bluuebunny/crossref_metadata_2025 huggingface dataset:
Wave-Driven Inner-Shelf Motions on the Oregon Coast*
Authors: Kirincich Anthony R. , Lentz Steven J. , Barth John A.
Published: May 2009

Recent work by S. Lentz et al. documents offshore transport in the inner shelf due to a wave-driven return flow associated with the Hasselmann wave stress (the Stokes–Coriolis force). This analysis is extended using observations from the central Oregon coast to identify the wave-driven return flow present and quantify the potential bias of wind-driven across-shelf exchange by unresolved wave-driven circulation. Using acoustic Doppler current profiler (ADCP) measurements at six stations, each in water depths of 13–15 m, observed depth-averaged, across-shelf velocities were generally correlated with theoretical estimates of the proposed return flow. During times of minimal wind forcing, across-shelf velocity profiles were vertically sheared, with stronger velocities near the top of the measured portion of the water column, and increased in magnitude with increasing significant wave height, consistent with circulation due to the Hasselmann wave stress. Yet velocity magnitudes and vertical shears were stronger than that predicted by linear wave theory, and more similar to the stratified “summer” velocity profiles described by S. Lentz et al. Additionally, substantial temporal and spatial variability of the wave-driven return flow was found, potentially due to changing wind and wave conditions as well as local bathymetric variability. Despite the wave-driven circulation found, subtracting estimates of the return flow from the observed across-shelf velocity had no significant effect on estimates of the across-shelf exchange due to along-shelf wind forcing at these water depths along the Oregon coast during summer.
From begums and bibis to abandoned females and idle women
Authors: Wald Erica
Published: May 2009

The late nineteenth and early twentieth centuries saw a proliferation of laws in colonial India which targeted women deemed to be prostitutes. As the number of laws grew, so too did the category of ‘prostitute’. Yet, before the nineteenth century, it would have been difficult to identify many of these women or their activities as criminal, or even immoral. This article examines how such legal boundaries and conceptualisations came to be formulated. It suggests that the ‘prostitute’ category in India was shaped by the repeated failure of the East India Company's surgeons and officers to control venereal disease among the European soldiery. Such attempts at disease control were experimented with from the late eighteenth century and, as this article argues, were keys in the later formulation of the Contagious Diseases Acts. This article traces the decline of long-term, monogamous relationships between European men and Indian women, and the corresponding rise in shorter-term sexual transactions in and around military cantonments. By grounding later legal shifts within the military medical context, we can clearly see the forces behind the social and moral changes surrounding this group of women in the early nineteenth century.
Poverty and Violent Conflict: A Micro-Level Perspective on the Causes and Duration of Warfare
Authors: Justino Patricia
Published: May 2009

This article discusses how endogenous mechanisms linking processes of violent conflict and the economic well-being of individuals and households in combat areas provide valuable micro foundations to the ongoing debate on the causes and duration of armed conflict. Notably, the endogenous relationship between conflict processes and household economic status leads to the emergence of symbiotic associations between armed groups and households living in areas they control that affect substantially the probability of a conflict starting and its effectiveness thereafter. Households in conflict areas draw on local armed groups to protect their economic status when anticipating violence and during the conflict, while armed groups make use of different levels of (either reluctant or voluntary) participation, support and cooperation from local populations to advance their strategic objectives at the onset and throughout the conflict. The level of household participation at the start and during the conflict is a function of two interdependent variables, namely household vulnerability to poverty and household vulnerability to violence. The poorer the household is at the start of the conflict, the higher is the probability of the household participating and supporting an armed group. The higher the risk of violence, the higher is the probability of the household participating and supporting armed groups. The interaction between these two variables varies with the conflict itself and is defined by the direct and indirect effects of conflict-induced violence on the economic behaviour and decisions of households in combat areas.
Livestock, Land and Political Power: The 1993 Killings in Burundi
Authors: Bundervoet Tom
Published: May 2009

This article examines the characteristics of the victims of the October 1993 massacres in Burundi. Using information on parents of the respondents of a 2002 demographic household survey, the author finds that the probability of a parent being killed during the events is significantly affected by age, sex and wealth, in the sense that older, wealthier and male persons were more likely to be killed. Using the median level of education of a parent's offspring to proxy the parental investment in human capital, the author finds that people who invested more in the human capital of their children ran a higher risk of being killed. The analysis also shows important spatial disparities in the killings. In trying to explain these locational effects, the author focus on two key hypotheses set forth with respect to the October 1993 events in Burundi: the land crisis and the questionable role played by the Front Démocratique du Burundi (FRODEBU), the dominant political actor at that time. The author finds that communal land pressure significantly increases the probability of being killed and that communal popular support for FRODEBU increases, in a non-linear fashion, the risk of being affected by the killings. The results are interpreted in light of the prevailing political economy of 1993 Burundi.
Civil Conflict and Displacement: Village-Level Determinants of Forced Migration in Aceh
Authors: Czaika Mathias , Kis-Katos Krisztina
Published: May 2009

