Showing papers by "University of Massachusetts Boston published in 2006"

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

Abstract: Over the last decade, the introduction of microarray technology has had a profound impact on gene expression research. The publication of studies with dissimilar or altogether contradictory results, obtained using different microarray platforms to analyze identical RNA samples, has raised concerns about the reliability of this technology. The MicroArray Quality Control (MAQC) project was initiated to address these concerns, as well as other performance and data analysis issues. Expression data on four titration pools from two distinct reference RNA samples were generated at multiple test sites using a variety of microarray-based and alternative technology platforms. Here we describe the experimental design and probe mapping efforts behind the MAQC project. We show intraplatform consistency across test sites as well as a high level of interplatform concordance in terms of genes identified as differentially expressed. This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings.

Calcium plus vitamin D supplementation and the risk of fractures.

Abstract: Background The efficacy of calcium with vitamin D supplementation for preventing hip and other fractures in healthy postmenopausal women remains equivocal. Methods We recruited 36,282 postmenopausal women, 50 to 79 years of age, who were already enrolled in a Women's Health Initiative (WHI) clinical trial. We randomly assigned participants to receive 1000 mg of elemental calcium as calcium carbonate with 400 IU of vitamin D3 daily or placebo. Fractures were ascertained for an average follow-up period of 7.0 years. Bone density was measured at three WHI centers. Results Hip bone density was 1.06 percent higher in the calcium plus vitamin D group than in the placebo group (P<0.01). Intention-to-treat analysis indicated that participants receiving calcium plus vitamin D supplementation had a hazard ratio of 0.88 for hip fracture (95 percent confidence interval, 0.72 to 1.08), 0.90 for clinical spine fracture (0.74 to 1.10), and 0.96 for total fractures (0.91 to 1.02). The risk of renal calculi increased with...

Evaluation of DNA microarray results with quantitative gene expression platforms.

Abstract: We have evaluated the performance characteristics of three quantitative gene expression technologies and correlated their expression measurements to those of five commercial microarray platforms, based on the MicroArray Quality Control (MAQC) data set. The limit of detection, assay range, precision, accuracy and fold-change correlations were assessed for 997 TaqMan Gene Expression Assays, 205 Standardized RT (Sta)RT-PCR assays and 244 QuantiGene assays. TaqMan is a registered trademark of Roche Molecular Systems, Inc. We observed high correlation between quantitative gene expression values and microarray platform results and found few discordant measurements among all platforms. The main cause of variability was differences in probe sequence and thus target location. A second source of variability was the limited and variable sensitivity of the different microarray platforms for detecting weakly expressed genes, which affected interplatform and intersite reproducibility of differentially expressed genes. From this analysis, we conclude that the MAQC microarray data set has been validated by alternative quantitative gene expression platforms thus supporting the use of microarray platforms for the quantitative characterization of gene expression.

Global bathymetric patterns of standing stock and body size in the deep-sea benthos

Abstract: We present the first global-scale analy- sis of standing stock (abundance and biomass) for 4 major size classes of deep-sea biota: bacteria, meta- zoan meiofauna, macrofauna and megafauna. The community standing stock decreases with depth; this is a universal phenomenon that involves a com- plex transition in the relative importance of the different size groups. Bacterial abundance and biomass show no decline with depth. All 3 animal size groups experience significant exponential de- creases in both abundance and biomass. The abun- dance of larger animals is significantly lower and decreases more rapidly than for smaller groups. The resulting drop in average body size with depth con- firms Thiel's size-structure hypothesis on very large spatial scales. In terms of their proportion of total community biomass, smaller size classes replace larger size classes. The upper continental slope is dominated by macrofaunal biomass, and the abyss by bacterial and meiofaunal biomass. The dramatic decrease in total community standing stock and the ascendancy of smaller organisms with depth has important implications for deep-sea biodiversity. The bathyal zone (200 to 4000 m) affords more eco- logical and evolutionary opportunity in the form of energy availability for larger organisms, and conse- quently supports higher macrofaunal and mega- faunal species diversity than the abyss (> 4000 m).

