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Dmtn-021: Implementation Of Image Difference Decorrelation

David J Reiss, Robert H Lupton
2016 Zenodo  
DIA Source measurement The measurement and classification of dipoles in image differences, described in Reiss (2016) is complicated by image difference decorrelation, because dipole fitting is constrained  ... 
doi:10.5281/zenodo.192833 fatcat:xdmvh7s7fndufbaehkimmsqmdu

Global analysis of mRNA stability in Mycobacterium tuberculosis

Tige R. Rustad, Kyle J. Minch, William Brabant, Jessica K. Winkler, David J. Reiss, Nitin S. Baliga, David R. Sherman
2012 Nucleic Acids Research  
Mycobacterium tuberculosis (MTB) is a highly successful pathogen that infects over a billion people. As with most organisms, MTB adapts to stress by modifying its transcriptional profile. Remodeling of the transcriptome requires both altering the transcription rate and clearing away the existing mRNA through degradation, a process that can be directly regulated in response to stress. To understand better how MTB adapts to the harsh environs of the human host, we performed a global survey of the
more » ... decay rates of MTB mRNA transcripts. Decay rates were measured for 2139 of the $4000 MTB genes, which displayed an average half-life of 9.5 min. This is nearly twice the average mRNA half-life of other prokaryotic organisms where these measurements have been made. The transcriptome was further stabilized in response to lowered temperature and hypoxic stress. The generally stable transcriptome described here, and the additional stabilization in response to physiologically relevant stresses, has far-ranging implications for how this pathogen is able to adapt in its human host.
doi:10.1093/nar/gks1019 pmid:23125364 pmcid:PMC3592478 fatcat:r36hho23tbg77khwf4fituei2y

Fannie Mae and Freddie Mac: Creatures of Regulatory Privilege [chapter]

David J. Reiss
2010 Financial Institutions and Markets  
Fannie Mae and Freddie Mac: Creatures of Regulatory Privilege 2/3/2010 David Reiss borrow at.  ...  Fannie Mae and Freddie Mac: Creatures of Regulatory Privilege 2/3/2010 David Reiss market, they are able to extract some economic rent.  ... 
doi:10.1057/9780230117365_7 fatcat:zqn2pxpkrzaxnmet4mfn7wcx2m

Neuroanatomical spatial patterns in Turner syndrome

Matthew J. Marzelli, Fumiko Hoeft, David S. Hong, Allan L. Reiss
2011 NeuroImage  
., 2004; Reiss et al., 1995) and enlargement of the amygdala (Good et al., 2003; Kesler et al., 2004) .  ... 
doi:10.1016/j.neuroimage.2010.12.054 pmid:21195197 pmcid:PMC3035734 fatcat:bmaecj6pxvbbnatcdh5xjewzqa

Reinventing Homeownership: A Compendium of Concepts to Consider

Denise Gabel, David J. Reiss
2012 Social Science Research Network  
David Reiss, JD, is a professor of law at Brooklyn Law School in New York. He concentrates on real estate finance and community development.  ...  David Reiss x The goal is to create a network of the passionate, next genera-tion of credit union voices, while connecting to the leadership and traditions of the past.  ... 
doi:10.2139/ssrn.2094376 fatcat:gk57zj76tzbxvfer2vsotp57zm

ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells [article]

Samuel Anthony Danziger, David L Gibbs, Ilya Shmulevich, Mark McConnell, Matthew WB Trotter, Frank Schmitz, David J Reiss, Alexander V Ratushny
2019 bioRxiv   pre-print
Summary: Immune cell infiltration of tumors can be an important component for determining patient outcomes, e.g. by inferring immune cell presence by deconvolving gene expression data drawn from a heterogenous mix of cell types. ADAPTS aids deconvolution by adding custom cell types to existing cell- type signature matrices or building new matrices de novo. This R package builds a custom signature matrix from purified cell type gene expression data by automatically determining genes that
more » ... identify each cell type. The package includes functions that call deconvolution algorithms which use the custom signature matrix to estimate the proportion of cell types present in heterogenous samples. Availability: The R packages ADAPTS, ADAPTSdata, and an instructional vignette are available on CRAN.
doi:10.1101/633958 fatcat:s7a6vsrvvrf7jklkt3vzac5me4

Opportunity Cost, Inattention and the Bidder's Curse

David Freeman, Erik O. Kimbrough, J. Philipp Reiss
2017 Social Science Research Network  
Kimbrough, J. Philipp Reiss: Opportunity cost, inattention and the bidder's curse, February 2017 Andranik S.  ...  ., 1987; Kagel and Levin, 1993; Cooper and Fang, 2008; Kagel and Levin, 1986; Klemperer, 2002; Levin and Reiss, 2017) .  ... 
doi:10.2139/ssrn.2915309 fatcat:7tovlgtchfasfnyspe32phqap4