The purpose of this article is to identify the determinants of displacement behavior based on various push and pull factors at the village level. The study concentrates on changes in village population during three years of civil conflict (1999—2002) in Aceh, Indonesia. The empirical analysis is based on a unique dataset from two census rounds of the Indonesian Village Potential Census (PODES). It uses data on around 5,200 Acehnese villages and relates village-level population change to conflict variables, geographic patterns, and traditional socio-economic determinants of migration. By applying quantile regressions, the push (outflow) factors and the pull (inflow) determinants of migration can also be distinguished. The authors identify the following factors as the main determinants of the Aceh migration pattern in this period. First, conflict clashes induced large rearrangements of the population between villages in highly affected districts, as well as strong village emigration from the geographically remote regions in Central Aceh towards the less conflict-affected coastal industrial areas. Besides conflict factors, an (ongoing) rural—urban migration process, driven by socio-economic factors, has taken place during the conflict period. Second, there is also evidence that security considerations, such as the presence of police in a village or neighborhood, were either emigration-reducing or immigration-inducing. Third, although the presence of ethnic Javanese has not been a primary cause of conflict incidence, their intimidation by the rebel movement has led to a significant outflow, primarily from conflict-affected villages in Central Aceh. These results reveal that, beside a conflict-induced fear of violence, population movements in Aceh have also been an outcome of traditional migration determinants.
Identifying Victims of Civil Conflicts: An Evaluation of Forced Displaced Households in Colombia
Authors: Ibáñez Ana María , Velásquez Andrea
Published: May 2009

Given that forced migration subjects households to extremely vulnerable conditions, the need to design particular policies for displaced populations is unquestionable. However, forced displacement poses several challenges to policymakers. In connection with low-intensity conflicts, such as in the case of Colombia, the main obstacle concerns the identification of households' victims of forced migration, so as to know to whom one should funnel aid. In such cases, inasmuch as victims migrate individually and tend to spread throughout a territory, identifying victims is difficult and channeling aid through supply-driven mechanisms is prohibitively expensive. To locate the households' victims of low intensity conflicts, an alternative — one adopted by the Colombia government — is to provide aid through demand-driven programs. This article evaluates whether demand-driven approaches aimed at assisting displaced households do in fact reach the entire displaced population. The study employs a survey applied to 1,553 households located in 48 Colombian municipalities. The authors identify to what extent a demand-driven approach excludes particular groups of households within the displaced population, examine what household characteristics determine the decision to declare one's eligibility for and final registration in RUPD, and analyze whether the exclusion of some groups of households is caused by the behavior of the relevant displaced households or by the deliberate targeting of these households by government offices. Results reveal that the exclusion of households from Colombia's RPUD program is mainly caused by lack of information regarding RUPD, with institutional determinants playing a lesser role.
Performance Measurement of Dynamic Structure DEVS for Large-Scale Cellular Space Models
Authors: Yi Sun  , Xiaolin Hu
Published: May 2009

Dynamic structure Discrete Event System Specification (DSDEVS) is an advanced modeling formalism that allows DEVS models and their couplings to be dynamically changed. The modeling power and advantages of DSDEVS have been well studied, however, the performance aspect is generally overlooked. This paper provides a comprehensive performance measurement of DSDEVS for a large-scale cellular space model. We consider the modeling and simulation layers for performance analysis, and carry out performance measurement based on a token ring model and a fire spread model. The results show that DS modeling can improve simulation performance for large-scale cellular space models, due to the fact that it makes the simulation focus only on those active models, and thus is more efficient than when the entire cellular space is loaded. On the other hand, the DS overhead cannot be ignored and can become significant and even dominant when a large number of cells are dynamically added/deleted.
Self-Esteem and Communal Responsiveness Toward a Flawed Partner: The Fair-Weather Care of Low-Self-Esteem Individuals
Authors: Lemay Edward P. , Clark Margaret S.
Published: May 2009

Three studies provide evidence that people with low self-esteem, but not those with high self-esteem, distance themselves from a flawed partner in situations in which the flaws seem likely to reflect negatively on them. Participants with low (but not high) self-esteem reduced their motivation to care for the partner's needs when they felt they might share a partner's salient flaws (Study 1), when they were primed to focus on similarities between themselves and a socially devalued partner (Study 2), and when they learned that their partner was socially incompetent (Study 3). In Study 3, individuals with low (but not high) self-esteem provided less emotional support and experienced more public image threat when they learned that partners were socially incompetent. In addition, all three studies provided evidence that participants' distancing reduced their confidence in the partner's motivation to care for them, suggesting that distancing involves a cost to the self.
Dollar Hegemony, Financialization, and the Credit Crisis
Authors: Vasudevan Ramaa
Published: May 2009

Countercyclical private capital flows to emerging markets have acted as a safety valve mechanism preserving the international role of the dollar and at the same time exporting fragility to the periphery. The revival of flows to the developing countries since 2002 has been different in that inflows to the United States have also been increasing. This suggests the emergence of a pattern of recycling that draws from the surplus countries in the periphery and channels these capital flows increasingly towards U.S. markets. The exploding of the bubble with the collapse of the subprime mortgage market is in that sense a result of the same recycling mechanisms that led to the debt crisis in the eighties and the Tequila and Asian crises in the nineties.
Qualitative Study of Breastfeeding After Childhood Sexual Assault
Authors: Coles Jan
Published: May 2009

