Showing papers by "Indiana University published in 2007"

Paclitaxel plus Bevacizumab versus Paclitaxel Alone for Metastatic Breast Cancer

Abstract: vs. 0.0%, P<0.001), proteinuria (3.6% vs. 0.0%, P<0.001), headache (2.2% vs. 0.0%, P = 0.008), and cerebrovascular ischemia (1.9% vs. 0.0%, P = 0.02) were more frequent in patients receiving paclitaxel plus bevacizumab. Infection was more common in patients receiving paclitaxel plus bevacizumab (9.3% vs. 2.9%, P<0.001), but febrile neutropenia was uncommon (<1% overall). Conclusions Initial therapy of metastatic breast cancer with paclitaxel plus bevacizumab prolongs progression-free survival, but not overall survival, as compared with paclitaxel alone. (ClinicalTrials.gov number, NCT00028990.)

Complexity of coupled human and natural systems

Abstract: Integrated studies of coupled human and natural systems reveal new and complex patterns and processes not evident when studied by social or natural scientists separately. Synthesis of six case studies from around the world shows that couplings between human and natural systems vary across space, time, and organizational units. They also exhibit nonlinear dynamics with thresholds, reciprocal feedback loops, time lags, resilience, heterogeneity, and surprises. Furthermore, past couplings have legacy effects on present conditions and future possibilities.

Resolution limit in community detection

Abstract: Detecting community structure is fundamental for uncovering the links between structure and function in complex networks and for practical applications in many disciplines such as biology and sociology. A popular method now widely used relies on the optimization of a quantity called modularity, which is a quality index for a partition of a network into communities. We find that modularity optimization may fail to identify modules smaller than a scale which depends on the total size of the network and on the degree of interconnectedness of the modules, even in cases where modules are unambiguously defined. This finding is confirmed through several examples, both in artificial and in real social, biological, and technological networks, where we show that modularity optimization indeed does not resolve a large number of modules. A check of the modules obtained through modularity optimization is thus necessary, and we provide here key elements for the assessment of the reliability of this community detection method.

A survey of image classification methods and techniques for improving classification performance

Abstract: Image classification is a complex process that may be affected by many factors. This paper examines current practices, problems, and prospects of image classification. The emphasis is placed on the summarization of major advanced classification approaches and the techniques used for improving classification accuracy. In addition, some important issues affecting classification performance are discussed. This literature review suggests that designing a suitable image-processing procedure is a prerequisite for a successful classification of remotely sensed data into a thematic map. Effective use of multiple features of remotely sensed data and the selection of a suitable classification method are especially significant for improving classification accuracy. Non-parametric classifiers such as neural network, decision tree classifier, and knowledge-based classification have increasingly become important approaches for multisource data classification. Integration of remote sensing, geographical information systems (GIS), and expert system emerges as a new research frontier. More research, however, is needed to identify and reduce uncertainties in the image-processing chain to improve classification accuracy.

A diagnostic approach for going beyond panaceas

Abstract: The articles in this special feature challenge the presumption that scholars can make simple, predictive models of social–ecological systems (SESs) and deduce universal solutions, panaceas, to problems of overuse or destruction of resources. Moving beyond panaceas to develop cumulative capacities to diagnose the problems and potentialities of linked SESs requires serious study of complex, multivariable, nonlinear, cross-scale, and changing systems. Many variables have been identified by researchers as affecting the patterns of interactions and outcomes observed in empirical studies of SESs. A step toward developing a diagnostic method is taken by organizing these variables in a nested, multitier framework. The framework enables scholars to organize analyses of how attributes of (i) a resource system (e.g., fishery, lake, grazing area), (ii) the resource units generated by that system (e.g., fish, water, fodder), (iii) the users of that system, and (iv) the governance system jointly affect and are indirectly affected by interactions and resulting outcomes achieved at a particular time and place. The framework also enables us to organize how these attributes may affect and be affected by larger socioeconomic, political, and ecological settings in which they are embedded, as well as smaller ones. The framework is intended to be a step toward building a strong interdisciplinary science of complex, multilevel systems that will enable future diagnosticians to match governance arrangements to specific problems embedded in a social–ecological context.

