules and root colonization by arbuscular mycorrhizal fungi in Plantago lanceolata
Authors: Sainz M. J. , González‐Penalta B. , Vilariño A.
Published: December 2005

Lindane (γ‐hexachlorocyclohexane or γ‐HCH) is an organochlorine insecticide previously used extensively for the control of agricultural pests. We studied the effects of soil HCH contamination on vegetation and its associated arbuscular mycorrhizas (AM). The polluted and unpolluted plots had similar plant cover, with the same species richness and abundance. Plantago lanceolata plants were selected for mycorrhizal analysis because of their presence in both plots and known mycotrophy. The presence of HCH appeared to have no significant effect on the extent of colonization of Plantago roots by AM, suggesting a similar functionality of the fungal symbionts. However, infective AM propagules, the density of AM spores and viable AM hyphae in the rhizosphere were much less in the HCH‐polluted soil than in the unpolluted plot. Pre‐inoculation of four plant species with an isolate of Glomus deserticola obtained from the HCH‐contaminated soil resulted in increased growth and fungal colonization of roots compared with plants pre‐inoculated with the introduced fungus G. macrocarpum or colonized by the consortium of indigenous AM fungal species, when those plants were transplanted to an HCH‐contaminated soil. This suggests that the fungus increases the tolerance of plants to the toxic soil environment. We conclude that herbaceous and woody plants can grow in soil with little P contaminated with <100 mg HCH kg−1 with the help of tolerant AM, despite the detrimental effect of HCH on AM fungal propagules in soil. The effects of AM fungi on plant growth and soil microbial community structure in HCH‐polluted sites could be important for remediation of the pollutant through the microbial activity in the rhizosphere.
Investigating microbial community structure in soils by physiological, biochemical and molecular fingerprinting methods
Authors: Singh B. K. , Munro S. , Reid E. , Ord B. , Potts J. M. , Paterson E. , Millard P.
Published: December 2005

Several biochemical and molecular methods are used to investigate the microbial diversity and changes in microbial community structure in rhizospheres and bulk soils resulting from changes in management. We have compared the effects of plants on the microbial community, using several methods, in three different types of soils. Pots containing soil from three contrasting sites were planted with Lolium perenne (rye grass). Physiological (Biolog), biochemical (PLFA) and molecular (DGGE and TRFLP) fingerprinting methods were employed to study the change in soil microbial communities caused by the growth of rye grass. Different methods of DNA extraction and nested PCR on TRFLP profiles were examined to investigate whether they gave different views of community structure. Molecular methods were used for both fungal and bacterial diversity. Principal component analysis of Biolog data suggested a significant effect of the plants on the microbial community structure. We found significant effects of both soil type and plants on microbial communities in PLFA data. Data from TRFLP of soil bacterial communities showed large effects of soil type and smaller but significant effects of plants. Effects of plant growth on soil fungal communities were measured by TRFLP and DGGE. Multiple Procrustes analysis suggested that both methods gave similar results, with only soil types having a significant effect on fungal communities. However, TRFLP was more discriminatory as it generated more ribotype fragments for each sample than the number of bands detected by DGGE. Neither methods of DNA extraction nor the nested PCR had any effect on the evaluation of soil microbial community structure. In conclusion, the different methods of microbial fingerprinting gave qualitatively similar results when samples were processed consistently and compatible statistical methods used. However, the molecular methods were more discriminatory than the physiological and biochemical approaches. We believe results obtained from this experiment will have a major impact on soil microbial ecology in general and rhizosphere–microbial interaction studies in particular, as we showed that the different fingerprinting methods for microbial communities gave qualitatively similar results.
Carbon dynamics in successional and afforested spruce stands in Thuringia and the Alps
Authors: THUILLE ANGELIKA , SCHULZE ERNST‐DETLEF
Published: December 2005

Changes in the carbon stocks of stem biomass, organic layers and the upper 50 cm of the mineral soil during succession and afforestation of spruce (Picea abies) on former grassland were examined along six chronosequences in Thuringia and the Alps. Three chronosequences were established on calcareous and three on acidic bedrocks. Stand elevation and mean annual precipitation of the chronosequences were different. Maximum stand age was 93 years on acid and 112 years on calcareous bedrocks. Stem biomass increased with stand age and reached values of 250–400 t C ha−1 in the oldest successional stands. On acidic bedrocks, the organic layers accumulated linearly during forest succession at a rate of 0.34 t C ha−1 yr−1. On calcareous bedrocks, a maximum carbon stock in the humus layers was reached at an age of 60 years.

