36,908 Works

Multi-view Clustering of Social-based Data

Iain Cruickshank
Real-world, social phenomena produce various types of data, like explicit networks or user-emitted text. When different sets of data describe the same entities, thedata is termed multi-view or multi-modal. A distinct advantage of multi-view data is that different views may better capture different aspects of the latent structure ofthe data. However, there are difficulties in combining that data to produce something like a clustering of the data. Multi-view clustering techniques, primarily developedfor image or biological...

The large-scale organization of shape processing in the ventral and dorsal pathways

Erez Freud, Jody Culham, David Plaut & Marlene Behrmann
This collection of dataset includes fMRI raw data for the paper entitled : The large-scale organization of shape processing in the ventral and dorsal pathways by Freud, Culham, Plaut and Behrmann. 10.7554/eLife.27576
The data include two experiments, 11 subjects each.
For each participant 8 functional runs and one anatomical run are included. In addition a readme file and a dcm headers file are included in each dataset. The protocols are included in a separate dataset.
For more...

Methods and metrics for the assessment of research data management maturity, adoption of software tools, and data sharing outcomes in neuroimaging

Ana Van Gulick & John Borghi
Poster presented at the 12th International Digital Curation Conference in Edinburgh, Scotland in February 2017.
The poster presents the methods and survey design for a project to assess the maturity of research data management practices among researchers using functional MRI to study human neuroscience. The survey asks researchers to rate and describe their practices throughout the research lifecycle including during planning, collection, analysis, and publication phases and to specify which digital platforms and software they...

Stakeholder perceptions of water systems and hydro-climate information in Guanacaste, Costa Rica

Matthew Babcock, Gabrielle Wong-Parodi, Mitchell Small & Iris Grossmann
In the face of changing environmental and socio-economic drivers, access to, understanding of, and the use of probabilistic climate forecasts and other sources of scientific hydro-climate information are important for informed decision making in the water sector. This paper characterizes and compares local perceptions of the water system and hydro-climate information in the seasonally dry province of Guanacaste, Costa Rica. Semi-structured interviews were conducted with a total of 40 participants from 7 water-related groups. Interview...

Integrability

Frederick Kazman, Philip Bianco, James Ivers & John Klein
This report summarizes how to systematically analyze a software architecture with respect to a quality attribute requirement for integrability. The report introduces integrability and common forms of integrability requirements for software architecture. It provides a set of definitions, core concepts, and a framework for reasoning about integrability and satisfaction (or not) of integrability requirements by an architecture and, eventually, a system. It describes a set of mechanisms, such as patterns and tactics, that are commonly...

Overview of Risks, Threats, and Vulnerabilities Faced in Moving to the Cloud

Timothy Morrow, , Carrie Lee & Donald Faatz
As organizations develop new applications in or migrate existing applications to cloud services, they face changes in securing their information and applications. This report examines the changes to risks, threats, and vulnerabilities when applications are deployed to cloud services. Five cloud-unique threats and risks are identified along with seven threats and risks that exist on-premises and in cloud computing. For each of these threats and risks, recommendations are made for managing and mitigating the threats...

Overview of Risks, Threats, and Vulnerabilities Faced in Moving to the Cloud

Timothy Morrow, , Carrie Lee & Donald Faatz
As organizations develop new applications in or migrate existing applications to cloud services, they face changes in securing their information and applications. This report examines the changes to risks, threats, and vulnerabilities when applications are deployed to cloud services. Five cloud-unique threats and risks are identified along with seven threats and risks that exist on-premises and in cloud computing. For each of these threats and risks, recommendations are made for managing and mitigating the threats...

Hybrid Thread Modeling Method

Nancy Mead, Forrest Shull, Ole Villadsen &
In FY 2016, the research team evaluated Security Cards, STRIDE (Spoofing identity, Tampering with data, Repudiation, Information disclosure, Denial of service, Elevation of privilege), and persona non grata (PnG) for effectiveness in threat identification. Security Cards is an approach that emphasizes creativity and brainstorming over more structured approaches such as checklists. STRIDE involves modeling a system and subsystem and related data flows. PnGs represent archetypal users who behave in unwanted, possibly nefarious ways. The team...

Incident Management Capability Assessment

Audrey Dorofee, Robin Ruefle, Mark Zajicek, Christopher Alberts, Samuel Perl, Carly Lauren Huth, Pennie Walters & David McIntire
Successful management of incidents that threaten an organization's computer security is a complex endeavor. Frequently an organization's primary focus is on the response aspects of security incidents, which results in its failure to manage incidents beyond simply reacting to threatening events.

Essays on the Economics of Health Care

Kole Reddig
This dissertation has two chapters on health care provider decision-making. The first chapter, titled “Designing Contracts for Multitasking Groups: A Structural Model of Accountable Care Organizations,” estimates a structural model of multitasking agents to investigate the cost-quality tradeoff in healthcare and design contracts for a large physician incentive program. The setting involves Medicare’s Accountable Care Organizations (ACOs), which are groups of healthcare providers that receive incentive pay for spending below a cost target on shared...