Evolution of genes and genomes on the Drosophila phylogeny.

Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Integrating Technology into K-12 Teaching and Learning: Current Knowledge Gaps and Recommendations for Future Research

Abstract: Although research studies in education show that use of technol- ogy can help student learning, its use is generally affected by certain barriers In this paper, we first identify the general barriers typically faced by K-12 schools, both in the United States as well as other countries, when integrating technology into the curriculum for instructional purposes, namely: (a) resources, (b) institution, (c) subject culture, (d) attitudes and beliefs, (e) knowledge and skills, and (f) assessment We then describe the strategies to overcome such barriers: (a) having a shared vision and technology integration plan, (b) overcoming the scarcity of resources, (c) changing attitudes and beliefs, (d) conducting professional development, and (e) reconsidering assessments Finally, we identify several current knowledge gaps pertaining to the barriers and strategies of technology integration, and offer pertinent recommendations for future research

Network structure of cerebral cortex shapes functional connectivity on multiple time scales.

Abstract: Neuronal dynamics unfolding within the cerebral cortex exhibit complex spatial and temporal patterns even in the absence of external input. Here we use a computational approach in an attempt to relate these features of spontaneous cortical dynamics to the underlying anatomical connectivity. Simulating nonlinear neuronal dynamics on a network that captures the large-scale interregional connections of macaque neocortex, and applying information theoretic measures to identify functional networks, we find structure-function relations at multiple temporal scales. Functional networks recovered from long windows of neural activity (minutes) largely overlap with the underlying structural network. As a result, hubs in these long-run functional networks correspond to structural hubs. In contrast, significant fluctuations in functional topology are observed across the sequence of networks recovered from consecutive shorter (seconds) time windows. The functional centrality of individual nodes varies across time as interregional couplings shift. Furthermore, the transient couplings between brain regions are coordinated in a manner that reveals the existence of two anticorrelated clusters. These clusters are linked by prefrontal and parietal regions that are hub nodes in the underlying structural network. At an even faster time scale (hundreds of milliseconds) we detect individual episodes of interregional phase-locking and find that slow variations in the statistics of these transient episodes, contingent on the underlying anatomical structure, produce the transfer entropy functional connectivity and simulated blood oxygenation level-dependent correlation patterns observed on slower time scales.

Mechanism of auxin perception by the TIR1 ubiquitin ligase

Abstract: Auxin is a pivotal plant hormone that controls many aspects of plant growth and development. Perceived by a small family of F-box proteins including transport inhibitor response 1 (TIR1), auxin regulates gene expression by promoting SCF ubiquitin-ligase-catalysed degradation of the Aux/IAA transcription repressors, but how the TIR1 F-box protein senses and becomes activated by auxin remains unclear. Here we present the crystal structures of the Arabidopsis TIR1-ASK1 complex, free and in complexes with three different auxin compounds and an Aux/IAA substrate peptide. These structures show that the leucine-rich repeat domain of TIR1 contains an unexpected inositol hexakisphosphate co-factor and recognizes auxin and the Aux/IAA polypeptide substrate through a single surface pocket. Anchored to the base of the TIR1 pocket, auxin binds to a partially promiscuous site, which can also accommodate various auxin analogues. Docked on top of auxin, the Aux/IAA substrate peptide occupies the rest of the TIR1 pocket and completely encloses the hormone-binding site. By filling in a hydrophobic cavity at the protein interface, auxin enhances the TIR1-substrate interactions by acting as a 'molecular glue'. Our results establish the first structural model of a plant hormone receptor.

Evolutionary and biomedical insights from the rhesus macaque genome

Abstract: The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species.

Identification and classification of hubs in brain networks.

