cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.4231/r7h41pbt
title: Position of MLL1 morphemes in human genomic DNA

description: &lt;p&gt;[[Link(http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&amp;db=hg19&amp;position=chr7&amp;hgt.customText=https://purr.purdue.edu/publications/1639/serve?v=1 Open in genome browser)]]&lt;/p&gt;

&lt;p&gt;Mixed Lineage Leukemia 1 (MLL or MLL1) may play a central role in the recruitment of transcription factors to chromatin to regulate the expression of genes associated with !CpG islands. We have previously shown that MLL1 binds specific DNA sequence elements known as morphemes: &lt;a href="http://www.biomedcentral.com/content/pdf/1471-2164-14-927.pdf" target="_blank"&gt;Bina et. al, BMC Genomics 14:927 (2013)&lt;/a&gt;&lt;/p&gt;

&lt;p&gt;This publication provides a file (Bina_MLL_morphemes_hg19.bed) to display the position of MLL1 morphemes in the human genome browser at UCSC (hg19). You can obtain a copy of the bed file (txt format) by clicking on download. Alternatively, you can use the link below to view the position of MLL1 morphemes directly on a track in the browser at UCSC. While using the genome browser, select Dense for viewing morpheme positions in genomic DNA. Select pack when zooming to short DNA segments.&lt;/p&gt;

&lt;p&gt;[[Link(http://genome.ucsc.edu/cgi-bin/hgTracks?org=human&amp;db=hg19&amp;position=chr7&amp;hgt.customText=https://purr.purdue.edu/publications/1639/serve?v=1 Open the position of MLL1 morphemes in hg19 at the UCSC genome browser.)]]&lt;/p&gt;

&lt;p&gt;If you use the data in your research, please cite the primary publication by Bina et al., published in BMC Genomics. 2013 Dec 28;14:927.&lt;/p&gt;
description: Supplementary materials for the publication entitled “Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin.” Bina M, Wyss P, et al. BMC Genomics. 14:927 (2013).
DOI: 10.4231/r77p8w9j
title: Biological, chemical and flow characteristics of five river sampling sites in the Wabash River watershed near Lafayette, Indiana – 2010.

description: &lt;p&gt;This dataset includes water quality data collected from five sites located in the Lafayette area watershed in 2010. Two of the sites are located upstream and downstream of Lafayette on the Wabash River. The other three sites are located on Little Pine Creek, Little Wea Creek, and Elliot Ditch. Data includes 15 minute flow data collected by the United States Geological Survey (USGS).&lt;/p&gt;
description: Water quality data collected from the Lafayette area watershed in 2010. There are five samples sites located on Little Pine Creek, Elliot Ditch, Little Wea Creek and two sites on the Wabash River.
DOI: 10.4231/r73x84k6
title: Biological, chemical and flow characteristics of five river sampling sites in the Wabash River watershed near Lafayette, Indiana – 2011.

description: &lt;p&gt;This dataset includes water quality data collected from five sites located in the Lafayette area watershed in 2011. Two of the sites are located upstream and downstream of Lafayette on the Wabash River. The other three sites are located on Little Pine Creek, Little Wea Creek, and Elliot Ditch. Data includes 15 minute flow data collected by the United States Geological Survey (USGS).&lt;/p&gt;
description: Water quality data collected from the Lafayette area watershed in 2011. There are five samples sites located on Little Pine Creek, Elliot Ditch, Little Wea Creek and two sites on the Wabash River.
DOI: 10.4231/r7057cvs
title: Arrival Performance Measures at a Diverging Diamond Interchange

description: &lt;p&gt;[[Video(https://www.youtube.com/watch?v=RhazZu4xMeA)]]&lt;/p&gt;

&lt;p&gt;Diverging diamond interchanges (DDI) are a relatively recent adaptation of signalized interchanges. This video shows several cycles of a diverging diamond interchange at SR-201 / Bangerter in Salt Lake City, Utah on December 18, 2013. The video observes southbound traffic and how the vehicles arrive at the downstream stop bar. The upper plot is a Flow Profile Diagram and the lower graph is a Purdue Coordination Diagram (PCD). Both are used to assess arrival on green performance. &#39;&#39;&#39;Latitude/Longitude:&#39;&#39;&#39; 40.725819&deg; / -111.986311&deg;&lt;/p&gt;
description: This video shows several cycles of a diverging diamond interchange at SR-201 / Bangerter in Salt Lake City, Utah on December 18, 2013.
DOI: 10.4231/r7vd6wch
title: Sequence and Offset Optimization at a Diamond Interchange

description: &lt;p&gt;[[Video(https://www.youtube.com/watch?v=qi8oOfUFblY)]]&lt;/p&gt;

