bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of the California Project LEAN School Board Member Social Marketing Campaign
Authors: McDermott Robert J. , Berends Victoria , Brown Kelli R. McCormack , Agron Peggy , Black Karen M. , Barnes Seraphine Pitt
Published: September 2005

The prevalence of overweight youth in the United States has increased remarkably over the last two decades. Overweight and obese youth are at elevated risk for chronic diseases and other adverse health conditions. The foods and beverages that youth access at school (e.g., in a la carte food lines, in vending machines, and in school stores) contribute to overweight and obesity. Enacting policy to ban or restrict unhealthy food and beverage products at school can play a role in managing the epidemic of obesity. School board members are, therefore, a priority audience for introducing healthier food and beverage alternatives through articulation of specific policy initiatives. Under the leadership of California Project LEAN (Leaders Encouraging Activity and Nutrition), a social marketing campaign was directed at California school board members to motivate them to advance nutrition-related policy issues at school board meetings, and to enact and enforce school policies that support healthy eating. In less than two years after implementing the campaign, a significant increase in nutrition-related issues on school board meeting agendas occurred, more favorable nutrition-related policies became enacted, and school board members reported greater readiness to support school nutrition-related issues. Details of campaign development, implementation, and impact are reported.
Prison health care and the extent of prison overcrowding
Authors: Warmsley Roy
Published: September 2005

Overcrowding in prisons has a negative impact on health care and consequently the international standards insist that accommodation for prisoners must include sufficient space. Despite this, the article shows that overcrowded prison systems, defined as those holding more prisoners than they are intended to accommodate, are to be found in every part of the world; indeed, almost 70% are overcrowded, and many others are overcrowded in some prisons. Moreover, overcrowding is not just widespread; it is often severe, with many prison systems having levels of occupancy that far exceed the official capacity. Furthermore, the official capacities of prisons often allow insufficient space per prisoner, so that there is in fact overcrowding even in prison systems where the prison population is lower than the officially stated capacity. Again, prison populations continue to rise, often without parallel increases in the space available. It is suggested that attempts to improve prison health should include strategies to reduce prison populations and eliminate overcrowding.
Prisoner health care provision: Reflections from Australia
Authors: Levy Michael
Published: September 2005

Australian prisons are organised around eight state and territory jurisdictions, and a number of private prison operators. A broad range of structures have evolved over 200 years around correctional management in Australia, including the arrangements for the provision of prisoner health. This paper highlights a large number of issues to argue the complex interactions between prisoner health and “public health.” The Australian context provides the backdrop for this discussion.
Drinking, violence, and prisoners’ health
Authors: McMurran Mary
Published: September 2005

There is abundant evidence that excessive alcohol use can adversely affect physical and mental health. Prior to incarceration, heavy drinking is common among prisoners. In this study, AUDIT information was examined in a sample of 126 male prisoners. Hazardous drinking was identified in 81%, and half had severe alcohol problems. Perpetrators of alcohol‐related violence are the most problematic drinkers of all. Examination of lifetime alcohol‐related violence indicated that those who are violent when intoxicated had more frequently been the cause of concern to others. These results are discussed in relation to alcohol treatments in the Prison Service for England and Wales.
Managing the mentally ill in the prisons of Berlin
Authors: Konrad Norbert
Published: September 2005

A high and possibly increasing prevalence of mental disorders in prisoners has been demonstrated in recent surveys. Psychiatric care of prisoners is subject to wide regional variations in Germany, especially regarding inpatient treatment. Although hospitalized psychiatric patients in prison closely resemble those in forensic psychiatric secure hospitals with regard to socio‐demographic (percentage of women, age peak) and forensic characteristics (delinquency, prison experience), marked discrepancies in the diagnostic spectrum necessitate very different treatment planning based on general clinical psychiatry when considering the approach and especially the treatment duration. In Berlin, we try to develop a care structure within the prison system, which addresses inmate‐specific problems and circumstances as well as the possibility of inpatient and outpatient treatment and semihospitalization according to the principle of “equivalence”.
Hepatitis C treatment in a Canadian federal correctional population: Preliminary feasibility and outcomes
Authors: Farley John , Vasdev Shawn , Fischer Benedikt , Rehm Jürgen , Haydon Emma
Published: September 2005

Hepatitis C virus (HCV) infection is a major public health concern in Canada, which now mostly affects marginalized populations, including correctional inmates. These populations ‐ until recently ‐ have largely been excluded from HCV pharmacotherapy. We report preliminary data on HCV treatment in a federal correctional population sample in British Columbia (BC), using Pegetron combination therapy. HCV RNA results are presented at week 12 of treatment, a strong predictor of treatment outcome. Just over four‐fifths (80.8%) of inmate patients had no detectable HCV RNA at week 12; inmates with genotype 2 and 3 fared better than those with genotype 1. These preliminary results suggest that HCV treatment is feasible and promises to be efficacious in correctional populations.
Influenza control in Australian prison settings: Cost ‐ benefit analysis of major strategies
Authors: Awofeso Niyi , Rawlinson William D.
Published: September 2005