Childhood sexual assault (CSA) is a common experience for women. Little research has explored the breastfeeding experience of CSA survivors who successfully breastfeed. The objective of this study is to explore the experience of successful breastfeeding with mothers with a history of CSA. Eleven women are interviewed after responding to a community-based advertisement. The women self-identify as having experienced CSA by a family member. Semistructured interviews are conducted by the author. Interviews are transcribed, coded, and analyzed for themes. Four key themes are identified: enhancement of the mother— baby relationship, validation of the maternal body, splitting of the breasts' dual role as maternal and sexual objects, and exposure and control when breastfeeding in public. Healthcare professionals should be aware of these maternal issues when promoting breastfeeding and counseling breastfeeding women. J Hum Lact. 25(3):317-324.
The Use of the Modified Telephone Interview for Cognitive Status (TICS-M) in the Detection of Amnestic Mild Cognitive Impairment
Authors: Cook Sarah E. , Marsiske Michael , McCoy Karin J. M.
Published: May 2009

Many screening tools for detecting cognitive decline require in-person assessment, which is often not cost-effective or feasible for those with physical limitations. The Modified Telephone Interview for Cognitive Status has been used for screening dementia, but little is known about its usefulness in detecting amnestic mild cognitive impairment. Community-dwelling participants (mean age = 74.9, mean education = 16.1 years) were administered the Modified Telephone Interview for Cognitive Status during initial screening and subsequently given a multidomain neuropsychological battery. Participants were classified by consensus panel as cognitively normal older adult (noMCI, N = 54) or amnestic mild cognitive impairment (N = 17) based on neuropsychological performance and Clinical Dementia Rating Scale interview, but independent of Modified Telephone Interview for Cognitive Status score. There was a significant difference between groups in Modified Telephone Interview for Cognitive Status score (t = 8.04, P < .01, noMCI range 32-43, mean [SD] = 37.4 [2.5], amnestic mild cognitive impairment range 25-37, mean [SD] = 31.2 [3.5]). Discriminant function analysis revealed that TICS-M alone correctly classified 85.9% of participants into their respective diagnostic classification (sensitivity = 82.4%, specificity = 87.0%). Receiver operating characteristics analysis resulted in cutoff score of 34 that optimized sensitivity and specificity of amnestic mild cognitive impairment classification. The Modified Telephone Interview for Cognitive Status is a brief, cost-effective screening measure for identifying those with and without amnestic mild cognitive impairment.
Cohesion and Performance
Authors: Chiocchio François , Essiembre Hélène
Published: May 2009

The management of project teams is evolving from managing technical processes to focusing on psychosocial determinants of performance. This trend puts a strain on project management theory and practice. Past meta-analyses on the cohesion—performance relationship show a positive correlation. However, they integrate effect sizes across different types of teams and settings. To clarify this issue for project teams, this meta-analysis differentiates 33 cohesion—performance correlations depending on whether teams are project, production, or service teams in organizational or academic settings. Results show that types of teams and settings are moderators. Project teams in organizational and academic settings show large effect sizes and differ from other teams. Theoretical considerations point to five interrelated modifiers: task uncertainty, task versus outcome performance, student samples' mental representation of the project outcome, and group heterogeneity.
Project Management in Real Time: A Service-Learning Project
Authors: Larson Erik , Drexler John A.
Published: May 2009

This article describes a service-learning assignment for a project management course. It is designed to facilitate hands-on student learning of both the technical and the interpersonal aspects of project management, and it involves student engagement with real customers and real stakeholders in the creation of real events with real outcomes. As such, it helps students internalize project management principles and value project management tools. Student teams design and implement plans for events intended to result in significant contributions in support of various charitable organizations. They create the planning and execution documents required of project management teams. The article describes the assignment and its results and discusses some cautions and alternatives.
Two Hours or More Away From Most Things
Authors: Haywood Rolling James , Brogden Lace Marie
Published: May 2009

How do we construe and re:construe the (archi)textures of (written) life? What is belonging when identities are temporal and where naming remains elusive or unknown? This article plays writing collaborative writing, deconstructing textual hierarchies between the “main” text body and footnoted text as a means of interrogating ways identities are written/performed. It is inspired by correspondences between the authors, generated in relation to three previous works published in Qualitative Inquiry, James Haywood Rolling, Jr.’s “Messing Around with Identity Constructs: Pursuing a Poststructuralist and Poetic Aesthetic,” “Searching Self-image: Identities to be Self-evident,” and Lace Marie Brogden’s “Not Quite Acceptable: Re:Reading my Father in Qualitative Inquiry.” We share correspondences between academics, using spaces created in writing “between friends” while constantly becoming through the re:writing of our identities from no fixed address.
Ethnic Differences in Parental Beliefs of Attention-Deficit/Hyperactivity Disorder and Treatment
Authors: Pham Andy V. , Carlson John S. , Kosciulek John F.
Published: May 2009

