Showing papers by "Indiana University published in 2013"

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Abstract: De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.

Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical Practice Guideline Update

Abstract: Purpose.—To update the American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guideline recommendations for human epidermal growth factor receptor 2 (HER2) testing in b...

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs

Abstract: Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.

Bridging the qualitative-quantitative divide: guidelines for conducting mixed methods research in information systems

Abstract: Mixed methods research is an approach that combines quantitative and qualitative research methods in the same research inquiry. Such work can help develop rich insights into various phenomena of interest that cannot be fully understood using only a quantitative or a qualitative method. Notwithstanding the benefits and repeated calls for such work, there is a dearth of mixed methods research in information systems. Building on the literature on recent methodological advances in mixed methods research, we develop a set of guidelines for conducting mixed methods research in IS. We particularly elaborate on three important aspects of conducting mixed methods research: (1) appropriateness of a mixed methods approach; (2) development of meta-inferences (i.e., substantive theory) from mixed methods research; and (3) assessment of the quality of meta-inferences (i.e., validation of mixed methods research). The applicability of these guidelines is illustrated using two published IS papers that used mixed methods.

The Drama of the Commons

Abstract: 1 Front Matter 2 1 The Drama of the Commons 3 Part I: Resource Users, Resource Systems, and Behavior in the Drama of the Commons 4 2 Common Resources and Institutional Sustainability 5 3 Unequal Irrigators: Heterogeneity and Commons Management in Large-Scale 6 4 Factors Influencing Cooperation in Commons Dilemmas: A Review of Experimental Psychological Research 7 5 Appropriating the Commons: A Theoretical Explanation 8 Part II: Privatization and Its Limitations 9 6 The Tradable Permits Approach to Protecting the Commons: What Have We Learned? 10 7 Common Property, Regulatory Property, and Environmental Protection: Comparing Community-Based Management to Tradable Environmental Allowances 11 Part III: Cross-Scale Linkages and Dynamic Interactions 12 8 Institutional Interplay: The Environmental Consequences of Cross-Scale Interactions 13 9 Cross-Scale Institutional Linkages: Perspectives from the Bottom Up 14 Part IV: Emerging Issues 15 10 Scientific Uncertainty, Complex Systems, and the Design of Common-Pool Institutions 16 11 Emergence of Institutions for the Commons: Contexts, Situations, and Events 17 12 An Evolutionary Theory of Commons Management 18 13 Knowledge and Questions After 15 Years of Research 19 About the Contributors 20 Index

Principled missing data methods for researchers.

Abstract: The impact of missing data on quantitative research can be serious, leading to biased estimates of parameters, loss of information, decreased statistical power, increased standard errors, and weakened generalizability of findings. In this paper, we discussed and demonstrated three principled missing data methods: multiple imputation, full information maximum likelihood, and expectation-maximization algorithm, applied to a real-world data set. Results were contrasted with those obtained from the complete data set and from the listwise deletion method. The relative merits of each method are noted, along with common features they share. The paper concludes with an emphasis on the importance of statistical assumptions, and recommendations for researchers. Quality of research will be enhanced if (a) researchers explicitly acknowledge missing data problems and the conditions under which they occurred, (b) principled methods are employed to handle missing data, and (c) the appropriate treatment of missing data is incorporated into review standards of manuscripts submitted for publication.

What is network science

Abstract: This is the beginning of Network Science. The journal has been created because network science is exploding. As is typical for a field in formation, the discussions about its scope, contents, and foundations are intense. On these first few pages of the first issue of our new journal, we would like to share our own vision of the emerging science of networks.

Bayesian Estimation Supersedes the t Test

Abstract: Bayesian estimation for 2 groups provides complete distributions of credible values for the effect size, group means and their difference, standard deviations and their difference, and the normality of the data. The method handles outliers. The decision rule can accept the null value (unlike traditional t tests) when certainty in the estimate is high (unlike Bayesian model comparison using Bayes factors). The method also yields precise estimates of statistical power for various research goals. The software and programs are free and run on Macintosh, Windows, and Linux platforms.

Pathways of Antigen Processing

Abstract: T cell recognition of antigen-presenting cells depends on their expression of a spectrum of peptides bound to major histocompatibility complex class I (MHC-I) and class II (MHC-II) molecules. Conversion of antigens from pathogens or transformed cells into MHC-I- and MHC-II-bound peptides is critical for mounting protective T cell responses, and similar processing of self proteins is necessary to establish and maintain tolerance. Cells use a variety of mechanisms to acquire protein antigens, from translation in the cytosol to variations on the theme of endocytosis, and to degrade them once acquired. In this review, we highlight the aspects of MHC-I and MHC-II biosynthesis and assembly that have evolved to intersect these pathways and sample the peptides that are produced.