What is housing affordability? The case for the residual income approach

Abstract: This article seeks to increase the awareness of and support for the residual income approach to housing affordability indicators and standards, especially in the United States. It begins with an overview of various semantic, substantive, and definitional issues relating to the notion of affordability, leading to an argument supporting the conceptual soundness of the residual income approach. The concept is then briefly set into the historical context of U.S. and British debates on affordability measures. This description is followed by a discussion of two of the principal issues involved in crafting an operational residual income standard: the selection of a normative standard for nonhousing items and the treatment of taxes. The article concludes by considering some of the potential implications of the residual income paradigm for the analysis of housing problems and needs, for housing subsidy policy, and for mortgage underwriting practice.

A model for the influence of mentoring relationships on youth development

Abstract: Anecdotal reports of the protective qualities of mentoring relationships for youth are corroborated by a growing body of research. What is missing, however, is research on the processes by which mentors influence developmental outcomes. In this article, we present a conceptual model of the mentoring process along with a delineation of some of the current research on what makes for more effective mentoring relationships. A set of recommendations for future research is offered. © 2006 Wiley Periodicals, Inc.

Condition indices for conservation: new uses for evolving tools

Abstract: Biologists have developed a wide range of morphological, biochemical and physiological metrics to assess the health and, in particular, the energetic status of individual animals. These metrics originated to quantify aspects of human health, but have also proven useful to address questions in life history, ecology and resource management of game and commercial animals. We review the application of condition indices (CI) for conservation studies and focus on measures that quantify fat reserves, known to be critical for energetically challenging activities such as migration, reproduction and survival during periods of scarcity. Standard methods score fat content, or rely on a ratio of body mass rationalized by some measure of size, usually a linear dimension such as wing length or total body length. Higher numerical values of these indices are interpreted to mean an animal has greater energy reserves. Such CIs can provide predictive information about habitat quality and reproductive output, which in turn can help managers with conservation assessments and policies. We review the issues about the methods and metrics of measurement and describe the linkage of CIs to measures of body shape. Debates in the literature about the best statistical methods to use in computing and comparing CIs remain unresolved. Next, we comment on the diversity of methods used to measure body composition and the diversity of physiological models that compute body composition and CIs. The underlying physiological regulatory systems that govern the allocation of energy and nutrients among compartments and processes within the body are poorly understood, especially for field situations, and await basic data from additional laboratory studies and advanced measurement systems including telemetry. For now, standard physiological CIs can provide supporting evidence and mechanistic linkages for population studies that have traditionally been the focus of conservation biology. Physiologists can provide guidance for the field application of conditions indices with validation studies and development of new instruments.

Can distributed software development be agile

Abstract: Three organizations studied here suggest the answer is "yes," when the unique characteristics of both environments are successfully blended.

Evidence of Broad Deficits in Emotion Regulation Associated with Chronic Worry and Generalized Anxiety Disorder

Abstract: This study examined the relationship between emotion regulation deficits and GAD-related outcomes in an analogue sample. Consistent with hypotheses, general emotion dysregulation was associated with reports of chronic worry and with analogue GAD status. Also, specific regulation deficits, including deficits in emotional clarity, acceptance of emotions, ability to engage in goal directed behaviors when distressed, impulse control, and access to effective regulation strategies, were associated with worry and analogue GAD above and beyond variance contributed by negative affectivity. These findings provide additional preliminary evidence for an emotion regulation deficit model of GAD and are discussed in terms of clinical implications and directions for future research.

The impact of child symptom severity on depressed mood among parents of children with ASD: the mediating role of stress proliferation.

Abstract: Stress proliferation (the tendency of stressors to engender additional stressors in other life domains) is explored in a sample of 68 parents of children identified with ASD. Regression analyses showed that parent depression was predicted by both child symptom severity and by stress proliferation and that stress proliferation partially mediated the effect of child symptom severity on parent depression. In addition, informal social support was found to reduce levels of parent stress proliferation and parent depression; however, contrary to the stress buffering hypothesis, the ameliorative effect of support on stress proliferation was shown to be greatest when reported child symptomatology was less (rather than more) severe. Study implications for future research and practice are discussed.

Financial ties between DSM-IV panel members and the pharmaceutical industry.