Total carbon stocks in stem biomass, organic layers and the mineral soil increased during forest development from 75 t C ha−1 in the meadows to 350 t C ha−1 in the oldest successional forest stands (2.75 t C ha−1 yr−1). Carbon sequestration occurred in stem biomass and in the organic layers (0.34 t C ha−1 yr−1on acid bedrock), while mineral soil carbon stocks declined.

Mineral soil carbon stocks were larger in areas with higher precipitation. During forest succession, mineral soil carbon stocks of the upper 50 cm decreased until they reached approximately 80% of the meadow level and increased slightly thereafter. Carbon dynamics in soil layers were examined by a process model. Results showed that sustained input of meadow fine roots is the factor, which most likely reduces carbon losses in the upper 10 cm. Carbon losses in 10–20 cm depth were lower on acidic than on calcareous bedrocks. In this depth, continuous dissolved organic carbon inputs and low soil respiration rates could promote carbon sequestration following initial carbon loss.

At least 80 years are necessary to regain former stock levels in the mineral soil. Despite the comparatively larger amount of carbon stored in the regrowing vegetation, afforestation projects under the Kyoto protocol should also aim at the preservation or increase of carbon in the mineral soil regarding its greater stability of compared with stocks in biomass and humus layers. If grassland afforestation is planned, suitable management options and a sufficient rotation length should be chosen to achieve these objectives. Maintenance of grass cover reduces the initial loss.
Contrasting stream water NO3− and Ca2+ in two nearly adjacent catchments: the role of soil Ca and forest vegetation
Authors: CHRISTOPHER SHEILA F. , PAGE BLAIR D. , CAMPBELL JOHN L. , MITCHELL MYRON J.
Published: December 2005

Two nearly adjacent subcatchments, located in the Adirondack Mountains of New York State, US, with similar atmospheric inputs of N (0.6 kmol ha−1 yr−1), but markedly different stream water solute concentrations, provided a unique opportunity to evaluate the mechanisms causing this variation. Subcatchment 14 (S14) had much greater stream water Ca2+ and NO3− concentrations (851 and 73 μmolc L−1, respectively) than Subcatchment 15 (S15) (427 and 26 μmolc L−1, respectively). To elucidate factors affecting the variability in stream water concentrations, soil and forest floor samples from each subcatchment were analyzed for total elemental cations and extractable N species. Mineral soil samples were also analyzed for exchangeable cations. Tree species composition was characterized in each subcatchment and potential differences in land use history and hydrology were also assessed. Compared with S15, soils in S14 had significantly higher total elemental Ca2+ in the forest floor (380 vs. 84 μmol g−1), Bs horizon (e.g. 1361 vs. 576 μmol g−1) and C horizon (1340 vs. 717 μmol g−1). Exchangeable Ca2+ was also significantly higher in the mineral soil (64 μmol g−1 in S14 vs. 8 μmol g−1 in S15). Extractable NO3− was higher in S14 compared with S15 in both the forest floor (0.1 vs. 0.01 μmol g−1) and Bs horizon (0.2 vs. 0.07 μmol g−1) while extractable NH4+ was higher in S14 vs. S15 in the forest floor (7 vs. 5 μmol g−1). The total basal area of ‘base‐rich indicator’ tree species (e.g. sugar maple, American basswood, eastern hophornbeam) was significantly greater in S14 compared with S15, which had species characteristic of sites with lower base concentrations (e.g. American beech and eastern white pine). The disparity in stream water Ca2+ and NO3−, concentrations and fluxes between S14 and S15 were explained by differences in tree species composition and soil properties rather than differences in land use or hydrology. The marked difference in soil Ca2+ concentrations in S14 vs. S15 corresponded to the higher stream water Ca2+ and the larger contribution of base‐rich tree species to the overstory biomass in S14. Soil under such species is associated with higher net mineralization and nitrification and likely contributed to the higher NO3− concentrations in the drainage waters of S14 vs. S15. Studies investigating differences in spatial and temporal patterns of the effects of chronic N deposition on surface water chemistry need to account for changes in tree species composition and how vegetation composition is influenced by soil properties, as well as climatic and biotic changes.
The effects of enterprise resource planning implementation strategy on cross‐functionality
Authors: El Amrani Redouane , Rowe Frantz , Geffroy‐Maronnat Bénédicte
Published: December 2005