Plant–soil feedbacks: the past, the present and future challenges

Abstract: Summary Plant–soil feedbacks is becoming an important concept for explaining vegetation dynamics, the invasiveness of introduced exotic species in new habitats and how terrestrial ecosystems respond to global land use and climate change. Using a new conceptual model, we show how critical alterations in plant–soil feedback interactions can change the assemblage of plant communities. We highlight recent advances, define terms and identify future challenges in this area of research and discuss how variations in strengths and directions of plant–soil feedbacks can explain succession, invasion, response to climate warming and diversity-productivity relationships. While there has been a rapid increase in understanding the biological, chemical and physical mechanisms and their interdependencies underlying plant–soil feedback interactions, further progress is to be expected from applying new experimental techniques and technologies, linking empirical studies to modelling and field-based studies that can include plant–soil feedback interactions on longer time scales that also include long-term processes such as litter decomposition and mineralization. Significant progress has also been made in analysing consequences of plant–soil feedbacks for biodiversity-functioning relationships, plant fitness and selection. To further integrate plant–soil feedbacks into ecological theory, it will be important to determine where and how observed patterns may be generalized, and how they may influence evolution. Synthesis. Gaining a greater understanding of plant–soil feedbacks and underlying mechanisms is improving our ability to predict consequences of these interactions for plant community composition and productivity under a variety of conditions. Future research will enable better prediction and mitigation of the consequences of human-induced global changes, improve efforts of restoration and conservation and promote sustainable provision of ecosystem services in a rapidly changing world.

Sentinel Lymph Node Surgery After Neoadjuvant Chemotherapy in Patients With Node-Positive Breast Cancer: The ACOSOG Z1071 (Alliance) Clinical Trial

Abstract: IMPORTANCE Sentinel lymph node (SLN) surgery provides reliable nodal staging information with less morbidity than axillary lymph node dissection (ALND) for patients with clinically node-negative (cN0) breast cancer. The application of SLN surgery for staging the axilla following chemotherapy for women who initially had node-positive cN1 breast cancer is unclear because of high false-negative results reported in previous studies.

Cognition assessment using the NIH Toolbox

Abstract: Motor function involves complex physiologic processes and requires the integration of multiple systems, including neuromuscular, musculoskeletal, and cardiopulmonary, and neural motor and sensory-perceptual systems. Motor-functional status is indicative of current physical health status, burden of disease, and long-term health outcomes, and is integrally related to daily functioning and quality of life. Given its importance to overall neurologic health and function, motor function was identified as a key domain for inclusion in the NIH Toolbox for Assessment of Neurological and Behavioral Function (NIH Toolbox). We engaged in a 3-stage developmental process to: 1) identify key subdomains and candidate measures for inclusion in the NIH Toolbox, 2) pretest candidate measures for feasibility across the age span of people aged 3 to 85 years, and 3) validate candidate measures against criterion measures in a sample of healthy individuals aged 3 to 85 years (n = 340). Based on extensive literature review and input from content experts, the 5 subdomains of dexterity, strength, balance, locomotion, and endurance were recommended for inclusion in the NIH Toolbox motor battery. Based on our validation testing, valid and reliable measures that are simultaneously low-cost and portable have been recommended to assess each subdomain, including the 9-hole peg board for dexterity, grip dynamometry for upper-extremity strength, standing balance test, 4-m walk test for gait speed, and a 2-minute walk test for endurance.

A bright monomeric green fluorescent protein derived from Branchiostoma lanceolatum.

Abstract: We report a monomeric yellow-green fluorescent protein, mNeonGreen, derived from a tetrameric fluorescent protein from the cephalochordate Branchiostoma lanceolatum. mNeonGreen is the brightest monomeric green or yellow fluorescent protein yet described to our knowledge, performs exceptionally well as a fusion tag for traditional imaging as well as stochastic single-molecule superresolution imaging and is an excellent fluorescence resonance energy transfer (FRET) acceptor for the newest cyan fluorescent proteins.

Bibliometrics: Global gender disparities in science

Abstract: Cassidy R. Sugimoto and colleagues present a bibliometric analysis confirming that gender imbalances persist in research output worldwide.