Abstract: Brain regions in the mammalian cerebral cortex are linked by a complex network of fiber bundles. These inter-regional networks have previously been analyzed in terms of their node degree, structural motif, path length and clustering coefficient distributions. In this paper we focus on the identification and classification of hub regions, which are thought to play pivotal roles in the coordination of information flow. We identify hubs and characterize their network contributions by examining motif fingerprints and centrality indices for all regions within the cerebral cortices of both the cat and the macaque. Motif fingerprints capture the statistics of local connection patterns, while measures of centrality identify regions that lie on many of the shortest paths between parts of the network. Within both cat and macaque networks, we find that a combination of degree, motif participation, betweenness centrality and closeness centrality allows for reliable identification of hub regions, many of which have previously been functionally classified as polysensory or multimodal. We then classify hubs as either provincial (intra-cluster) hubs or connector (inter-cluster) hubs, and proceed to show that lesioning hubs of each type from the network produces opposite effects on the small-world index. Our study presents an approach to the identification and classification of putative hub regions in brain networks on the basis of multiple network attributes and charts potential links between the structural embedding of such regions and their functional roles.

Cholangiocarcinoma: Thirty-one-Year Experience With 564 Patients at a Single Institution

Abstract: Objective:To assess long-term survival and prognostic factors in a large series of patients with bile duct cancer.Summary Background Data:The incidence of bile duct cancer is low but increasing. Determinants of survival vary in the literature, due to a lack of sufficient numbers of patients in most

Social phishing

Abstract: Sometimes a "friendly" email message tempts recipients to reveal more online than they otherwise would, playing right into the sender's hand.

Going beyond panaceas.

Abstract: In the context of governance of human-environment interactions, a panacea refers to a blueprint for a single type of governance system (e.g., government ownership, privatization, community property) that is applied to all environmental problems. The aim of this special feature is to provide theoretical analysis and empirical evidence to caution against the tendency, when confronted with pervasive uncertainty, to believe that scholars can generate simple models of linked social-ecological systems and deduce general solutions to the overuse of resources. Practitioners and scholars who fall into panacea traps falsely assume that all problems of resource governance can be represented by a small set of simple models, because they falsely perceive that the preferences and perceptions of most resource users are the same. Readers of this special feature will become acquainted with many cases in which panaceas fail. The articles provide an excellent overview of why they fail. Furthermore, the articles in this special feature address how scholars and public officials can increase the prospects for future sustainable resource use by facilitating a diagnostic approach in selecting appropriate starting points for governance and monitoring, as well as by learning from the outcomes of new policies and adapting in light of effective feedback.

Candidate mechanisms for chemotherapy-induced cognitive changes.

Abstract: The mechanism(s) for chemotherapy-induced cognitive changes are largely unknown; however, several candidate mechanisms have been identified. We suggest that shared genetic risk factors for the development of cancer and cognitive problems, including low-efficiency efflux pumps, deficits in DNA-repair mechanisms and/or a deregulated immune response, coupled with the effect of chemotherapy on these systems, might contribute to cognitive decline in patients after chemotherapy. Furthermore, the genetically modulated reduction of capacity for neural repair and neurotransmitter activity, as well as reduced antioxidant capacity associated with treatment-induced reduction in oestrogen and testosterone levels, might interact with these mechanisms and/or have independent effects on cognitive function.

Copula Modeling: An Introduction for Practitioners

Abstract: This article explores the copula approach for econometric modeling of joint parametric distributions. Although theoretical foundations of copulas are complex, this paper demonstrates that practical implementation and estimation are relatively straightforward. An attractive feature of parametrically specified copulas is that estimation and inference are based on standard maximum likelihood procedures, and thus copulas can be estimated using desktop econometric software. This represents a substantial advantage of copulas over recently proposed simulationbased approaches to joint modeling.

Impact of data sources on citation counts and rankings of LIS faculty: Web of science versus scopus and google scholar

Abstract: The Institute for Scientific Information's (ISI, now Thomson Scientific, Philadelphia, PA) citation databases have been used for decades as a starting point and often as the only tools for locating citations andsor conducting citation analyses. The ISI databases (or Web of Science [WoS]), however, may no longer be sufficient because new databases and tools that allow citation searching are now available. Using citations to the work of 25 library and information science (LIS) faculty members as a case study, the authors examine the effects of using Scopus and Google Scholar (GS) on the citation counts and rankings of scholars as measured by WoS. Overall, more than 10,000 citing and purportedly citing documents were examined. Results show that Scopus significantly alters the relative ranking of those scholars that appear in the middle of the rankings and that GS stands out in its coverage of conference proceedings as well as international, non-English language journals. The use of Scopus and GS, in addition to WoS, helps reveal a more accurate and comprehensive picture of the scholarly impact of authors. The WoS data took about 100 hours of collecting and processing time, Scopus consumed 200 hours, and GS a grueling 3,000 hours. © 2007 Wiley Periodicals, Inc.