Objective: A survey study was conducted to explore ethnic differences in parental beliefs about the causes and treatments of ADHD and whether these beliefs predicted treatment preference. Method: Ethnically diverse parents of 5- to 12-year-old children with ADHD ( n = 58) and without ADHD ( n = 61) completed a questionnaire developed by the authors that asked them to rate statements about biological and psychological causes of ADHD and their beliefs about medication and behavioral treatment. Results: There were no significant ethnic differences in how parents viewed causes of ADHD. Beliefs about behavioral treatment revealed significant group differences, as ethnic minority (e.g., African American, Latino) parents rated behavioral treatments more positively than did Caucasian parents. Beliefs about biological causes predicted medication treatment and combined treatment use. Conclusion: Dissemination of information regarding evidence-based treatments should be given special attention as it may influence parents’ decisions to pursue specific treatments based on their beliefs. (J. of Att. Dis. 2010; 13(6) 584-591)
Predicting Performance on High-Stakes Assessment for Proficient Students and Students At Risk With Oral Reading Fluency Growth
Authors: Ditkowsky Ben , Koonce Danel A.
Published: May 2009

The current study examines the predictive relationship of Dynamic Indicators of Basic Early Literacy Skills oral reading fluency (DORF) scores to high-stakes test performance. Data were collected from 423 students. The participants were divided into three groups based on the level of progress that was made from the fall to the spring benchmark period. A descriptive, nonexperimental design was followed by a quasiexperimental examination of the relations between progress measured by DORF and results of high-stakes testing. Results indicate that progress in oral reading is meaningful in terms of fluency and high-stakes outcomes. In addition, progress measured using oral reading fluency increases the chances of students with special education needs meeting standards on high-stakes tests. Implications of the findings are presented.
Prevalence of Antiretroviral Drug Resistance in Antiretroviral-Naive Individuals
Authors: James Christopher W. , Moffett Lee E. , Szabo Susan
Published: May 2009

Transmitted antiretroviral drug resistance has been an ongoing consideration even in patients who are treatment naive. The authors retrospectively selected all eligible patients from a US-based urban HIV clinic who had a genotypic resistance assay performed prior to the initiation of antiretroviral therapy. Clinically significant resistance was detected in 8% of assays, and was comparable when stratified by duration of time from diagnosis to genotypic resistance assay.
Known to Be Positive But Not in Care: A Pilot Study From Thailand
Authors: Rithpho Pratuma , Grimes Deanna E. , Grimes Richard M. , Senaratana Wilawan
Published: May 2009

This study was designed to describe persons with HIV/ AIDS (PWHAs) in Thailand who have not disclosed their HIV status to the government HIV clinics to receive medical care. Objectives were to (1) demonstrate a way to access these persons, and (2) describe their characteristics, HIV status, reasons for nondisclosure, and problems related to their self-care. Two nongovernmental organizations (NGOs) serving the nonmedical needs of PWHAs were used. In all, 22 PWHAs participated. Approximately 80% have known their HIV status for more than 1 year and 30% for more than 5 years. Almost 60% currently used recreational drugs. Reasons for not disclosing their HIV status included that they were still healthy (81.8%) and worried about stigma (77.3%). Two thirds will disclose when a serious problem occurs. This study demonstrates that this population can be accessed and studied through NGOs and that this population differs slightly from PWHAs in Thailand studied at initiation of medical care.
Financialisation and Derivatives: Constructing an Artifice of Indifference
Authors: Wigan Duncan
Published: May 2009

This paper accords derivatives a central role in defining the character and dynamics of financialised accumulation. Under the guise of financial precision and a progressive innovation spiral, financial derivatives have instrumentalised risk so that ownership and property take a novel form. The advent of limited liability and absentee ownership in the second half of the nineteenth century marked the start of this process of transformation. At that stage, ownership became fleeting and its relationship to the underlying technical process uncertain, loose and complex. Risk management through derivatives takes this a stage further. Derivatives imply that ownership can take a form wherein there are no direct ties to a particular asset, and therefore no possibility of a conceptual link between property and stewardship. Instead, ownership proceeds on the basis of disengagement and financialisation proceeds via the construction of indifference to the exigencies of ‘real’ economic competition.
Novel modelling approach to optimisation of welding conditions and heat treatment schedules for age hardening Al alloys
Authors: Myhr O. R. , Grong Ø.
Published: May 2009