Increase in forest water-use efficiency as atmospheric carbon dioxide concentrations rise

Abstract: Terrestrial plants remove CO2 from the atmosphere through photosynthesis, a process that is accompanied by the loss of water vapour from leaves. The ratio of water loss to carbon gain, or water-use efficiency, is a key characteristic of ecosystem function that is central to the global cycles of water, energy and carbon. Here we analyse direct, long-term measurements of whole-ecosystem carbon and water exchange. We find a substantial increase in water-use efficiency in temperate and boreal forests of the Northern Hemisphere over the past two decades. We systematically assess various competing hypotheses to explain this trend, and find that the observed increase is most consistent with a strong CO2 fertilization effect. The results suggest a partial closure of stomata-small pores on the leaf surface that regulate gas exchange-to maintain a near-constant concentration of CO2 inside the leaf even under continually increasing atmospheric CO2 levels. The observed increase in forest water-use efficiency is larger than that predicted by existing theory and 13 terrestrial biosphere models. The increase is associated with trends of increasing ecosystem-level photosynthesis and net carbon uptake, and decreasing evapotranspiration. Our findings suggest a shift in the carbon- and water-based economics of terrestrial vegetation, which may require a reassessment of the role of stomatal control in regulating interactions between forests and climate change, and a re-evaluation of coupled vegetation-climate models.

The International Society of Urological Pathology (ISUP) Vancouver classification of renal neoplasia

Abstract: The classification working group of the International Society of Urological Pathology consensus conference on renal neoplasia was in charge of making recommendations regarding additions and changes to the current World Health Organization Classification of Renal Tumors (2004). Members of the group performed an exhaustive literature review, assessed the results of the preconference survey and participated in the consensus conference discussion and polling activities. On the basis of the above inputs, there was consensus that 5 entities should be recognized as new distinct epithelial tumors within the classification system: tubulocystic renal cell carcinoma (RCC), acquired cystic disease-associated RCC, clear cell (tubulo) papillary RCC, the MiT family translocation RCCs (in particular t(6;11) RCC), and hereditary leiomyomatosis RCC syndrome-associated RCC. In addition, there are 3 rare carcinomas that were considered as emerging or provisional new entities: thyroid-like follicular RCC; succinate dehydrogenase B deficiency-associated RCC; and ALK translocation RCC. Further reports of these entities are required to better understand the nature and behavior of these highly unusual tumors. There were a number of new concepts and suggested modifications to the existing World Health Organization 2004 categories. Within the clear cell RCC group, it was agreed upon that multicystic clear cell RCC is best considered as a neoplasm of low malignant potential. There was agreement that subtyping of papillary RCC is of value and that the oncocytic variant of papillary RCC should not be considered as a distinct entity. The hybrid oncocytic chromophobe tumor, which is an indolent tumor that occurs in 3 settings, namely Birt-Hogg-Dube Syndrome, renal oncocytosis, and as a sporadic neoplasm, was placed, for the time being, within the chromophobe RCC category. Recent advances related to collecting duct carcinoma, renal medullary carcinoma, and mucinous spindle cell and tubular RCC were elucidated. Outside of the epithelial category, advances in our understanding of angiomyolipoma, including the epithelioid and epithelial cystic variants, were considered. In addition, the apparent relationship between cystic nephroma and mixed epithelial and stromal tumor was discussed, with the consensus that these tumors form a spectrum of neoplasia. Finally, it was thought that the synovial sarcoma should be removed from the mixed epithelial and mesenchymal category and placed within the sarcoma group. The new classification is to be referred to as the International Society of Urological Pathology Vancouver Classification of Renal Neoplasia.

Prevention, diagnosis, and treatment of the overtraining syndrome: joint consensus statement of the European College of Sport Science and the American College of Sports Medicine.

Abstract: Successful training not only must involve overload but also must avoid the combination of excessive overload plus inadequate recovery. Athletes can experience short-term performance decrement without severe psychological or lasting other negative symptoms. This functional overreaching will eventually lead to an improvement in performance after recovery. When athletes do not sufficiently respect the balance between training and recovery, nonfunctional overreaching (NFOR) can occur. The distinction between NFOR and overtraining syndrome (OTS) is very difficult and will depend on the clinical outcome and exclusion diagnosis. The athlete will often show the same clinical, hormonal, and other signs and symptoms. A keyword in the recognition of OTS might be "prolonged maladaptation" not only of the athlete but also of several biological, neurochemical, and hormonal regulation mechanisms. It is generally thought that symptoms of OTS, such as fatigue, performance decline, and mood disturbances, are more severe than those of NFOR. However, there is no scientific evidence to either confirm or refute this suggestion. One approach to understanding the etiology of OTS involves the exclusion of organic diseases or infections and factors such as dietary caloric restriction (negative energy balance) and insufficient carbohydrate and/or protein intake, iron deficiency, magnesium deficiency, allergies, and others together with identification of initiating events or triggers. In this article, we provide the recent status of possible markers for the detection of OTS. Currently, several markers (hormones, performance tests, psychological tests, and biochemical and immune markers) are used, but none of them meet all the criteria to make their use generally accepted.