Repeated influenza outbreaks are surprisingly rare in prison settings worldwide, a factor that has made it superfluous, to date, to develop contingency plans for responding to prison‐based influenza epidemics. However, the influenza outbreak that occurred in an Australian prison in 2000 has highlighted the appropriateness of developing an outbreak plan, not least because of the security implications of a widespread prison influenza epidemic. Using reported attack rates and morbidity profiles of the 2000 Australian prison influenza outbreak to develop scenarios, the authors estimated the cost ‐ benefit of mass vaccination and antiviral chemotherapy approaches for the control of hypothetical widespread influenza outbreaks in New South Wales prisons, occurring at an average frequency of once every 10 years. It was concluded that, from the perspectives of maintaining
prison security as well as health care services’ provision to prisoners, early antiviral chemotherapy for symptomatic individuals will have more favourable cost ‐ benefit ratios than a mass vaccination approach for controlling prison‐based influenza outbreaks that occur in line with this model.
Taking action to reduce injecting drug‐related harms in prisons: The evidence of effectiveness of prison needle exchange in six countries
Authors: Lines Rick , Jürgens Ralf , Betteridge Glen , Stöver Heino
Published: September 2005

This article examines the issue of prison needle‐exchange programmes (PNEP) based upon the international experience and evidence in six countries. A review of existing literature was undertaken together with original research comprising site visits to prison needle‐exchange programmes in four countries operating such initiatives in October 2002. During the course of the research, prison needle exchange programmes were initiated in two other countries, Kyrgyzstan and Belarus. Site visits were not possible in respect of these two countries, and data was gathered via conversations with staff and funding organisations involved and by the examination of documentary evidence. The paper presents
an overview of the PNEP initiated and a commentry on the outcomes. Based upon the evidence emerging from the investigation, the paper concludes that while prison syringe‐exchange programmes have been implemented in diverse environments and under differing circumstances, the results of the programmes have been remarkably consistent. Improved prisoner health and reduction of needle sharing have been achieved. Fears of violence, increased drug consumption, and other negative consequences have not materialised. Based on the evidence and experience, it can be concluded unequivocally that prison needle‐exchange programmes effectively address the health‐related harms
associated with needle sharing in prisons and do not undermine institutional safety or security.
Dual Diagnosis within Italian prisons ‐ some preliminary data
Authors: Berto Daniele , Tartari Morena , Tabacchi Barbara , Gerra Gilberto , Tamburino Giovanni
Published: September 2005

Dual Diagnosis (DD) is a double pathology afflicting drug users that involves both addiction and psychiatric diseases. This specific condition is currently attracting attention from the scientific community. There are limited data available relating to this area and even less specifically relating to problematic drug use and addiction among prisoners and the general lack of adequate treatments and therapeutic tools that are required by this population. This study is divided into four phases, and this article discusses only the preliminary data. Each prisoner in the sample with addiction problems was subjected to an initial screening, and if the slightest element of DD was highlighted, the client was assessed with specific clinical tools (MMPI‐2, SCID II) and an interview with a psychiatrist. The data collected from the Minnesota Multiphasic Personality Inventory (MMPI‐2) test highlighted that the most recurrent disorder in both of the sample prisons was borderline personality disorder with the majority of the subjects presenting personality disorders in axis II of the DSM‐IV TR, using the Structured Clinical Interview Diagnosis II (SCID II). The data gathered demonstrated that two‐thirds
of the prisoners with addiction in these prisons suffer from a DD, and it is therefore important to distinguish the addiction from the psychiatric diagnoses and the DD condition in order to decide the specific treatment. This research suggests that in cases of Dual Diagnosis, both clinical conditions must be addressed, or there is a risk that these prisoners will only be partially treated, and this will create further difficulties in their rehabilitation.
Effects of self‐modeling on figure skating jump performance and psychological variables
Authors: Law Barbi , Ste‐Marie Diane M.
Published: September 2005

This study investigated whether self‐modeling plus physical practice would improve intermediate level figure skaters’ jump performance, as well as their self‐efficacy, motivation, and state anxiety, when compared to physical practice alone. Twelve female figure skaters (M=13.4 years of age, SD=1.4) participated in a within‐participant design where they received a self‐modeling intervention for one jump and a control condition for another jump. They were also compared with a separate control group of 7 skaters (M=14.2 years of age, SD=2.35) who received no intervention. We hypothesized that skaters would show greater improvement in physical and psychological performance scores for jumps in the self‐modeling condition than for jumps in the control conditions. We also hypothesized that increased self‐efficacy and motivation and decreased state anxiety would mediate the relationship between self‐modeling and physical performance. Counter to our predictions, no differences existed between the two conditions for the self‐modeling group or between the self‐modeling group and the control group. Despite the lack of statistical support for our hypotheses, skaters’ evaluation of the intervention was very positive and suggests possible explanations for the results.
Injuries in handball: Examination of the risk factors
Authors: Tsigilis Nikolaos , Hatzimanouil Dimitrios
Published: September 2005