Abstract: Background: Increasing attention has been given to the transparency of potential confl icts of interest in clinical medicine and biomedical sciences, particularly in journal publishing and science advisory panels. The authors examined the degree and type of fities to the pharmaceutical industry of panel members responsible for revisions of the Diagnostic and Statistical Manual of Mental Disorders (DSM) . Methods: By using multimodal screening techniques the authors investigated the fi nancial ties to the pharmaceutical industry of 170 panel members who contributed to the diagnostic criteria produced for the DSM-IV and the DSM-IV-TR. Results: Of the 170 DSM panel members 95 (56%) had one or more fi nancial associations with companies in the pharmaceutical industry. One hundred percent of the members of the panels on ‘Mood Disorders’ and ‘Schizophrenia and Other Psychotic Disorders’ had fi nancial ties to drug companies. The leading categories of fiinterest held by panel members were research funding (42%), consultan

The effect of loans on the persistence and attainment of community college students

Abstract: This study informs public policies regarding the use of subsidized loans as financial aid for community college students. Using logistic regression, it analyzes the National Center for Education Statistics’ Beginning Postsecondary Students (BPS 90/94) data to predict persistence to the second year of college and associate’s degree attainment over five years. During the period under study, loans did not contribute to higher persistence and attainment rates. Loans are observed to have a negative effect on persistence and no effect on degree attainment. Estimates of the interaction effects of borrowing and income status are insignificant but demonstrate the need for further testing. The findings are attributed to a combination of the high uncertainty of degree completion among community college students and the negative affective component of indebtedness.

A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies

Abstract: Over the last decade, gene expression microarrays have had a profound impact on biomedical research. The diversity of platforms and analytical methods available to researchers have made the comparison of data from multiple platforms challenging. In this study, we describe a framework for comparisons across platforms and laboratories. We have attempted to include nearly all the available commercial and 'in-house' platforms. Using probe sequences matched at the exon level improved consistency of measurements across the different microarray platforms compared to annotation-based matches. Generally, consistency was good for highly expressed genes, and variable for genes with lower expression values as confirmed by quantitative real-time (QRT)-PCR. Concordance of measurements was higher between laboratories on the same platform than across platforms. We demonstrate that, after stringent preprocessing, commercial arrays were more consistent than in-house arrays, and by most measures, one-dye platforms were more consistent than two-dye platforms.

Population growth, human development, and deforestation in biodiversity hotspots.

Abstract: Human population and development activities affect the rate of deforestation in biodiversity hotspots. We quantified the effect of human population growth and development on rates of deforestation and analyzed the relationship between these causal factors in the 1980s and 1990s. We compared the averages of population growth, human development index (HDI, which measures income, health, and education), and deforestation rate and computed correlations among these variables for countries that contain biodiversity hotspots. When population growth was high and HDI was low there was a high rate of deforestation, but when HDI was high, rate of deforestation was low, despite high population growth. The correlation among variables was significant for the 1990s but not for the 1980s. The relationship between population growth and HDI had a regional pattern that reflected the historical process of development. Based on the changes in HDI and deforestation rate over time, we identified two drivers of deforestation: policy choice and human-development constraints. Policy choices that disregard conservation may cause the loss of forests even in countries that are relatively developed. Lack of development in other countries, on the other hand, may increase the pressure on forests to meet the basic needs of the human population. Deforestation resulting from policy choices may be easier to fix than deforestation arising from human development constraints. To prevent deforestation in the countries that have such constraints, transfer of material and intellectual resources from developed countries may be needed. Popular interest in sustainable development in developed countries can facilitate the transfer of these resources.

Using RNA sample titrations to assess microarray platform performance and normalization techniques

Abstract: We have assessed the utility of RNA titration samples for evaluating microarray platform performance and the impact of different normalization methods on the results obtained. As part of the MicroArray Quality Control project, we investigated the performance of five commercial microarray platforms using two independent RNA samples and two titration mixtures of these samples. Focusing on 12,091 genes common across all platforms, we determined the ability of each platform to detect the correct titration response across the samples. Global deviations from the response predicted by the titration ratios were observed. These differences could be explained by variations in relative amounts of messenger RNA as a fraction of total RNA between the two independent samples. Overall, both the qualitative and quantitative correspondence across platforms was high. In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples.