&lt;p&gt;Signalized diamond interchanges are unique pairs of intersections characterized by interlocked left turns and relatively close spacing between ramps. A diamond interchange has four external entry points (origins) and four external exit points (destinations). To effectively operate a diamond interchange, it is critical to examine the external origin-destination paths and evaluate their impact on the interior storage and progression. This video demonstrates the optimized performance at a diamond interchange at I-69 / 96^th^ Street in northeast Indianapolis, IN. The movement observed is the westbound thru movement and depicts an animated time space diagram based on high-resolution event-based data. &#39;&#39;&#39;Latitude/Longitude:&#39;&#39;&#39; 39.927108&deg; / -86.029641&deg;&lt;/p&gt;
description: This video demonstrates the optimized performance at a diamond interchange at I-69 / 96th Street in northeast Indianapolis, IN.
DOI: 10.4231/r7kw5cxf
title: Localization of MLL1 morphemes in mouse mm9 genomic DNA

description: &lt;p&gt;&lt;a href="http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&amp;db=mm9&amp;position=chr1&amp;hgt.customText=https://purr.purdue.edu/publications/1648/serve?v=1" target="_blank"&gt;Access in genome browser&lt;/a&gt;. Mixed Lineage Leukemia 1 (MLL or MLL1) plays central roles in the regulation of protein-coding genes. Previous studies of mice have established that MLL1 controls key developmental pathways including the formation of body plan during the early stages of embryogenesis. Even though MLL1 is best known for catalyzing methylation of lysine 4 in histone H3 (H3K4), reported data indicate that MLL1 performs histone methyltransferase-independent functions including gene-bookmarking during mitosis, favoring genes that were highly transcribed during interphase, to accelerate reactivation of transcription following mitotic exit (Blobel &#39;&#39;et al&#39;&#39;., &#39;&#39;Mol Cell&#39;&#39;. 2009). By analyzing results of reported DNA binding and chromatin immunoprecipitation assays, we have uncovered the DNA sequence elements that bind the MT-domain in MLL1: &lt;a href="http://www.biomedcentral.com/content/pdf/1471-2164-14-927.pdf" target="_blank"&gt;Bina et. al, BMC Genomics 14:927 (2013)&lt;/a&gt;. We describe these elements as minimal units or morphemes: the smallest &lsquo;words&rsquo; in DNA that selectively bind the MLL1 MT-domain. This publication provides a file (BINA_MLL_morphemes_mm9.bed) to display the position of MLL1 morphemes in the genome browser at UCSC. You can obtain a copy of the bed file (in text format) by clicking on download. Alternatively, you can use the link below to view the position of MLL1 morphemes directly on a track in the browser at UCSC. While using the genome browser, select Dense to view morpheme positions in genomic DNA. Select pack when zooming to short DNA segments. &lt;a href="http://genome.ucsc.edu/cgi-bin/hgTracks?org=mouse&amp;db=mm9&amp;position=chr1&amp;hgt.customText=https://purr.purdue.edu/publications/1648/serve?v=1" target="_blank"&gt;Open the position of MLL1 morphemes in the mouse built mm9 genomic DNA&lt;/a&gt;. If you use the data in your research, please cite the primary publication by Bina et al., published in BMC Genomics 14:927 (2013).&lt;/p&gt;
description: Supplementary materials for the publication entitled “Discovery of MLL1 binding units, their localization to CpG Islands, and their potential function in mitotic chromatin.” Bina M, Wyss P, et al. BMC Genomics. 14:927 (2013)
DOI: 10.4231/r72z13fc
title: Indiana Department of Agriculture Debrief - 2013 Engineering Technology Summit