Unraveling feng-shui

Ramesh Krishnamurti
This paper comes in three parts. First, relevant principles of fēng-shuǐ are enunciated and examined. Second, these principles are applied to procedures to compute two parameters of predesign behaviour in Chinese traditional architectural practice: the fortunate orientation for a building site and an auspicious date for the start of its construction. Third, an interactive computer implementation is described that incorporates these procedures

Unraveling feng-shui

Ramesh Krishnamurti
This paper comes in three parts. First, relevant principles of fēng-shuǐ are enunciated and examined. Second, these principles are applied to procedures to compute two parameters of predesign behaviour in Chinese traditional architectural practice: the fortunate orientation for a building site and an auspicious date for the start of its construction. Third, an interactive computer implementation is described that incorporates these procedures

Single-Cell Genetic Analysis Reveals Insights into Clonal Development of Prostate Cancers and Indicates Loss of PTEN as a Marker of Poor Prognosis.

Kerstin M. Heselmeyer-Haddad, Lissa Y. Berroa Garcia, Amanda Bradley, , Yue Hu, Jens K. Habermann, Christoph Dumke, Christoph Thorns, Sven Perner, Ekaterina Pestova, Catherine Burke, Salim A. Chowdhury, Russell Schwartz, Alejandro H. Schäffer, Pamela L. Paris & Thomas Ried
Gauging the risk of developing progressive disease is a major challenge in prostate cancer patient management. We used genetic markers to understand genomic alteration dynamics during disease progression. By using a novel, advanced, multicolor fluorescence in situ hybridization approach, we enumerated copy numbers of six genes previously identified by array comparative genomic hybridization to be involved in aggressive prostate cancer [TBL1XR1, CTTNBP2, MYC (alias c-myc), PTEN, MEN1, and PDGFB] in six nonrecurrent and seven recurrent...

Site mutations disrupt inter-helical H-bonds (alpha14W-alpha67T and beta15W-beta72S) involved in kinetic steps in the hemoglobin R-->T transition without altering the free energies of oxygenation.

, Virgil Simplaceanu, Nancy T. Ho, , , Thomas G. Spiro & Chien Ho
Three recombinant mutant hemoglobins (rHbs) of human normal adult hemoglobin (Hb A), rHb (alphaT67V), rHb (betaS72A), and rHb (alphaT67V, betaS72A), have been constructed to test the role of the tertiary intra-subunit H-bonds between alpha67T and alpha14W and between beta72S and beta15W in the cooperative oxygenation of Hb A. Oxygen-binding studies in 0.1 M sodium phosphate buffer at 29 degrees C show that rHb (alphaT67V), rHb (betaS72A), and rHb (alphaT67V, betaS72A) exhibit oxygen-binding properties similar to...

Stochastic steady state gain in a gene expression process with mRNA degradation control.

Hiroyuki Kuwahara & Russell Schwartz
Recent analyses with high-resolution single-molecule experimental methods have shown highly irregular and variable bursting of mRNA in a wide range of organisms. Noise in gene expression is thought to be beneficial in cell fate specifications, as it can lay a foundation for phenotypic diversification of isogenetic cells in the homogeneous environment. However, because the stability of proteins is, in many cases, higher than that of mRNAs, noise from transcriptional bursting can be considerably buffered at...

The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA.

Arnon Henn, , David Hackney & Enrique M. De La Cruz
DEAD-box proteins are ATPase enzymes that destabilize and unwind duplex RNA. Quantitative knowledge of the ATPase cycle parameters is critical for developing models of helicase activity. However, limited information regarding the rate and equilibrium constants defining the ATPase cycle of RNA helicases is available, including the distribution of populated biochemical intermediates, the catalytic step(s) that limits the enzymatic reaction cycle, and how ATP utilization and RNA interactions are linked. We present a quantitative kinetic and...

The expression and distribution of Wnt and Wnt receptor mRNAs during early sea urchin development.

Rachel E. Stamateris, Kiran Rafiq & Charles A. Ettensohn
The protein beta-catenin plays a critically important role in establishing axial polarity during early animal development. In many organisms, beta-catenin is degraded preferentially on one side of the cleavage stage embryo. On the opposite side of the embryo, beta-catenin is stabilized and accumulates in the nucleus, where it functions in concert with members of the LEF/TCF family to activate the transcription of diverse target genes. Genes that are activated by beta-catenin play an essential role...