Physical Activity of Adults with Mental Retardation: Review and Research Needs:

Abstract: Objective To characterize physical activity levels of adults with mental retardation and identify limitations in published research. Data Sources Key word searches for “mental retardation,” “intellectual disability,” “learning disability,” or “developmental disability” combined with “physical activity” or “habitual exercise” identified articles from MEDLINE, Academic Search Elite, Psych Articles, Health Source, and SPORT Discus. This produced a total of 801 citations. Study Inclusion and Exclusion Criteria Published English-language literature that quantitatively measured physical activity levels of adults with mental retardation was included in this review. Fourteen articles met this criterion. Data Extraction Characteristics of participants, study design, outcome measures, methods of analyses, and findings in terms of percentages, step counts, and accelerometer output were extracted. Data Synthesis Data were synthesized to identify the percentage of adults with mental retardation who met publis...

The Love of a Good Man? Romantic Relationships as a Source of Support or Hindrance for Female Ex-Offenders

Abstract: This article explores the impact of romantic relationships on the reentry experiences of female ex-offenders. Although attachment to a prosocial spouse is an important social bond in the desistance of male offenders, male and female offenders have different offending and life experiences and are likely to draw romantic partners from very different groups. This article addresses this issue through an analysis of qualitative interviews with 49 female ex-offenders and their romantic partners. These women most often have relationships with recovering drug users and/or ex-offenders, not purely prosocial men or women. These relationships are dynamic and may be both destructive and conventionalizing at different points in time. Many women also consciously avoid romantic relationships, at least temporarily. These patterns of romantic relationships for female ex-offenders add to our understanding of the role of social bonds in desistance. This article emphasizes the need to look at relationships as processes rathe...

Organizational Commitment of Teachers in Urban Schools Examining the Effects of Team Structures

Abstract: This study examines the effects of four team-based structures on the organizational commitment of elementary teachers in an urban school district. The study model focuses on organizational commitment and includes three intervening, endogenous variables: teacher empowerment, school communication, and work autonomy. Team teaching had both direct and indirect effects on commitment to the school. Curriculum teamwork, governance teamwork, and community-relations teamwork each contributed indirectly to higher levels of teacher commitment. Research results suggest the need for organizational designs and procedures that reinforce teacher identification with and involvement in the school organization.

Cross-layer-based modeling for quality of service guarantees in mobile wireless networks

Abstract: In this article we propose a cross-layer approach to investigate the impact of the physical-layer infrastructure on the data-link-layer QoS performance in mobile wireless networks. At the physical layer, we take the MIMO diversity schemes as well its AMC into account. At the data-link layer, our focus is on how this physical-layer infrastructure influences the real-time multimedia QoS provisioning performance such as delay-bound violation and buffer-overflow probabilities. To achieve this goal, we first model the physical-layer service process as a finite state Markov chain. Based on this FSMC model, we then characterize the QoS performance at the data-link layer using the effective capacity approach, which turns out to be critically important for the statistical QoS guarantees in mobile wireless networks. The numerical and simulation results obtained demonstrate that the proposed cross-layer model can efficiently characterize the interaction between the physical layer infrastructure and upper layer protocols' QoS provisioning performance.

Biodiversity in Agricultural Landscapes: Saving Natural Capital without Losing Interest

Abstract: Old-growth forest of the Hoh River Valley, Olympic National Park, Washington (U.S.A.). For decades the U.S. Pacific Norwest has been a center of controversy over logging and endangered species. This special section explores progress made by the Northwest Forest Plan?a global example of land-use planning?a decade after it was established to end the stalemate over logging and endangered species. Authors include some of the key architects involved in its creation and implementation. Photo by Kevin Schafer.