In the present paper the general purpose finite element code WELDSIM, equipped with a new natural aging model, is used to calculate the minimum heat affected zone (HAZ) strength level σ min and the equivalent half width of the reduced strength zone Δyeq red of strength σ min during single pass butt welding of Al–Mg–Si alloys. In particular, it is illustrated how the resulting strength loss depends on the interplay between the base metal chemistry and the initial temper condition on the one hand and the net arc power q 0, the welding speed v, the plate thickness d and the effective heat transfer coefficient h between the Al plate and the steel backing on the other hand. Assuming one-dimensional heat flow and pseudosteady state, the former parameters can be combined in a single group variable q 0/ vd, which uniquely defines the HAZ thermal programme when welding is performed without the use of steel backing. Taking this as the main variable controlling the strength loss, the simulation results can be condensed into two-dimensional process diagrams, showing the variation in the design parameters σ min and Δyeq red with q 0/ vd for different combinations of h and d. The output data from WELDSIM are, in turn, used as inputs to mechanical models to predict the resulting design stress under different loading conditions. It is concluded that significant weight reductions and cost savings can be achieved by minimising the strength loss after welding, provided that the design parameters σ min and Δyeq red are calculated on the basis of the actual yield strength profile within the weld HAZ, as obtained from WELDSIM.
Tyrosine kinase inhibitor–induced platelet dysfunction in patients with chronic myeloid leukemia
Authors: Quintás-Cardama Alfonso , Han Xin , Kantarjian Hagop , Cortes Jorge
Published: May 2009

Dasatinib is associated with increased risk of bleeding among patients with chronic myeloid leukemia, even in the absence of thrombocytopenia, suggesting the presence of a hemostatic defect. We tested platelet aggregation in 91 patients with chronic myeloid leukemia in chronic phase either off-therapy (n = 4) or receiving dasatinib (n = 27), bosutinib (n = 32), imatinib (n = 19), or nilotinib (n = 9). All but 3 patients simultaneously receiving imatinib and warfarin had normal coagulation studies. All 4 patients off therapy had normal platelet aggregation. Impaired platelet aggregation on stimulation with arachidonic acid, epinephrine, or both was observed in 70%, 85%, and 59% of patients on dasatinib, respectively. Eighty-five percent of patients on bosutinib, 100% on nilotinib, and 33% on imatinib had normal platelet aggregation. Dasatinib 400 nM induced rapid and marked prolongation of closure time to collagen/epinephrine in normal whole blood on the PFA-100 system. In conclusion, dasatinib and, to some extent, imatinib produce abnormalities in platelet aggregometry testing.
Genetic variation in caspase genes and risk of non-Hodgkin lymphoma: a pooled analysis of 3 population-based case-control studies
Authors: Lan Qing , Morton Lindsay M. , Armstrong Bruce , Hartge Patricia , Menashe Idan , Zheng Tongzhang , Purdue Mark P. , Cerhan James R. , Zhang Yawei , Grulich Andrew , Cozen Wendy , Yeager Meredith , Holford Theodore R. , Vajdic Claire M. , Davis Scott , Leaderer Brian , Kricker Anne , Schenk Maryjean , Zahm Shelia H. , Chatterjee Nilanjan , Chanock Stephen J. , Rothman Nathaniel , Wang Sophia S.
Published: May 2009

Caspases play a critical role in regulation of apoptosis, cell differentiation, inflammation, and innate immunity, and several are mutated or have altered expression in non-Hodgkin lymphoma (NHL). To study the impact of genetic variation in caspases on NHL risk, we analyzed tag single nucleotide polymorphisms (SNPs) in 12 caspase and related genes in 3 population-based case-control studies (1946 cases and 1808 controls). Gene-based analysis, adjusting for the number of tagSNPs genotyped in each gene, showed significant associations for CASP8, CASP9, and CASP1. SNP-based analysis showed that CASP8 rs6736233 (odds ratio (OR) CG = 1.21; ORCC = 2.13; P trend = .011); CASP9 rs4661636 (ORCT = 0.89; ORTT = 0.77; P trend = .011); and CASP1 rs1785882 (ORAT = 1.12; ORAA = 1.30; P trend = .0054) were significantly associated with NHL risk and consistent across studies. It is noteworthy that genetic variants in CASP8 were associated with risk of all major NHL subtypes. Our findings suggest that genetic variation in caspases may play an important role in lymphomagenesis.
Fucosylated chondroitin sulfate inhibits plasma thrombin generation via targeting of the factor IXa heparin-binding exosite
Authors: Buyue Yang , Sheehan John P.
Published: May 2009

Depolymerized holothurian glycosaminoglycan (DHG) is a fucosylated chondroitin sulfate with antithrombin-independent antithrombotic properties. Heparin cofactor II (HCII)-dependent and -independent mechanisms for DHG inhibition of plasma thrombin generation were evaluated. When thrombin generation was initiated with 0.2 pM tissue factor (TF), the half maximal effective concentration (EC50) for DHG inhibition was identical in mock- or HCII-depleted plasma, suggesting a serpin-independent mechanism. In the presence of excess TF, the EC50 for DHG was increased 13- to 27-fold, suggesting inhibition was dependent on intrinsic tenase (factor IXa-factor VIIIa) components. In factor VIII–deficient plasma supplemented with 700 pM factor VIII or VIIIa, and factor IX–deficient plasma supplemented with plasma-derived factor IX or 100 pM factor IXa, the EC50 for DHG was similar. Thus, cofactor and zymogen activation did not contribute to DHG inhibition of thrombin generation. Factor IX–deficient plasma supplemented with mutant factor IX(a) proteins demonstrated resistance to DHG inhibition of thrombin generation [factor IX(a) R233A > R170A > WT] that inversely correlated with protease-heparin affinity. These results replicate the effect of these mutations with purified intrinsic tenase components, and establish the factor IXa heparin-binding exosite as the relevant molecular target for inhibition by DHG. Glycosaminoglycan-mediated intrinsic tenase inhibition is a novel antithrombotic mechanism with physiologic and therapeutic applications.
De novo deletion 17p13.1 chronic lymphocytic leukemia shows significant clinical heterogeneity: the M. D. Anderson and Mayo Clinic experience
Authors: Tam Constantine S. , Shanafelt Tait D. , Wierda William G. , Abruzzo Lynne V. , Van Dyke Daniel L. , O'Brien Susan , Ferrajoli Alessandra , Lerner Susan A. , Lynn Alice , Kay Neil E. , Keating Michael J.
Published: May 2009