This paper examines the influence of selected risk factors on injuries among male players of competition handball. Data relating to risk factors were collected using a self‐report questionnaire. The factors that were examined were age, height, weight, body mass index, field position, past sport experience, level of competition, pre‐season conditioning, number of practices per week, frequency of participation in games, use of prophylactic equipment, use of stretching exercises, and technical training. The questionnaire was administered to 216 male handball players. Nearly half of the players (42.6% or n=92) reported that they had been injured during the previous two years. The injury incidence was 8.14 injuries per 1,000 game hours for the preceding two years. Logistic regression analysis revealed that the variables “use of prophylactic equipment” and the “number of practices per week” contributed significantly to the prediction of an injury in handball players. The results of this study suggest that it is possible to reduce injury occurrence by giving specific attention to players using prophylactic equipment and to the lower‐competition‐level players.
The response of intracellular signaling and muscle‐protein metabolism to nutrition and exercise
Authors: Tipton Kevin D. , Sharp Carwyn P.
Published: September 2005

In recent years, a body of literature examining the response of muscle‐protein metabolism to exercise and nutrition has arisen. Developments in methods, especially stable isotopic tracer methodology, have allowed much information to be gathered in vivo in humans. The metabolic mechanism behind increased muscle mass requires that muscle‐protein synthesis exceeds breakdown, i.e., net muscle‐protein synthesis. Increased net muscle‐protein balance may occur due to exercise, but net synthesis may occur only with the addition of nutrients, particularly a source of amino acids. The major impact of increased amino acid availability on net muscle‐protein balance is due to stimulation of muscle‐protein synthesis and less to inhibition of muscle‐protein breakdown. Amino acids seem to stimulate muscle‐protein synthesis, not only by mass action, i.e., providing substrate, but also as signals for initiation of protein synthesis. Stimulation of muscle‐protein synthesis by amino acid ingestion may be linked to increased intracellular amino acid levels and/or to changing amino acid levels in the blood. Carbohydrate ingestion, most likely through the action of insulin, also may play a role in the response of muscle to exercise and nutrition. There is very little research in humans in vivo on the intracellular signaling that is linked to muscle‐protein synthesis. It is clear that intracellular signaling responds to both insulin and amino acids, but the interactions with exercise are not well known; however, the details of the pathways have only just begun to be investigated, especially in humans. Delineation of these pathways is complicated, and there is little doubt that multiple intracellular signaling pathways with several levels of communication are involved in the hypertrophy process in response to nutrition and exercise. A systematic investigation of the relationship of the signaling to insulin and amino acids combined with exercise will provide important information, especially for populations vulnerable to muscle loss.
Debilitative interpretations of competitive anxiety: A qualitative examination of elite performers
Authors: Hanton Sheldon , Wadey Ross , Connaughton Declan
Published: September 2005

Research has not accounted for a small but significant proportion of elite performers who consistently report debilitative interpretations of competitive anxiety‐related symptoms. Interviews were used to investigate elite athletes’ precompetitive thoughts, feelings, and mental strategies underlying symptom interpretation. Six male athletes, from a variety of sports (M age = 23.3, SD=2.2), who were currently competing within the UK, were found to hold debilitative interpretations. Data were drawn from verbatim transcripts and the content analysed. Four general dimensions traced the participants’ precompetitive states and mental skills from early competitive experiences to the present day. Findings indicated that the participants reported early debilitating symptoms, which became habituated throughout their respective careers. Possible explanations as to why these elite performers consistently reported negative interpretations related to mental preparation and effectiveness, psychological skills, coping strategies, perceptions of control, and perceived self‐confidence levels. The way in which the athletes are able to compete at an elite level, despite reporting debilitative interpretations, is also discussed.
Working memory capacity and the construction of spatial mental models in comprehension and deductive reasoning
Authors: Oberauer Klaus , Weidenfeld Andrea , Hörnig Robin
Published: September 2005

We asked 149 high-school students who were pretested for their working memory capacity (WMC) to read spatial descriptions relating to five objects and to evaluate conclusions asserting an unmentioned relationship between two of the objects. Unambiguous descriptions were compatible with a single spatial arrangement, whereas ambiguous descriptions permitted two arrangements; a subset of the ambiguous descriptions still determined the relation asserted in the conclusion, whereas another subset did not. Two groups of participants received different instructions: The deduction group should accept conclusions only if they followed with logical necessity from the description, whereas the comprehension group should accept a conclusion if it agreed with their representation of the arrangement. Self-paced reading times increased on sentences that introduced an ambiguity, replicating previous findings in deductive reasoning experiments. This effect was also found in the comprehension group, casting doubt on the interpretation that people consider multiple possible arrangements online. Responses to conclusions could be modelled by a multinomial processing model with four parameters: the probability of constructing a correct mental model, the probability of detecting an ambiguity, and two guessing parameters. Participants with high and with low WMC differed mainly in the probability of successfully constructing a mental model.
Continuous control of autoimmune disease by antigen-dependent polyclonal CD4+CD25+ regulatory T cells in the regional lymph node
Authors: Samy Eileen T. , Parker Lucy A. , Sharp Colin P. , Tung Kenneth S.K.
Published: September 2005