A large-scale evaluation of computational protein function prediction

Abstract: Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report the results from the first large-scale community-based critical assessment of protein function annotation (CAFA) experiment. Fifty-four methods representing the state of the art for protein function prediction were evaluated on a target set of 866 proteins from 11 organisms. Two findings stand out: (i) today's best protein function prediction algorithms substantially outperform widely used first-generation methods, with large gains on all types of targets; and (ii) although the top methods perform well enough to guide experiments, there is considerable need for improvement of currently available tools.

Do Altmetrics Work? Twitter and Ten Other Social Web Services

Abstract: Altmetric measurements derived from the social web are increasingly advocated and used as early indicators of article impact and usefulness. Nevertheless, there is a lack of systematic scientific evidence that altmetrics are valid proxies of either impact or utility although a few case studies have reported medium correlations between specific altmetrics and citation rates for individual journals or fields. To fill this gap, this study compares 11 altmetrics with Web of Science citations for 76 to 208,739 PubMed articles with at least one altmetric mention in each case and up to 1,891 journals per metric. It also introduces a simple sign test to overcome biases caused by different citation and usage windows. Statistically significant associations were found between higher metric scores and higher citations for articles with positive altmetric scores in all cases with sufficient evidence (Twitter, Facebook wall posts, research highlights, blogs, mainstream media and forums) except perhaps for Google+ posts. Evidence was insufficient for LinkedIn, Pinterest, question and answer sites, and Reddit, and no conclusions should be drawn about articles with zero altmetric scores or the strength of any correlation between altmetrics and citations. Nevertheless, comparisons between citations and metric values for articles published at different times, even within the same year, can remove or reverse this association and so publishers and scientometricians should consider the effect of time when using altmetrics to rank articles. Finally, the coverage of all the altmetrics except for Twitter seems to be low and so it is not clear if they are prevalent enough to be useful in practice.

Best-Practice Recommendations for Defining, Identifying, and Handling Outliers

Abstract: The presence of outliers, which are data points that deviate markedly from others, is one of the most enduring and pervasive methodological challenges in organizational science research. We provide evidence that different ways of defining, identifying, and handling outliers alter substantive research conclusions. Then, we report results of a literature review of 46 methodological sources (i.e., journal articles, book chapters, and books) addressing the topic of outliers, as well as 232 organizational science journal articles mentioning issues about outliers. Our literature review uncovered (a) 14 unique and mutually exclusive outlier definitions, 39 outlier identification techniques, and 20 different ways of handling outliers; (b) inconsistencies in how outliers are defined, identified, and handled in various methodological sources; and (c) confusion and lack of transparency in how outliers are addressed by substantive researchers. We offer guidelines, including decision-making trees, that researchers can...

Bias in peer review

Abstract: Research on bias in peer review examines scholarly communication and funding processes to assess the epistemic and social legitimacy of the mechanisms by which knowledge communities vet and self-regulate their work. Despite vocal concerns, a closer look at the empirical and methodological limitations of research on bias raises questions about the existence and extent of many hypothesized forms of bias. In addition, the notion of bias is predicated on an implicit ideal that, once articulated, raises questions about the normative implications of research on bias in peer review. This review provides a brief description of the function, history, and scope of peer review; articulates and critiques the conception of bias unifying research on bias in peer review; characterizes and examines the empirical, methodological, and normative claims of bias in peer review research; and assesses possible alternatives to the status quo. We close by identifying ways to expand conceptions and studies of bias to contend with the complexity of social interactions among actors involved directly and indirectly in peer review. © 2013 Wiley Periodicals, Inc.

Observation of a charged charmoniumlike structure in e+ e- → (D* D*)± π∓ at √s = 4.26 GeV.

Abstract: We study the process e(+)e(-) -> pi(+)pi(-) J/psi at a center-of-mass energy of 4.260 GeV using a 525 pb(-1) data sample collected with the BESIII detector operating at the Beijing Electron Positron Collider. The Born cross section is measured to be (62.9 +/- 1.9 +/- 3.7) pb, consistent with the production of the Y(4260). We observe a structure at around 3.9 GeV/c(2) in the pi(+/-) J/psi mass spectrum, which we refer to as the Z(c)(3900). If interpreted as a new particle, it is unusual in that it carries an electric charge and couples to charmonium. A fit to the pi(+/-) J/psi invariant mass spectrum, neglecting interference, results in a mass of (3899.0 +/- 3.6 +/- 4.9) MeV/c(2) and a width of (46 +/- 10 +/- 20) MeV. Its production ratio is measured to be R = (sigma(e(+)e(-) -> pi(+/-) Z(c)(3900)(-/+) -> pi(+)pi(-) J/psi)/sigma(e(+)e(-) -> pi(+)pi(-) J/psi)) = (21.5 +/- 3.3 +/- 7.5)%. In all measurements the first errors are statistical and the second are systematic.