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis

Serdar Turkarslan, Eliza J R Peterson, Tige R Rustad, Kyle J Minch, David J Reiss, Robert Morrison, Shuyi Ma, Nathan D Price, David R Sherman, Nitin S Baliga
2015 Scientific Data  
Mycobacterium tuberculosis (MTB) is a pathogenic bacterium responsible for 12 million active cases of tuberculosis (TB) worldwide. The complexity and critical regulatory components of MTB pathogenicity are still poorly understood despite extensive research efforts. In this study, we constructed the first systemsscale map of transcription factor (TF) binding sites and their regulatory target proteins in MTB. We constructed FLAG-tagged overexpression constructs for 206 TFs in MTB, used ChIP-seq
more » ... identify genomewide binding events and surveyed global transcriptomic changes for each overexpressed TF. Here we present data for the most comprehensive map of MTB gene regulation to date. We also define elaborate quality control measures, extensive filtering steps, and the gene-level overlap between ChIP-seq and microarray datasets. Further, we describe the use of TF overexpression datasets to validate a global gene regulatory network model of MTB and describe an online source to explore the datasets. Design Type(s) ChIP-chip by tiling array design • systems biology analysis Measurement Type(s) transcription factor binding site identification • transcription profiling assay Technology Type(s) ChIP assay • tiling microarray Factor Type(s) Sample Characteristic(s) Mycobacterium tuberculosis H37Rv
doi:10.1038/sdata.2015.10 pmid:25977815 pmcid:PMC4413241 fatcat:nlh27ehml5bfxanexr7yet5xra

Unsupervised imaging, registration and archiving of tissue microarrays

Wenjin Chen, David J Foran, Michael Reiss
2002 Proceedings. AMIA Symposium  
Tissue microarray (TMA) technology offers several advantages over traditional methods of specimen preparation by maximizing limited tissue resources and providing the means for visualizing molecular targets. Currently, the primary methods used to evaluate arrays involves the interactive review of TMA samples while they are viewed by microscope and are subjectively evaluated and scored. The process is slow, tedious and prone to error. In order to facilitate large-scale, multi-institutional
more » ... s a more automated and reliable means for processing tissue microarrays is needed. We have developed a web-based prototype which features automated imaging, registration and intelligent archiving of tissue microarrays in multi-user, network environments.
pmid:12463802 pmcid:PMC2244557 fatcat:3o2ijlgixfcwrot4c2kysq7adm

Multi-species integrative biclustering

Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns, David J Reiss, Patrick Eichenberger, Richard Bonneau
2010 Genome Biology  
For each organism j (j {U, V}), [20] .  ...  g ik j ik , is defined as in the SSCM algorithm, as: g r r s s q q ik j ik j ik j n nik j n N = ( ) + ( ) + ( ) ∈ ∑ 0 0 0 log log log    where  r ik j ,  ... 
doi:10.1186/gb-2010-11-9-r96 pmid:20920250 pmcid:PMC2965388 fatcat:uiwrcsusx5bttmslq2gum43q44

Alterations of Smad signaling in human breast carcinoma are associated with poor outcome: a tissue microarray study

Wen Xie, Joachim C Mertens, Daniel J Reiss, David L Rimm, Robert L Camp, Bruce G Haffty, Michael Reiss
2002 Cancer Research  
Reiss, unpublished observations. 6 T. V. Parekh, P. Gama, W. Xie, R. Demopoulos, J. S. Munger, M. L. Carcangiu, M. Reiss, and L. I. Gold.  ...  Reiss. Molecular analysis of transforming growth factor-␤ signaling pathway in colorectal cancer using tissue microarrays, manuscript in preparation.  ... 
pmid:11809701 fatcat:f7nbeyklm5hk7g7cys6ckinyry

Comment on the Use of Eminent Domain to Restructure Performing Loans

David J. Reiss
2012 Social Science Research Network  
Sincerely, /s/ David Reiss PROFESSOR 250 JORALEMON STREET • BROOKLYN, NEW YORK 11201 • 718 -780 -0636 • FAX: 718 -780 -0376 DAVID.REISS@BROOKLAW.EDU FHFA has significant concerns about the use of eminent  ...  D A V I D J . R E I S S (1984) , provides further support for the use of eminent domain to assist a broad swath of the public when faced with a market failure.  ... 
doi:10.2139/ssrn.2144786 fatcat:pp2kxg7hgzfgzm56k26ydbiuzy

Rating Agencies: Facilitators of Predatory Lending in the Subprime Market [chapter]

David J. Reiss
2011 Lessons from the Financial Crisis  
Mortgage Market: A Model of Dueling Charters, 11 J. HOUSING RES. 233, 233-34 (2000). excessive interest ‡ U.S. GEN.  ... 
doi:10.1002/9781118266588.ch25 fatcat:lpio3e7qpbcshf67awidzqvhee

The DNA-binding network of Mycobacterium tuberculosis

Kyle J. Minch, Tige R. Rustad, Eliza J. R. Peterson, Jessica Winkler, David J. Reiss, Shuyi Ma, Mark Hickey, William Brabant, Bob Morrison, Serdar Turkarslan, Chris Mawhinney, James E. Galagan (+3 others)
2015 Nature Communications  
doi:10.1038/ncomms6829 pmid:25581030 pmcid:PMC4301838 fatcat:hariktkptfd6nhyuufgc4nodua

The Federal Housing Administration (FHA) and Private Mortgage Insurance (PMI): A Bibliography

David J. Reiss
2016 Social Science Research Network  
Freund, David M.P. (2006). Marketing the Free Market: State Intervention and the Politics of Prosperity in Metropolitan American in Kevin M. Kurse & Thomas J. Sugrue. (Eds.).  ...  Courchane, Marsha J. et al. (2009). From FHA to Subprime and Back? Retrieved from Social Science Research Network website: http://papers.ssrn.com/sol3/papers.cfm?  ... 
doi:10.2139/ssrn.2743957 fatcat:ikzbhaovdvasrhrwf2gum2l2ty
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