This study investigated the unresolved issue of antigen-dependency and antigen-specificity of autoimmune disease suppression by CD4+CD25+ T cells (T regs). Based on autoimmune ovarian disease (AOD) in day 3 thymectomized (d3tx) mice and polyclonal T regs expressing the Thy1.1 marker, we determined: (a) the location of recipient T cell suppression, (b) the distribution of AOD-suppressing T regs, and (c) the relative efficacy of male versus female T regs. Expansion of recipient CD4+ T cells, activation/memory marker expression, and IFN-γ production were inhibited persistently in the ovary-draining LNs but not elsewhere. The cellular changes were reversed upon Thy1.1+ T reg depletion, with emergence of potent pathogenic T cells and severe AOD. Similar changes were detected in the regional LNs during autoimmune dacryoadenitis and autoimmune prostatitis suppression. Although the infused Thy1.1+ T regs proliferated and were disseminated in peripheral lymphoid organs, only those retrieved from ovary-draining LNs adoptively suppressed AOD at a suboptimal cell dose. By depriving d3tx recipients of ovarian antigens, we unmasked the supremacy of ovarian antigen-exposed female over male T regs in AOD suppression. Thus, disease suppression by polyclonal T regs depends on endogenous antigen stimulation; this occurs in a location where potent antigen-specific T regs accumulate and continuously negate pathogenic T cell response.
Eosinophil adhesion under flow conditions activates mechanosensitive signaling pathways in human endothelial cells
Authors: Cuvelier Susan L. , Paul Smitha , Shariat Neda , Colarusso Pina , Patel Kamala D.
Published: September 2005

Leukocyte transmigration can be affected by shear stress; however, the mechanisms by which shear stress modulates transmigration are unknown. We found that adhesion of eosinophils or an eosinophilic cell line to intereukin 4–stimulated endothelial cells led to a shear-dependent increase in endothelial cell intracellular calcium and increased phosphorylation of extracellular signal-regulated kinase (ERK) 2, but not c-Jun NH2-terminal kinase or p38 mitogen-activated protein kinase. Latex beads coated with antibodies were used to characterize the role of specific endothelial cell surface molecules in initiating signaling under shear conditions. We found that ligation of either vascular cell adhesion molecule–1 or E-selectin, but not major histocompatibility complex class I, induced a shear-dependent increase in ERK2 phosphorylation in cytokine-stimulated endothelial cells. Disassembly of the actin cytoskeleton with latrunculin A prevented ERK2 phosphorylation after adhesion under flow conditions, supporting a role for the cytoskeleton in mechanosensing. Rapid phosphorylation of focal adhesion kinase and paxillin occurred under identical conditions, suggesting that focal adhesions were also involved in mechanotransduction. Finally, we found that Rho-associated protein kinase and calpain were both critical in the subsequent transendothelial migration of eosinophils under flow conditions. These data suggest that ligation of leukocyte adhesion molecules under flow conditions leads to mechanotransduction in endothelial cells, which can regulate subsequent leukocyte trafficking.
A role for TSLP in the development of inflammation in an asthma model
Authors: Al-Shami Amin , Spolski Rosanne , Kelly John , Keane-Myers Andrea , Leonard Warren J.
Published: September 2005

Thymic stromal lymphopoietin (TSLP) is a cytokine that promotes CD4+ T cell homeostasis. We now demonstrate that TSLP is required to mount a normal CD4+ T cell–mediated inflammatory response. TSLP acts directly on naive, but not, memory CD4+ T cells, and promotes their proliferation in response to antigen. In addition, TSLP exerts an effect indirectly through DCs to promote Th2 differentiation of CD4+ T cells. Correspondingly, TSLP receptor (TSLPR) knockout (KO) mice exhibit strong Th1 responses, with high levels of interleukin (IL)-12, interferon-γ, and immunoglobulin (Ig) G2a, but low production of IL-4, -5, -10, -13, and IgE; moreover, CD4+ T cells from these animals proliferate less well in response to antigen. Furthermore, TSLPR KO mice fail to develop an inflammatory lung response to inhaled antigen unless supplemented with wild-type CD4+ T cells. This underscores an important role for this cytokine in the development of inflammatory and/or allergic responses in vivo.
Dual phase regulation of experimental allergic encephalomyelitis by platelet-activating factor
Authors: Kihara Yasuyuki , Ishii Satoshi , Kita Yoshihiro , Toda Akiko , Shimada Atsuyoshi , Shimizu Takao
Published: September 2005

Experimental allergic encephalomyelitis (EAE) serves as a model for multiple sclerosis and is considered to be a CD4+ Th1 cell–mediated autoimmune disease. To investigate the role of platelet-activating factor (PAF) in this disease, PAF receptor (PAFR) KO (PAFR-KO) and wild-type (WT) mice, on a C57BL/6 genetic background, were immunized with myelin oligodendrocyte glycoprotein 35–55. The levels of PAF production and PAFR mRNA expression in the spinal cord (SC) correlated with the EAE symptoms. PAFR-KO mice showed lower incidence and less severe symptoms in the chronic phase of EAE than WT mice. However, no difference was observed in T cell proliferation, Th1-cytokine production, or titer of IgG2a between both genotypes. Before onset, as revealed by microarray analysis, mRNAs of inflammatory mediators and their receptors—including IL-6 and CC chemokine receptor 2—were down-regulated in the SC of PAFR-KO mice compared with WT mice. Moreover, in the chronic phase, the severity of inflammation and demyelination in the SC was substantially reduced in PAFR-KO mice. PAFR-KO macrophages reduced phagocytic activity and subsequent production of TNF-α. These results suggest that PAF plays a dual role in EAE pathology in the induction and chronic phases through the T cell–independent pathways.
Cytosolic phospholipase A2α–deficient mice are resistant to experimental autoimmune encephalomyelitis
Authors: Marusic Suzana , Leach Michael W. , Pelker Jeffrey W. , Azoitei Mihai L. , Uozumi Naonori , Cui Junqing , Shen Marina W.H. , DeClercq Charlene M. , Miyashiro Joy S. , Carito Brenda A. , Thakker Paresh , Simmons David L. , Leonard John P. , Shimizu Takao , Clark James D.
Published: September 2005