Abstract.  Enterprise resource planning (ERP) systems are characterized by specific features such as the scope of the ERP modules, interdependent relationships, single database and standard management and processing rules, all of which are capable of causing various degrees of change within the company and, potentially, encourage a more cross‐functional overview of it. This paper develops a theoretical distinction between cross‐functional integration and cross‐functionality as it raises people's awareness of the transverse and coupled nature of work process across different organizational units. It aims to test and discuss the impact of ERP implementation strategy (organizational vision, process re‐engineering, the scope of the ERP modules implemented and speed) on cross‐functionality. The methodology is basically based on a survey of 100 French companies, of which the results are further discussed in five case studies. The results show that all previously mentioned factors play significant roles. These roles should be addressed in future research.
The challenges of redressing the digital divide: a tale of two US cities
Authors: Kvasny Lynette , Keil Mark
Published: December 2005

Abstract.  In this paper, we examine efforts undertaken by two cities – Atlanta and LaGrange, Georgia – to redress the digital divide. Atlanta's initiative has taken the form of community technology centres where citizens can come to get exposure to the internet, and learn something about computers and their applications. LaGrange has taken a very different approach, providing free internet access to the home via a digital cable set‐top box. Using theoretical constructs from Bourdieu, we analysed how the target populations and service providers reacted to the two initiatives, how these reactions served to reproduce the digital divide, and the lessons for future digital divide initiatives. In our findings and analysis, we see a reinforcement of the status quo. When people embrace these initiatives, they are full of enthusiasm, and there is no question that some learning occurs and that the programmes are beneficial. However, there is no mechanism for people to go to the next step, whether that is technical certification, going to college, buying a personal computer or escaping the poverty that put them on the losing end of the divide in the first place. This leads us to conclude that the Atlanta and LaGrange programmes could be classified as successes in the sense that they provided access and basic computer literacy to people lacking these resources. However, both programmes were, at least initially, conceived rather narrowly and represent short‐term, technology‐centric fixes to a problem that is deeply rooted in long‐standing and systemic patterns of spatial, political and economic disadvantage. A persistent divide exists even when cities are giving away theoretically ‘free’ goods and services.
Are Chilean coastal forests pre‐Pleistocene relicts? Evidence from foliar physiognomy, palaeoclimate, and phytogeography
Authors: Hinojosa Luis Felipe , Armesto Juan J. , Villagrán Carolina
Published: December 2005

Aim We ask whether contemporary forests of the Chilean Coastal Range can be considered to be direct and conservative descendants of pre‐Pleistocene palaeofloras that occurred in southern South America from the Palaeogene to early Neogene periods (65–10 Ma), maintaining foliar physiognomies that do not match their present‐day climate. We also identify the most likely ancestors of present‐day coastal forests.

Location Coastal Range of south‐central Chile (33–40° S).

Methods We compared leaf morphology between five representative modern floras from mid‐latitude forests of the Chilean Coastal Range, and 14 Palaeogene–early Neogene palaeofloras from southern South America. We also compared the composition of biogeographical elements (defined by the modern distribution of plant genera) between fossil and present‐day assemblages. Palaeoclimatic reconstructions were based on a canonical correspondence analysis between leaf morphology of modern assemblages and eight climatic variables, and tested by a Monte Carlo permutation test. We compared the relative positions of fossil and modern floras on the environmental vector space defined by Canoco, and on axes defined by instrumental and estimated temperature and precipitation data.

Results According to foliar characters, Palaeogene palaeofloras were strikingly divergent from present‐day coastal forests of central Chile. In contrast, two extant forest floras of the Chilean Coastal Range have a foliar morphology that resembles some late Eocene to early Miocene mixed palaeofloras, at least 23 Myr older. These two modern sites are representative of an area of the Coastal Range (36–37° S) that has been highlighted for its relictual character. None of the 14 fossil floras corresponded exactly to the modern composition of phytogeographic elements, although correspondence analyses showed that mixed and Neogene subtropical fossil floras were compositionally close to the extant woody floras of coastal forests in central Chile.

Main Conclusions Contemporary forests of the Chilean Coastal Range exhibit strong physiognomic resemblance to the mixed palaeofloras from 33°57′ to 41°15′ S, which may be the closest ancestor of the deciduous and endemic‐rich Maulino forest, presently restricted to coastal areas between 36° and 38° S. In turn, the Neogene subtropical palaeoflora that occurred in the Proto‐Andean foothills of central Chile is the likely predecessor of Mediterranean‐type sclerophyllous forests of central Chile (32–33° S). Despite foliar resemblance between the late pre‐Pleistocene and extant forest floras, our palaeoclimatic reconstructions suggest that modern assemblages exist under climatic conditions that do not match their foliar physiognomy. We attribute this convergence in foliar morphology to the ‘evolutionary inertia’ of surviving lineages, favoured by the buffering effect of the coastal environment on climatic variability.