The Statistical Significance of Max-Gap Clusters

Rose Hoberman, David Sankoff & Dannie Durand
Identifying gene clusters, genomic regions that share local similarities in gene organization, is a prerequisite for many different types of genomic analyses, including operon prediction, reconstruction of chromosomal rearrangements, and detection of whole-genome duplications. A number of formal definitions of gene clusters have been proposed, as well as methods for finding such clusters and/or statistical tests for determining their significance. Unfortunately, there is very little overlap between previously published rigorous analytical statistical tests and the...

Adult neurogenesis and specific replacement of interneuron subtypes in the mouse main olfactory bulb.

Joshua Bagley, Gregory Larocca, Daniel A. Jimenez & Nathan Urban
BACKGROUND: New neurons are generated in the adult brain from stem cells found in the subventricular zone (SVZ). These cells proliferate in the SVZ, generating neuroblasts which then migrate to the main olfactory bulb (MOB), ending their migration in the glomerular layer (GLL) and the granule cell layer (GCL) of the MOB. Neuronal populations in these layers undergo turnover throughout life, but whether all neuronal subtypes found in these areas are replaced and when neurons...

Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates.

Rory A. Eutsey, Natalia Hiller, Joshua P. Earl, Benjamin A. Janto, Margaret E. Dahlgren, Azad Ahmed, Evan Powell, Matthew P. Schultz, Janet R. Gilsdorf, , Arnold Smith, Timothy F. Murphy, Sanjay Sethi, Kai Shen, , Fen Z. Hu & Garth D. Ehrlich
BACKGROUND: Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates. RESULTS: We describe and validate a Haemophilus influenzae supragenome hybridization...

Developmental expression of transcription factor genes in a demosponge: insights into the origin of metazoan multicellularity.

Claire Larroux, Bryony Fahey, Danielle Liubicich, Veronica F. Hinman, Marie Gauthier, Milena Gongora, Kathryn Green, Gert Wörheide, Sally P. Leys & Bernard M. Degnan
Demosponges are considered part of the most basal evolutionary lineage in the animal kingdom. Although the sponge body plan fundamentally differs from that of other metazoans, their development includes many of the hallmarks of bilaterian and eumetazoan embryogenesis, namely fertilization followed by a period of cell division yielding distinct cell populations, which through a gastrulation-like process become allocated into different cell layers and patterned within these layers. These observations suggest that the last common ancestor...

Drosophila APC2 and APC1 play overlapping roles in wingless signaling in the embryo and imaginal discs.

Kathryn Akong, Elizabeth E. Grevengoed, Meredith H. Price, Brooke M. McCartney, Melissa A. Hayden, Jan C. DeNofrio & Mark Peifer
The regulation of signal transduction plays a key role in cell fate choices, and its disregulation contributes to oncogenesis. This duality is exemplified by the tumor suppressor APC. Originally identified for its role in colon tumors, APC family members were subsequently shown to negatively regulate Wnt signaling in both development and disease. The analysis of the normal roles of APC proteins is complicated by the presence of two APC family members in flies and mice....

Drosophila APC2 and APC1 play overlapping roles in wingless signaling in the embryo and imaginal discs.

Kathryn Akong, Elizabeth E. Grevengoed, Meredith H. Price, Brooke M. McCartney, Melissa A. Hayden, Jan C. DeNofrio & Mark Peifer
The regulation of signal transduction plays a key role in cell fate choices, and its disregulation contributes to oncogenesis. This duality is exemplified by the tumor suppressor APC. Originally identified for its role in colon tumors, APC family members were subsequently shown to negatively regulate Wnt signaling in both development and disease. The analysis of the normal roles of APC proteins is complicated by the presence of two APC family members in flies and mice....

Drosophila ventral furrow morphogenesis: a proteomic analysis.

Lei Gong, Mamta Puri, Mustafa Unlu, Margaret Young, Katherine Robertson, Surya Viswanathan, Arun Krishnaswamy, Susan R. Dowd & Jonathan Minden
Ventral furrow formation is a key morphogenetic event during Drosophila gastrulation that leads to the internalization of mesodermal precursors. While genetic analysis has revealed the genes involved in the specification of ventral furrow cells, few of the structural proteins that act as mediators of ventral cell behavior have been identified. A comparative proteomics approach employing difference gel electrophoresis was used to identify more than fifty proteins with altered abundance levels or isoform changes in ventralized...

Drosophila ventral furrow morphogenesis: a proteomic analysis.

Lei Gong, Mamta Puri, Mustafa Unlu, Margaret Young, Katherine Robertson, Surya Viswanathan, Arun Krishnaswamy, Susan R. Dowd & Jonathan Minden
Ventral furrow formation is a key morphogenetic event during Drosophila gastrulation that leads to the internalization of mesodermal precursors. While genetic analysis has revealed the genes involved in the specification of ventral furrow cells, few of the structural proteins that act as mediators of ventral cell behavior have been identified. A comparative proteomics approach employing difference gel electrophoresis was used to identify more than fifty proteins with altered abundance levels or isoform changes in ventralized...

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