Experimental autoimmune encephalomyelitis (EAE), a Th1-mediated inflammatory disease of the central nervous system (CNS), is a model of human multiple sclerosis. Cytosolic phospholipase A2α (cPLA2α), which initiates production of prostaglandins, leukotrienes, and platelet-activating factor, is present in EAE lesions. Using myelin oligodendrocyte glycoprotein (MOG) immunization, as well as an adoptive transfer model, we showed that cPLA2α−/− mice are resistant to EAE. Histologic examination of the CNS from MOG-immunized mice revealed extensive inflammatory lesions in the cPLA2α+/− mice, whereas the lesions in cPLA2α−/− mice were reduced greatly or completely absent. MOG-specific T cells generated from WT mice induced less severe EAE in cPLA2α−/− mice compared with cPLA2α+/− mice, which indicates that cPLA2α plays a role in the effector phase of EAE. Additionally, MOG-specific T cells from cPLA2α−/− mice, transferred into WT mice, induced EAE with delayed onset and lower severity compared with EAE that was induced by control cells; this indicates that cPLA2α also plays a role in the induction phase of EAE. MOG-specific T cells from cPLA2α−/− mice were deficient in production of Th1-type cytokines. Consistent with this deficiency, in vivo administration of IL-12 rendered cPLA2α−/− mice susceptible to EAE. Our data indicate that cPLA2α plays an important role in EAE development and facilitates differentiation of T cells toward the Th1 phenotype.
Modifier loci condition autoimmunity provoked by Aire deficiency
Authors: Jiang Wenyu , Anderson Mark S. , Bronson Roderick , Mathis Diane , Benoist Christophe
Published: September 2005

Loss of function mutations in the autoimmune regulator (Aire) gene in autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy patients and mutant mice lead to autoimmune manifestations that segregate as a monogenic trait, but with wide variation in the spectrum of organs targeted. To investigate the cause of this variability, the Aire knockout mutation was backcrossed to mice of diverse genetic backgrounds. The background loci strongly influenced the pattern of organs that were targeted (stomach, eye, pancreas, liver, ovary, thyroid, and salivary gland) and the severity of the targeting (particularly strong on the nonobese diabetic background, but very mild on the C57BL/6 background). Autoantibodies mimicked the disease pattern, with oligoclonal reactivity to a few antigens that varied between Aire-deficient strains. Congenic analysis and a whole genome scan showed that autoimmunity to each organ had a distinctive pattern of genetic control and identified several regions that controlled the pattern of targeting, including the major histocompatibility complex and regions of Chr1 and Chr3 previously identified in controlling type 1 diabetes.
The structure of human CD23 and its interactions with IgE and CD21
Authors: Hibbert Richard G. , Teriete Peter , Grundy Gabrielle J. , Beavil Rebecca L. , Reljić Rajko , Holers V. Michael , Hannan Jonathan P. , Sutton Brian J. , Gould Hannah J. , McDonnell James M.
Published: September 2005

The low-affinity immunoglobulin E (IgE) receptor, CD23 (FcεRII), binds both IgE and CD21 and, through these interactions, regulates the synthesis of IgE, the antibody isotype that mediates the allergic response. We have determined the three-dimensional structure of the C-type lectin domain of CD23 in solution by nuclear magnetic resonance spectroscopy. An analysis of concentration-dependent chemical shift perturbations have allowed us to identify the residues engaged in self-association to the trimeric state, whereas ligand-induced changes have defined the binding sites for IgE and CD21. The results further reveal that CD23 can bind both ligands simultaneously. Despite the C-type lectin domain structure, none of the interactions require calcium. We also find that IgE and CD23 can interact to form high molecular mass multimeric complexes. The interactions that we have described provide a solution to the paradox that CD23 is involved in both up- and down-regulation of IgE and provide a structural basis for the development of inhibitors of allergic disease.
Dragon Plant Biology Explorer. A Text-Mining Tool for Integrating Associations between Genetic and Biochemical Entities with Genome Annotation and Biochemical Terms Lists
Authors: Bajic Vladimir B. , Veronika Merlin , Veladandi Pardha Sarathi , Meka Archana , Heng Mok-Wei , Rajaraman Kanagasabai , Pan Hong , Swarup Sanjay
Published: September 2005