To determine the clinical fate of patients with de novo deletion 17p13.1 (17p−) chronic lymphocytic leukemia (CLL), we retrospectively studied the outcome of 99 treatment-naive 17p− CLL patients from the M. D. Anderson Cancer Center (n = 64) and the Mayo Clinic (n = 35). Among 67 asymptomatic patients followed for progression, 53% developed CLL requiring treatment over 3 years. Patients who had not progressed by 18 months subsequently had stable disease, with 3 of 19 patients progressing after follow-up of up to 70 months. Risk factors for progressive disease were Rai stage of 1 or higher and unmutated immunoglobulin variable region heavy chain (IgVH). The overall survival rate was 65% at 3 years. Rai stage 1 or higher, unmutated IgVH, and 17p− in 25% or more of nuclei were adverse factors for survival. The 3-year survival rates of patients with 1 or fewer, 2, and 3 of these factors were 95%, 74%, and 22%, respectively (P < .001). Response rates to therapy with rituximab (n = 6); purine analogues and rituximab (n = 25); and purine analogues, rituximab, and alemtuzumab (n = 16) combinations were 50%, 72%, and 81%, respectively. Patients with 17p− CLL exhibit clinical heterogeneity, with some patients experiencing an indolent course. Survival can be predicted using clinical and biologic characteristics.
Weak preservation of local neutral substitution rates across mammalian genomes
Authors: Imamura Hideo , Karro John E , Chuang Jeffrey H
Published: May 2009

Background

The rate at which neutral (non-functional) bases undergo substitution is highly dependent on their location within a genome. However, it is not clear how fast these location-dependent rates change, or to what extent the substitution rate patterns are conserved between lineages. To address this question, which is critical not only for understanding the substitution process but also for evaluating phylogenetic footprinting algorithms, we examine ancestral repeats: a predominantly neutral dataset with a significantly higher genomic density than other datasets commonly used to study substitution rate variation. Using this repeat data, we measure the extent to which orthologous ancestral repeat sequences exhibit similar substitution patterns in separate mammalian lineages, allowing us to ascertain how well local substitution rates have been preserved across species.

Results

We calculated substitution rates for each ancestral repeat in each of three independent mammalian lineages (primate – from human/macaque alignments, rodent – from mouse/rat alignments, and laurasiatheria – from dog/cow alignments). We then measured the correlation of local substitution rates among these lineages. Overall we found the correlations between lineages to be statistically significant, but too weak to have much predictive power (r
2 <5%). These correlations were found to be primarily driven by regional effects at the scale of several hundred kb or larger. A few repeat classes (e.g. 7SK, Charlie8, and MER121) also exhibited stronger conservation of rate patterns, likely due to the effect of repeat-specific purifying selection. These classes should be excluded when estimating local neutral substitution rates.

Conclusion

Although local neutral substitution rates have some correlations among mammalian species, these correlations have little predictive power on the scale of individual repeats. This indicates that local substitution rates have changed significantly among the lineages we have studied, and are likely to have changed even more for more diverged lineages. The correlations that do persist are too weak to be responsible for many of the highly conserved elements found by phylogenetic footprinting algorithms, leading us to conclude that such elements must be conserved due to selective forces.
Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants
Authors: Li Wenyan , Liu Bing , Yu Lujun , Feng Dongru , Wang Hongbin , Wang Jinfa
Published: May 2009

Background

The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-bonds in α, β-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multigene families. Although discoveries about this family in Arabidopsis and other species have been reported in some studies, the evolution and function of multiple OPRs in plants are not clearly understood.

Results

A comparative genomic analysis was performed to investigate the phylogenetic relationship, structural evolution and functional divergence among OPR paralogues in plants. In total, 74 OPR genes were identified from 11 species representing the 6 major green plant lineages: green algae, mosses, lycophytes, gymnosperms, monocots and dicots. Phylogenetic analysis showed that seven well-conserved subfamilies exist in plants. All OPR genes from green algae were clustered into a single subfamily, while those from land plants fell into six other subfamilies, suggesting that the events leading to the expansion of the OPR family occurred in land plants. Further analysis revealed that lineage-specific expansion, especially by tandem duplication, contributed to the current OPR subfamilies in land plants after divergence from aquatic plants. Interestingly, exon/intron structure analysis showed that the gene structures of OPR paralogues exhibits diversity in intron number and length, while the intron positions and phase were highly conserved across different lineage species. These observations together with the phylogenetic tree revealed that successive single intron loss, as well as indels within introns, occurred during the process of structural evolution of OPR paralogues. Functional divergence analysis revealed that altered functional constraints have occurred at specific amino acid positions after diversification of the paralogues. Most notably, significant functional divergence was also found in all pairs, except for the II/IV, II/V and V/VI pairs. Strikingly, analysis of the site-specific profiles established by posterior probability revealed that the positive-selection sites and/or critical amino acid residues for functional divergence are mainly distributed in α-helices and substrate binding loop (SBL), indicating the functional importance of these regions for this protein family.