description: &lt;p&gt;Chad Laux, Assistant Professor from the Technology, Leadership, &amp; Innovation Department at Purdue University interviews Coty Back from the Indiana Department of Agriculture and Future Farmers of America regarding careers paths in agriculture.&lt;/p&gt;
description: An interview with Coty Back from the Indiana Department of Agriculture and Future Farmers of America.
DOI: 10.4231/r7sb43pz
title: INERFC: Evaluation of the Repeated Integrals of the Coerror Function by Half-Range Gauss-Hermite Quadrature

description: These Matlab codes and files are a companion piece to the paper
``Evaluation of the repeated integrals of the coerror function by half-range Gauss--Hermite quadrature", submitted for
publication.
description: INERFC: Evaluation of the Repeated Integrals of the Coerror Function by Half-Range Gauss-Hermite Quadrature
DOI: 10.4231/r7rb72jk
title: Outflow Boundary Condition and Algorithm for Single-Phase Incompressible Flows

description: &lt;p&gt;We present a robust and accurate outflow boundary condition and an associated numerical algorithm for incompressible flow simulations on unbounded physical domains, aiming at maximizing the domain truncation without adversely affecting the flow physics. The proposed outflow boundary condition allows for the influx of kinetic energy into the domain through the outflow  boundaries, and prevents un-controlled growth in the energy of the domain in such situations. The numerical algorithm for the outflow boundary condition is developed on top of a rotational velocity-correction type strategy to de-couple the pressure and velocity computations, and a special construction in the algorithmic formulation prevents the numerical locking at the outflow boundaries for time-dependent problems. Extensive numerical tests for flow problems with bounded and semi-bounded physical domains demonstrate that this outflow boundary condition and the numerical algorithm produce stable and accurate simulations  on even severely truncated computational domains, where strong vortices may be present at or exit the outflow boundaries. The method developed herein has the potential to significantly expedite simulations of incompressible flows involving outflow or open boundaries, and to enable such simulations at Reynolds numbers significantly higher than the state of the art.&lt;/p&gt;
description: We present an accurate and effective outflow boundary condition and numerical algorithm for achieving stability in the presence of strong vortices or backflows at the outflow boundaries.
DOI: 10.4231/r7mk69tv
title: Two-Phase Outflows: Boundary Conditions and Algorithm

description: &lt;p&gt;We present an effective outflow boundary condition, and an associated numerical algorithm, within the phase-field framework for dealing with two-phase outflows or open boundaries. The set of two-phase outflow boundary conditions for the phase-field and flow variables are designed to prevent the un-controlled growth in the total energy of the two-phase system, even in situations where strong backflows or vortices may be present at the outflow  boundaries. We also present an additional boundary condition for the phase field function, which together with the usual Dirichlet condition can work effectively as the phase-field inflow conditions. The numerical algorithm for dealing with these boundary conditions is developed on top of a strategy for de-coupling the computations of all flow variables and for overcoming the performance bottleneck caused by variable coefficient matrices associated with variable density/viscosity. The algorithm contains special constructions, for treating the variable dynamic viscosity in the outflow boundary condition, and for preventing a numerical locking at the outflow boundaries for time-dependent problems. Extensive numerical tests  with incompressible two-phase flows involving inflow and outflow boundaries demonstrate that, the two-phase outflow boundary conditions and the numerical algorithm developed herein allow for the fluid interface and the  two-phase flow to pass through the outflow or open boundaries in a smooth and seamless fashion, and that our method produces stable  simulations when large density ratios and large viscosity ratios are involved and when strong backflows are present at the outflow boundaries.&lt;/p&gt;
description: We present an effective outflow boundary condition, and an associated numerical algorithm, within the phase field framework for dealing with two-phase outflows or open boundaries.
DOI: 10.4231/r7gt5k3j
title: Biological, chemical and flow characteristics of five river sampling sites in the Wabash River watershed near Lafayette, Indiana – 2012.