We introduce a tool for text mining, Dragon Plant Biology Explorer (DPBE) that integrates information on Arabidopsis (Arabidopsis thaliana) genes with their functions, based on gene ontologies and biochemical entity vocabularies, and presents the associations as interactive networks. The associations are based on (1) user-provided PubMed abstracts; (2) a list of Arabidopsis genes compiled by The Arabidopsis Information Resource; (3) user-defined combinations of four vocabulary lists based on the ones developed by the general, plant, and Arabidopsis GO consortia; and (4) three lists developed here based on metabolic pathways, enzymes, and metabolites derived from AraCyc, BRENDA, and other metabolism databases. We demonstrate how various combinations can be applied to fields of (1) gene function and gene interaction analyses, (2) plant development, (3) biochemistry and metabolism, and (4) pharmacology of bioactive compounds. Furthermore, we show the suitability of DPBE for systems approaches by integration with “omics” platform outputs. Using a list of abiotic stress-related genes identified by microarray experiments, we show how this tool can be used to rapidly build an information base on the previously reported relationships. This tool complements the existing biological resources for systems biology by identifying potentially novel associations using text analysis between cellular entities based on genome annotation terms. Thus, it allows researchers to efficiently summarize existing information for a group of genes or pathways, so as to make better informed choices for designing validation experiments. Last, DPBE can be helpful for beginning researchers and graduate students to summarize vast information in an unfamiliar area. DPBE is freely available for academic and nonprofit users at http://research.i2r.a-star.edu.sg/DRAGON/ME2/.
RNA Silencing of Single and Multiple Members in a Gene Family of Rice
Authors: Miki Daisuke , Itoh Rika , Shimamoto Ko
Published: September 2005

RNA silencing with inverted repeat (IR) constructs has been used to suppress gene expression in various organisms. However, the transitive RNA-silencing effect described in plants may preclude the use of RNA silencing for a gene family. Here, we show that, in rice (Oryza sativa), transitive RNA silencing (spreading of double-stranded RNA along the target mRNA) occurred with the green fluorescent protein transgene but not with the endogenous phytoene desaturase gene. We fused IR copies of unique 3′ untranslated regions derived from the rice OsRac gene family to a strong promoter and stably introduced them into rice. Each of the seven members of the OsRac gene family was specifically suppressed by its respective IR construct. We also examined IR constructs in which multiple 3′ untranslated regions were fused and showed that three members of the OsRac gene family were effectively suppressed by a single construct. Using highly conserved regions of the two members of the OsRac gene family, we also suppressed the expression of all members of the gene family with variable efficiencies. These results suggest that RNA silencing is a useful method for the functional analysis of gene families in rice and other plants.
Plant Virus RNAs. Coordinated Recruitment of Conserved Host Functions by (+) ssRNA Viruses during Early Infection Events
Authors: Thivierge Karine , Nicaise Valérie , Dufresne Philippe J. , Cotton Sophie , Laliberté Jean-François , Le Gall Olivier , Fortin Marc G.
Published: September 2005

Positive-sense single-stranded RNA viruses have developed strategies to exploit cellular resources at the expense of host mRNAs. The genomes of these viruses display a variety of structures at their 5′ and 3′ ends that differentiate them from cellular mRNAs. Despite this structural diversity, viral RNAs are still circularized by juxtaposition of their 5′ and 3′ ends, similar to the process used by cellular mRNAs. Also reminiscent of the mechanisms used by host mRNAs, translation of viral RNAs involves the recruitment of translation initiation factors. However, the roles played by these factors likely differ from those played by cellular mRNAs. In keeping with the general parsimony typical of RNA viruses, these host factors also participate in viral RNA replication. However, the dual use of host factors requires that viral RNA template utilization be regulated to avoid conflict between replication and translation. The molecular composition of the large ribonucleoprotein complexes that form the viral RNA replication and translation machineries likely evolves over the course of infection to allow for switching template use from translation to replication.
Measuring Similarity Among Various Shapes Based on Geometric Matching
Authors: Zhao Zuoquan , Stough Roger R.
Published: September 2005

The purpose of this article is to examine how to measure the degree of similarity among various shapes, including for the first time those that are fragmented and perforated, by the overlap‐based elongation index. It is argued that complete removal of the effects of position, size, and orientation on shape, which is essential for the calibration of shape similarity, can be achieved by a shape similarity index that varies continuously with changes in shape. After examining the characteristics of shape change, it is demonstrated that the elongation index is sensitive to changes in the shape of two spatial objects only when the centroids of the two objects are coincident. Two related rules of shape similarity are then presented. The applicability of the elongation index is evaluated by comparing several simple and complex shapes. The principal contribution of this article is that for the first time similarity among various shapes, fragmented or perforated, can be identified using the elongation index.
Dispersion of Nodes Added to a Network
Authors: Kuby Michael , Lim Seow , Upchurch Christopher
Published: September 2005