Conclusion

This study highlights the molecular evolution of the OPR gene family in all plant lineages and indicates critical amino acid residues likely relevant for the distinct functional properties of the paralogues. Further experimental verification of these findings may provide valuable information on the OPRs' biochemical and physiological functions.
Association of IL-10 and IL-10Rβ gene polymorphisms with graft-versus-host disease after haematopoietic stem cell transplantation from an HLA-identical sibling donor
Authors: Sivula Jyrki , Turpeinen Hannu , Volin Liisa , Partanen Jukka
Published: May 2009

Background

Extensive allelic matching in the human leukocyte antigen (HLA) genes is regarded as a prerequisite for good clinical success of allogeneic haematopoietic stem cell transplantation (HSCT). Also other genetic factors can be assumed to play a role in preventing and controlling the complications associated with allogeneic HSCT, in particular graft-versus-host disease (GvHD). Interleukin-10 (IL-10) and its receptor (IL-10R), key regulators of the immune response, are among these candidates. We studied the association of IL-10 and IL-10Rβ gene polymorphisms with the occurrence of GvHD in 309 HLA-identical sibling donor and recipient pairs.

Results

The difference in genotypic IL-10 production between patient and donor in combination with patient IL-10Rβ A/A genotype predisposed strongly to acute GvHD (OR = 7.15, p = 0.000023). On the other hand, a combination of same genotypic IL-10 production with patient IL-10Rβ A/A genotype protected from chronic GvHD (OR = 0.407, p = 0.0097).

Conclusion

Our results suggest that IL-10 and IL-10Rβ genes have a synergistic effect on the risk of GvHD.
Human sex hormone-binding globulin gene expression- multiple promoters and complex alternative splicing
Authors: Nakhla Atif M , Hryb Daniel J , Rosner William , Romas Nicholas A , Xiang Zhaoying , Kahn Scott M
Published: May 2009

Background

Human sex hormone-binding globulin (SHBG) regulates free sex steroid concentrations in plasma and modulates rapid, membrane based steroid signaling. SHBG is encoded by an eight exon-long transcript whose expression is regulated by a downstream promoter (PL). The SHBG gene was previously shown to express a second major transcript of unknown function, derived from an upstream promoter (PT), and two minor transcripts.

Results

We report that transcriptional expression of the human SHBG gene is far more complex than previously described. PL and PT direct the expression of at least six independent transcripts each, resulting from alternative splicing of exons 4, 5, 6, and/or 7. We mapped two transcriptional start sites downstream of PL and PT, and present evidence for a third SHBG gene promoter (PN) within the neighboring FXR2 gene; PN regulates the expression of at least seven independent SHBG gene transcripts, each possessing a novel, 164-nt first exon (1N). Transcriptional expression patterns were generated for human prostate, breast, testis, liver, and brain, and the LNCaP, MCF-7, and HepG2 cell lines. Each expresses the SHBG transcript, albeit in varying abundance. Alternative splicing was more pronounced in the cancer cell lines. PL- PT- and PN-derived transcripts were most abundant in liver, testis, and prostate, respectively. Initial findings reveal the existence of a smaller immunoreactive SHBG species in LNCaP, MCF-7, and HepG2 cells.

Conclusion

These results extend our understanding of human SHBG gene transcription, and raise new and important questions regarding the role of novel alternatively spliced transcripts, their function in hormonally responsive tissues including the breast and prostate, and the role that aberrant SHBG gene expression may play in cancer.
Application of biomedical informatics to chronic pediatric diseases: a systematic review
Authors: Moeinedin Fatemeh , Moineddin Rahim , Jadad Alejandro R , Hamid Jemila S , To Teresa , Beyene Joseph
Published: May 2009

Background

Chronic diseases affect millions of children worldwide leading to substantial disease burden to the children and their families as well as escalating health care costs. The increasing trend in the prevalence of complex pediatric chronic diseases requires innovative and optimal delivery of care. Biomedical informatics applications play an important role in improving health outcomes while being cost-effective. However, their utility in pediatric chronic diseases has not been studied in a comprehensive and systematic way. The objective of this study was to conduct a systematic review of the effects of biomedical informatics applications in pediatric chronic diseases.

Methods

A comprehensive literature search was conducted using MEDLINE, the Cochrane Library and EMBASE databases from inception of each database to September 2008. We included studies of any methodological type and any language that applied biomedical informatics to chronic conditions in children and adolescents 18 years of age or younger. Two independent reviewers carried out study selection and data extraction. Quality assessment was performed using a study design evaluation instrument to appraise the strength of the studies and their methodological adequacy. Because of heterogeneity in the conditions and outcomes we studied, a formal meta-analysis was not performed.