DisProt: the Database of Disordered Proteins

Abstract: The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs). Intrinsically disordered proteins do not form a fixed three-dimensional structure under physiological conditions, either in their entireties or in segments or regions. We define IDP as a protein that contains at least one experimentally determined disordered region. Although lacking fixed structure, IDPs and regions carry out important biological functions, being typically involved in regulation, signaling and control. Such functions can involve high-specificity low-affinity interactions, the multiple binding of one protein to many partners and the multiple binding of many proteins to one partner. These three features are all enabled and enhanced by protein intrinsic disorder. One of the major hindrances in the study of IDPs has been the lack of organized information. DisProt was developed to enable IDP research by collecting and organizing knowledge regarding the experimental characterization and the functional associations of IDPs. In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at http://www.disprot.org.

Coupled Human and Natural Systems

Abstract: Humans have continuously interacted with natural systems, resulting in the formation and development of coupled human and natural systems (CHANS). Recent studies reveal the complexity of organizational, spatial, and temporal couplings of CHANS. These couplings have evolved from direct to more indirect interactions, from adjacent to more distant linkages, from local to global scales, and from simple to complex patterns and processes. Untangling complexities, such as reciprocal effects and emergent properties, can lead to novel scientific discoveries and is essential to developing effective policies for ecological and socioeconomic sustainability. Opportunities for truly integrating various disciplines are emerging to address fundamental questions about CHANS and meet society's unprecedented challenges.

Reaction–diffusion processes and metapopulation models in heterogeneous networks

Abstract: Dynamical reaction–diffusion processes and metapopulation models are standard modelling approaches for a wide array of phenomena in which local quantities—such as density, potentials and particles—diffuse and interact according to the physical laws. Here, we study the behaviour of the basic reaction–diffusion process (given by the reaction steps B→A and B+A→2B) defined on networks with heterogeneous topology and no limit on the nodes’ occupation number. We investigate the effect of network topology on the basic properties of the system’s phase diagram and find that the network heterogeneity sustains the reaction activity even in the limit of a vanishing density of particles, eventually suppressing the critical point in density-driven phase transitions, whereas phase transition and critical points independent of the particle density are not altered by topological fluctuations. This work lays out a theoretical and computational microscopic framework for the study of a wide range of realistic metapopulation and agent-based models that include the complex features of real-world networks.

Modeling the Worldwide Spread of Pandemic Influenza: Baseline Case and Containment Interventions

Abstract: Background The highly pathogenic H5N1 avian influenza virus, which is now widespread in Southeast Asia and which diffused recently in some areas of the Balkans region and Western Europe, has raised a public alert toward the potential occurrence of a new severe influenza pandemic. Here we study the worldwide spread of a pandemic and its possible containment at a global level taking into account all available information on air travel. Methods and Findings We studied a metapopulation stochastic epidemic model on a global scale that considers airline travel flow data among urban areas. We provided a temporal and spatial evolution of the pandemic with a sensitivity analysis of different levels of infectiousness of the virus and initial outbreak conditions (both geographical and seasonal). For each spreading scenario we provided the timeline and the geographical impact of the pandemic in 3,100 urban areas, located in 220 different countries. We compared the baseline cases with different containment strategies, including travel restrictions and the therapeutic use of antiviral (AV) drugs. We investigated the effect of the use of AV drugs in the event that therapeutic protocols can be carried out with maximal coverage for the populations in all countries. In view of the wide diversity of AV stockpiles in different regions of the world, we also studied scenarios in which only a limited number of countries are prepared (i.e., have considerable AV supplies). In particular, we compared different plans in which, on the one hand, only prepared and wealthy countries benefit from large AV resources, with, on the other hand, cooperative containment scenarios in which countries with large AV stockpiles make a small portion of their supplies available worldwide. Conclusions We show that the inclusion of air transportation is crucial in the assessment of the occurrence probability of global outbreaks. The large-scale therapeutic usage of AV drugs in all hit countries would be able to mitigate a pandemic effect with a reproductive rate as high as 1.9 during the first year; with AV supply use sufficient to treat approximately 2% to 6% of the population, in conjunction with efficient case detection and timely drug distribution. For highly contagious viruses (i.e., a reproductive rate as high as 2.3), even the unrealistic use of supplies corresponding to the treatment of approximately 20% of the population leaves 30%–50% of the population infected. In the case of limited AV supplies and pandemics with a reproductive rate as high as 1.9, we demonstrate that the more cooperative the strategy, the more effective are the containment results in all regions of the world, including those countries that made part of their resources available for global use.