For location problems in which optimal locations can be at nodes or along arcs but no finite dominating set has been identified, researchers may desire a method for dispersing p additional discrete candidate sites along the m arcs of a network. This article develops and tests minimax and maximin models for solving this continuous network location problem, which we call the added‐node dispersion problem (ANDP). Adding nodes to an arc subdivides it into subarcs. The minimax model minimizes the maximum subarc length, while the maximin model maximizes the minimum subarc length. Like most worst‐case objectives, the minimax and maximin objectives are plagued by poorly behaved alternate optima. Therefore, a secondary MinSumMax objective is used to select the best‐dispersed alternate optima. We prove that equal spacing of added nodes along arcs is optimal to the MinSumMax objective. Using this fact we develop greedy heuristic algorithms that are simple, optimal, and efficient (O(mp)). Empirical results show how the maximum subarc, minimum subarc, and sum of longest subarcs change as the number of added nodes increases. Further empirical results show how using the ANDP to locate additional nodes can improve the solutions of another location problem. Using the p‐dispersion problem as a case study, we show how much adding ANDP sites to the network vertices improves the p‐dispersion objective function compared with (a) network vertices only and (b) vertices plus randomly added nodes. The ANDP can also be used by itself to disperse facilities such as stores, refueling stations, cell phone towers, or relay facilities along the arcs of a network, assuming that such facilities already exist at all nodes of the network.
Exploring Nonlinear Spatial Dependence in the Tails
Authors: Arbia Giuseppe , Lafratta Giovanni
Published: September 2005

In many instances it is of interest to measure the degree of similarity between neighboring regions. Spatial autocorrelation measures are the most popular means of doing it. However, such measures only capture a global linear relationship between regions, whereas in many circumstances a more general instrument is required. For instance, in economic poverty analysis or environmental applications (and in other cases where we are interested in extreme events and threshold exceedances) we should be more interested in the spatial pattern in the tails of the joint distributions. In this article we introduce some exploratory tool that focuses on the bivariate joint tails behavior to detect a pattern of spatial regularities. The method will be illustrated with reference to simulated environmental data.
Exploring Goodness‐of‐Fit and Spatial Correlation Using Components of Tango's Index of Spatial Clustering
Authors: Jackson Monica C. , Waller Lance A.
Published: September 2005

The ability to detect anomalies such as spatial clustering in data sets plays an important role in spatial data analysis, leading to interest in test statistics identifying patterns exhibiting significant levels of clustering. Toward this end, Tango (1995) proposed a statistic (and its associated distribution under a null hypothesis of no clustering) assessing overall patterns of spatial clustering in a set of observed regional counts. Rogerson (1999) observed that Tango's index may be decomposed into the summation of two distinct statistics, the first mirroring standard tests of goodness‐of‐fit (GOF), and the second an index of spatial association (SA) similar to Moran's I. In this article, we investigate the effectiveness of Rogerson's expression of Tango's statistic in separating GOF from SA in data sets containing clusters. We simulate data under the null hypothesis of no clustering as well as two alternative hypotheses. The first alternative hypothesis induces a poor fit from the null hypothesis while maintaining independent observations and the second alternative hypothesis induces spatial dependence while maintaining fit. Using Rogerson's decomposition and leukemia incidence data from upstate New York, we show graphically that one is unable to statistically distinguish poor fit from autocorrelation.
The absence of CD20 messenger RNA in recurrent cutaneous B‐cell lymphoma following rituximab therapy
Authors: Rawal Yeshwant B. , Nuovo Gerard J. , Frambach Gwyn E. , Porcu Pierluigi , Baiocchi Robert A. , Magro Cynthia M.
Published: September 2005

Background:  Rituximab has been used to treat relapsed low‐grade or advanced non‐Hodgkin's lymphoma since 1997, targeting the CD20 antigen expressed by B cells. Single‐agent rituximab therapy is safe and well tolerated. Recurrences showing a loss of CD20 expression following rituximab therapy have been reported.

Methods:  Four patients with CD20‐positive cutaneous B‐cell lymphoma received rituximab therapy with subsequent recurrences. The biopsies were assessed for cytoplasmic CD20 expression; CD20 messenger RNA was also assessed where tissue was available.

Results:  Cutaneous relapses occurring within 1.5–3 months following the last dose of rituximab were CD20 negative. In three cases, subsequent relapses showed renewed expression of CD20. Those biopsies demonstrating a loss of surface and cytoplasmic CD20 by immunohistochemistry also showed no evidence of messenger RNA for CD20 using an in situ polymerase chain reaction‐based methodology.

Conclusions:  Rituximab may be associated with the emergence of CD20‐negative B‐cell clones, potentially rendering a tumor insensitive to this drug. Conversely, following cessation of the drug, a re‐expression of CD20 within the neoplastic cells may occur allowing therapeutic intervention with this monoclonal antibody. The loss of CD20 expression appears to be a direct effect of the drug on CD20 messenger RNA synthesis.
De novo intraepidermal epithelioid melanocytic dysplasia as a marker of the atypical mole phenotype – a clinical and pathological study of 75 patients
Authors: Sachdeva Mandi , Frambach Gwyn E. , Crowson A. Neil , Deng April C. , Mihm Martin C. , Magro Cynthia M.
Published: September 2005

Background:  We encountered a distinctive pattern of dysplastic intraepidermal melanocytic proliferation, which defies classification as a dysplastic melanocytic nevus, but in which the morphologic features fall short of a diagnosis of melanoma in situ. We designate such lesions as de novo intraepidermal epithelioid melanocytic dysplasia.

Methods:  From 75 patients, 82 skin biopsies were encountered that showed this distinctive morphology. Hematoxylin‐ and eosin‐stained histologic sections were studied and the features were correlated with personal and family histories of dysplastic nevi and melanoma.