Results

Based on our search strategy, 655 titles and abstracts were reviewed. From this set we identified 27 relevant articles that met our inclusion criteria. The results from these studies indicated that biomedical informatics applications have favourable clinical and patient outcomes including, but not limited to, reduced number of emergency room visits, improved knowledge on disease management, and enhanced satisfaction. Seventy percent of reviewed papers were published after year 2000, 89% of users were patients and 11% were either providers or caregivers. The majority (96%) of the selected studies reported improved outcomes.

Conclusion

Published studies suggested positive impacts of informatics predominantly in pediatric asthma. As electronic tools become more widely adopted, there will be opportunities to improve patient care in a wide range of chronic illnesses through informatics solutions.
Test characteristics of two rapid antigen detection tests (SD FK50 and SD FK60) for the diagnosis of malaria in returned travellers
Authors: Van der Palen Mirna , Gillet Philippe , Bottieau Emmanuel , Cnops Lieselotte , Van Esbroeck Marjan , Jacobs Jan
Published: May 2009

Background

Two malaria rapid diagnostic tests were evaluated in a travel clinic setting: the SD FK50 Malaria Ag Plasmodium falciparum test (a two-band test) and the SD FK60 Malaria Ag P. falciparum/Pan test (a three-band test).

Methods

A panel of stored whole blood samples (n = 452 and n = 614 for FK50 and FK60, respectively) from returned travellers was used. The reference method was microscopy with PCR in case of discordant results.

Results

For both tests, overall sensitivity for the detection of P. falciparum was 93.5%, reaching 97.6% and 100% at parasite densities above 100 and 1,000/μl respectively. Overall sensitivities for Plasmodium vivax, Plasmodium ovale and Plasmodium malariae for the FK60 test were 87.5%, 76.3% and 45.2%, but they reached 92.6% and 90.5% for P. vivax and P. ovale at parasite densities above 500/μl. Specificities were above 95% for all species and both tests when corrected by PCR, with visible histidine-rich protein-2 lines for P. malariae (n = 3) and P. vivax and P. ovale (1 sample each). Line intensities were reproducible and correlated to parasite densities. The FK60 tests provided clues to estimate parasite densities for P. falciparum below or above 1,000/μl.

Conclusion

Both the FK50 and FK60 performed well for the diagnosis of P. falciparum in the present setting, and the FK60 for the diagnosis of P. vivax and P. ovale at parasite densities > 500/μl. The potential use of the FK60 as a semi-quantitative estimation of parasite density needs to be further explored.
Rate of red blood cell destruction varies in different strains of mice infected with Plasmodium berghei-ANKA after chronic exposure
Authors: Helegbe Gideon Kofi , Huy Nguyen T , Yanagi Tetsuo , Shuaibu Mohammed N , Yamazaki Akiko , Kikuchi Mihoko , Yasunami Michio , Hirayama Kenji
Published: May 2009

Background

Severe malaria anaemia in the semi-immune individuals in the holo-endemic area has been observed to occur at low parasite density with individual variation in the responses. Thus the following has been thought to be involved: auto-immune-mediated mechanisms of uninfected red blood cell destruction, and host genetic factors to explain the differences in individual responses under the same malaria transmission. In this study, the extent of red blood cell (RBC) destruction in different strains of semi-immune mice model at relatively low parasitaemia was studied.

Methodology

To generate semi-immunity, four strains of mice were taken through several cycles of infection and treatment. By means of immunofluorescent assay and ELISA, sera were screened for anti-erythrocyte auto-antibodies, and their relationship with haematological parameters and parasitaemia in the strains of semi-immune mice was investigated.

Results

Upon challenge withPlasmodium bergheiANKA after generating semi-immune status, different mean percentage haemoglobin (Hb) drop was observed in the mice strains (Balb/c = 47.1%; NZW = 30.05%; C57BL/6 = 28.44%; CBA = 25.1%), which occurred on different days for each strain (for Balb/c, mean period = 13.6 days; for C57BL/6, NZW, and CBA mean period = 10.6, 10.8, 10.9 days respectively). Binding of antibody to white ghost RBCs was observed in sera of the four strains of semi-immune mice by immunofluorescence. Mean percentage Hb drop per parasitaemia was highest in Balb/c (73.6), followed by C57BL/6 (8.6), CBA (6.9) and NZW (4.0), p = 0.0005. Consequently, auto-antibodies level to ghost RBC were correlated with degree of anaemia and were highest in Balb/c, when compared with the other strains, p < 0.001.

Conclusion

The results presented in this study seem to indicate that anti-RBC auto-antibodies may be involved in the destruction of uninfected RBC in semi-immune mice at relatively low parasite burden. Host genetic factors may also influence the outcome of auto-immune mediated destruction of RBC due to the variation in Hb loss per % parasitaemia and differences in antibody titer for each semi-immune mice strain. However, further studies at the molecular level ought to be carried out to confirm this.