A Systematic Review of School-Based Interventions to Prevent Bullying

Abstract: OBJECTIVE: To conduct a systematic review of rigorously evaluated school-based interventions to decrease bullying. DATA SOURCES: MEDLINE, PsycINFO, EMBASE, Educational Resources Information Center, Cochrane Collaboration, the Physical Education Index, and Sociology: A SAGE Full-Text Collection were searched for the terms bullying and bully. STUDY SELECTION: We found 2090 article citations and reviewed the references of relevant articles. Two reviewers critically evaluated 56 articles and found 26 studies that met the inclusion criteria. INTERVENTIONS: The types of interventions could be categorized as curriculum (10 studies), multidisciplinary or "whole-school" interventions (10 studies), social skills groups (4 studies), mentoring (1 study), and social worker support (1 study). MAIN OUTCOME MEASURES: Data were extracted regarding direct outcome measures of bullying (bullying, victimization, aggressive behavior, and school responses to violence) and outcomes indirectly related to bullying (school achievement, perceived school safety, self-esteem, and knowledge or attitudes toward bullying). RESULTS: Only 4 of the 10 curriculum studies showed decreased bullying, but 3 of those 4 also showed no improvement in some populations. Of the 10 studies evaluating the whole-school approach, 7 revealed decreased bullying, with younger children having fewer positive effects. Three of the social skills training studies showed no clear bullying reduction. The mentoring study found decreased bullying for mentored children. The study of increased school social workers found decreased bullying, truancy, theft, and drug use. CONCLUSIONS: Many school-based interventions directly reduce bullying, with better results for interventions that involve multiple disciplines. Curricular changes less often affect bullying behaviors. Outcomes indirectly related to bullying are not consistently improved by these interventions. Language: en

Biofilm Formation by Plant-Associated Bacteria

Abstract: Plants support a diverse array of bacteria, including parasites, mutualists, and commensals on and around their roots, in the vasculature, and on aerial tissues These microbes have a profound influence on plant health and productivity Bacteria physically interact with surfaces to form complex multicellular and often multispecies assemblies, including biofilms and smaller aggregates There is growing appreciation that the intensity, duration, and outcome of plant-microbe interactions are significantly influenced by the conformation of adherent microbial populations Biofilms on different tissues have unique properties, reflecting the prevailing conditions at those sites Attachment is required for biofilm formation, and bacteria interact with plant tissues through adhesins including polysaccharides and surface proteins, with initial contact often mediated by active motility Recognition between lectins and their cognate carbohydrates is a common means of specificity Biofilm development and the resulting intimate interactions with plants often require cell-cell communication between colonizing bacteria

Thoughts on Agenda Setting, Framing, and Priming

Abstract: This article discusses similarities and differences between “second-level” agenda setting and framing, and between priming and agenda setting. It presents data on the number of studies of agenda setting, framing, and priming indexed by Communication Abstract from 1971 to 2005, and it offers some conclusions about the cognitive processes involved in agenda setting, priming and framing.

Specialization and evolution of endogenous small RNA pathways.

Abstract: The specificity of RNA silencing is conferred by small RNA guides that are processed from structured RNA or dsRNA. The core components for small RNA biogenesis and effector functions have proliferated and specialized in eukaryotic lineages, resulting in diversified pathways that control expression of endogenous and exogenous genes, invasive elements and viruses, and repeated sequences. Deployment of small RNA pathways for spatiotemporal regulation of the transcriptome has shaped the evolution of eukaryotic genomes and contributed to the complexity of multicellular organisms.