Results:  The diagnosis of de novo melanocytic dysplasia was made in 27 male patients and 48 female patients (mean age: 44 years). The histologic hallmark was a pagetoid (single‐cell) array of moderately to severely atypical epithelioid melanocytes within the epidermis. Seventy‐three lesions were located on sun‐exposed skin and nine on sun‐protected skin. In 41 patients, there was an atypical mole phenotype, whereas 20 patients had a prior or subsequent diagnosis of melanoma with five of 16 patients questioned revealing a family history of melanoma.

Conclusions:  De novo intraepidermal epithelioid melanocytic dysplasia is a distinct entity associated with an atypical mole phenotype and a personal and/or family history of melanoma.
Retiform hemangioendothelioma: a case report and review of the literature
Authors: Tan Dongfeng , Kraybill William , Cheney Richard T. , Khoury Thaer
Published: September 2005

Background:  Retiform hemangioendothelioma (RH) is a rare, recently described vascular neoplasm of low malignant potential.

Methods:  We report a case of RH of the foot of a 19‐year‐old white female. Histologically, the tumor grew as numerous elongated vessels resembling the shape of rete testis with involvement of the skin adnexal structures and subcutaneous adipose tissue. No dissection of collagen by small groups of endothelial cells was seen. Wide local excision was performed and the patient was healthy with no metastasis at 14 months follow‐up.

Results and Conclusions:  Our case is discussed in the context of previously reported cases of RH; we also include a review of all cases of RH published to date.
Primary cutaneous carcinosarcoma arising in a patient with nevoid basal cell carcinoma syndrome
Authors: Bhattacharjee Pradip , Leffell David , McNiff Jennifer M.
Published: September 2005

Background:  Nevoid basal cell carcinoma syndrome (NBCC) is an autosomal dominant disorder characterized by developmental abnormalities and neoplasms including basal cell carcinoma (BCC) and sarcomas (i.e. leiomyosarcoma, rhabdomyosarcoma, and fibrosarcoma). Primary cutaneous carcinosarcoma (PCC), a rare tumor composed of malignant epithelial and mesenchymal components, has never been previously described in association with this syndrome.

Case report:  A 61‐year‐old Hispanic man with a history of NBCC presented with a 4 cm nodule on the right proximal medial thigh.

Pathologic findings:  Areas of typical BCC merged with intersecting fascicles of large atypical spindle cells that stained for vimentin and were negative for actin, desmin, CD‐34, and S‐100 protein. Scattered bizarre solitary cytokeratin‐positive epithelioid cells were embedded within the fibrocytic proliferation.

Conclusions:  Several carcinosarcomas have been reported to contain BCC as the malignant epithelial component, but to our knowledge, this is the first report of PCC associated with NBCC. Mutation in patched tumor suppressor gene on chromosome 9q occurs in BCCs of NBCC, and aberrancies on chromosome 9q are also reported in some carcinosarcomas. It is possible that the known genetic defect on chromosome 9 in this patient contributed to the development of carcinosarcoma.
Unusual histological variants of cutaneous malignant melanoma with some clinical and possible prognostic correlations
Authors: Rongioletti Franco , Smoller Bruce R.
Published: September 2005

Abstract:  Malignant melanoma is known for the wide range of histological patterns it can assume mimicking other malignant tumors. We present a review of most of the unusual histological variants of cutaneous melanoma and describe their immunohistochemical features, associate clinical findings, and possible behavior related to the histological subtype. In addition, we propose their classification into four groups corresponding to the (1) architectural patterns; (2) cytologic features; (3) stromal changes; and (4) the possible association of these findings (i.e. architectural + cytologic features). Although most of these unusual variants have the same prognosis as conventional melanomas, with Breslow thickness and ulceration, being the most important predictor of survival in clinical stage I, some of them have a peculiar biologic behavior that the clinicians and the dermatopathologists should know in order to give melanoma patients all educational information available.
Phase Equilibria, Oxygen Potentials, and Activities in the System Ni‐Co‐Si‐O at 1373 K
Authors: Jacob K. Thomas , Seetharaman Seshadri
Published: September 2005

In the system Ni‐Co‐Si‐O, the compositions of coexisting phases participating in two‐phase equilibria between the monoxide (NiyCo1‐yO) and orthosilicate (NizCo1‐zSi0.5O2) crystalline solutions, and alloy (NixCo1‐x) and orthosilicate phase, have been determined at 1373 K. The samples were equilibrated at 1373 K under argon gas, and the equilibrium compositions of the phases present after quenching were measured by electron probe microanalysis (EPMA). A solid‐state cell incorporating yttria‐stabilized zirconia as the solid electrolyte was used to measure the oxygen chemical potential corresponding to the three‐phase equilibrium between the alloy, orthosilicate solution, and quartz as a function of alloy composition. From these measurements, activity‐composition relationships in the alloy and orthosilicate solid solutions have been derived using a new method. Activities in the silicate solution have also been obtained independently using the mixing properties of the rock‐salt solid solution available in the literature and the tie‐line information obtained in this study. Both methods yield almost identical results. All three solid solution series‐alloy, monoxide, and orthosilicate‐exhibit mild positive derivations from ideality. The excess Gibbs free energy of mixing of the orthosilicate solid solution (NizCo1−zSi0.5O2) at 1373 K can be represented by the relation

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