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

Abstract: The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high ( h = 0.73) with pronounced population structure (Φ ST = 0.877) and highly significant geographic associations ( P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Health-promoting physical activity of adults with mental retardation

Abstract: This literature review describes the physical activity behavior of adults with mental retardation consistent with the U.S. Surgeon General's recommendation of 30 minutes of moderate intensity physical activity on 5 or more days per week. The proportion of participants achieving this criterion ranges from 17.5 to 33%. These data are likely to be generous estimates of activity as individuals included in physical activity studies to date have been relatively young and healthy volunteers with mild to moderate limitations. Major sources of physical activity were walking and cycling for transport, chores and work, dancing, and Special Olympics. There is a pressing need to conduct studies using appropriately powered representative samples and to validate measures that assess physical activity less directly; including methodologies in which proxy respondents are used. Accurate information about existing patterns of behavior will enhance the development of effective strategies to promote physical activity among persons with mental retardation.

A national survey of consumer attitudes towards companies that hire people with disabilities

Abstract: Employers' negative attitudes and fears have long been a barrier to the employment of individuals with disabilities Accordingly, attitude literature on the employment of people with disabilities has focused almost exclusively on employers However, due to their influence over business practices, the successful employment of people with disabilities is also contingent on the views of the consumer This study extends previous studies that focused on the attitudes of employers, and went directly to the consumer Consumer attitudes toward companies that hire individuals with disabilities were assessed through a national public survey (N = 803) Most of the participants (75%) had direct experience with people with disabilities in a work environment Moreover, these experiences were positive All participants responded positively towards companies that are socially responsible, including 92% of consumers who felt more favorable toward those that hire individuals with disabilities The participants also had strong positive beliefs about the value and benefits of hiring people with disabilities, with 87% specifically agreeing that they would prefer to give their business to companies that hire individuals with disabilities Implications of consumer support on company hiring practices are discussed

A Housing Affordability Standard for the UK

Abstract: Since 1990 there has been extensive exploration of the meaning of housing affordability by members of the academic, professional and advocacy communities in Britain. These debates have revealed weaknesses in the traditional ratio standard of affordability and led to arguments in support of an alternative, residual income concept of affordability. However, so far there has been only limited success in operationalising and applying the residual income approach in the UK. In the US, by contrast, arguments in support of a residual income approach to housing affordability emerged in the late 1960s and early 1970s, culminating in the formulation of operational standards utilising normative family budgets. This paper draws upon the US experience to formulate a residual income housing affordability standard for the UK that utilises the non-shelter components of the Family Budget Unit (FBU) 'Low Cost but Acceptable' budgets as the normative standard for minimum adequate residual income. The paper concludes by suggesting how use of such a 'shelter' poverty standard to assess housing affordability problems and needs in the UK might yield results that differ from those based on the ratio standard.

Organofluorine inhibitors of amyloid fibrillogenesis.

Abstract: The design and application of an effective, new class of organofluorine inhibitors of amyloid fibrillogenesis are described. Based on experimental evidence a core structure containing indol-3-yl, trifluoromethyl, hydroxyl, and carboxylic acid ester functions has been designed. Several substituted derivatives of this core structure have been synthesized, using various indole derivatives. While all inhibitor candidates have shown considerable effect (20−70% inhibition) in structure−activity relationship studies (inhibitor/Aβ = 10 ratio), several compounds have demonstrated excellent activity (93−96% inhibition). Using concentration dependence studies, the activity of the most active molecules have been quantified. These inhibitors practically completely block the fibril formation of Aβ1-40, as shown by maximum inhibition values (ICmax = 98−100%). The median inhibitor concentration values (IC50 = 0.23−0.53 molinhibitor/molAβ) demonstrate favorable stoichiometry for the inhibition. The respective elimination ...

What determines the slope of a plankton biomass spectrum

Abstract: A number of studies have been performed to understand the characteristics of biomass (size) spectra in aquatic plankton communities around the world. Although the area below a biomass spectrum curve represents the abundance or biomass of a plankton community, it has been hypothesized that the slope and shape of a biomass spectrum are determined by rates of growth, respiration, mortality and trophic dynamics. Observations of biomass spectra indicate that the slope of a biomass spectrum is around -1 on the logarithmic coordinates. Empirical hypotheses of growth-survival and the theoretical framework on biomass conservation based on the rates of individual body growth and abundance change have been developed for interpreting the slope and domes of a biomass spectrum. Here, a mathematical method is developed for estimating specific rates of body growth and abundance change from observations of biomass spectra, and a mathematical model is constructed for the relationship between a biomass spectrum slope, community assimilation efficiency and trophic levels.