description: &lt;p&gt;This dataset includes water quality data collected from five sites located in the Lafayette area watershed in 2012. Two of the sites are located upstream and downstream of Lafayette on the Wabash River. The other three sites are located on Little Pine Creek, Little Wea Creek, and Elliot Ditch. Data includes 15 minute flow data collected by the United States Geological Survey (USGS).&lt;/p&gt;
description: Water quality data collected from the Lafayette area watershed in 2012. There are three samples sites located on Little Pine Creek, Elliot Ditch, Little Wea Creek and two sites on the Wabash River.
DOI: 10.4231/r7zw1hv3
title: Painted Rumble Stripes: Alternative to Raised Pavement Markers (RPMs)

description: &lt;p&gt;[[Video(http://www.youtube.com/watch?v=bpuJgTDAIg8)]]     This video highlights research completed by the Joint Transportation Research Program led by Darcy Bullock, Lyles School of Civil Engineering, Purdue University, for JTRP Project SPR-3528, &quot;Alternatives to Raised Pavement Markers (RPMs).&quot; The video includes the six steps to installing rumble stripes with statistics on crash reductions provided by Indiana Department of Transportation.&lt;/p&gt;
description: This video highlights research completed by the Joint Transportation Research Program led by Darcy Bullock, Lyles School of Civil Engineering, Purdue University, for JTRP Project SPR-3528, "Alternatives to Raised Pavement Markers (RPMs)."
DOI: 10.4231/r7c24tc4
title: Three-Phase Operations at a Diverging Diamond Interchange Using an Unmanned Aerial Vehicle (UAV) Camera

description: &lt;p&gt;[[Video(http://www.youtube.com/watch?v=B6d7xeYlAiw)]] This video shows three-phase operations featuring a hold-back phase with data characterizing the southbound internal through movement (OL-C) on May 15, 2014, at the SR-201 / Bangerter DDI in Salt Lake City, Utah. The gray dots are associated with vehicles from the upstream ramp movement (OL-H) and the black dots are associated with vehicles from the upstream external through movement (OL-E). Radar detection was used, so closely spaced vehicles often generate one detection for the group instead of a unique detection for each vehicle. Latitude/Longitude: 40.726568&deg; / -111.9855606&deg;&lt;/p&gt;
description: This video shows three-phase operations featuring a hold-back phase with data characterizing the southbound internal through movement (OL-C) on May 15, 2014, at the SR-201 / Bangerter DDI in Salt Lake City, Utah.
DOI: 10.4231/r77d2s24
title: Cirrus SR-20 Traversing Saw Cut and Raised Rumble Strips at 15 Knots

description: &lt;p&gt;[[Video(http://www.youtube.com/watch?v=7dV9oHrOcfo)]]      This video documents a field test of a Cirrus SR-20 traversing both a saw cut and a raised rumble strip at the Purdue Airport (LAF). The audio track contains a qualitative report on ride quality as the aircraft traverses the rumble strips on a scale of 1-5. The report of a &ldquo;3&rdquo; and &ldquo;4&rdquo; indicate that both rumble strips are noticeable, but not excessive.  Latitude/Longitude: 40.415846,-86.929301&lt;/p&gt;
description: This video documents a field test of a Cirrus SR-20 traversing both a saw cut and a raised rumble strip at the Purdue Airport (LAF).
DOI: 10.4231/r73n21bs
title: Dramatic adaptive response of life history trait to reduced commercial harvest in a freshwater fish

description: Fisheries-induced evolution of exploited fish stocks toward maturation at smaller sizes and younger ages has been postulated to reduce stock productivity and depress the recovery of stocks after collapse.  Moreover, evidence from empirical and modeling research has shown that evolutionary changes in maturation may be very slow or impossible to reverse, even following complete fisheries closures.  We evaluated temporal trends in maturation of five Great Lakes stocks of yellow perch (Perca flavescens) using indices that reflect plastic (age at 50% maturity) and adaptive (probabilistic maturation reaction norms; PMRNs) variation in maturation schedules.  Four of the populations were fished commercially throughout the time series, while one (Lake Michigan) experienced a fisheries moratorium following collapse of the stock.  We documented a dramatic, adaptive increase in PMRNs of the Lake Michigan stock coincident with the closure of the commercial fishery, while populations that were continuously fished showed little change.  This evidence is among the first to suggest that fish life history traits have the potential to rapidly respond to fishing moratoriums and recover from previous, fisheries-induced changes, meaning some stocks may retain the evolutionary ability to recover from commercial overexploitation.
description: An analysis of maturation schedules of yellow perch in the Laurentian Great Lakes revealed rapid evolution in response to changes in commercial harvest.
DOI: 10.4231/r7qc01dr
title: Analytical database on noncompact and slender CFT members

description: &lt;p&gt;This analytical database presents the results from comprehensive parametric studies conducted using benchmarked finite element method (FEM) models developed by the author (Lai, 2014). These parametric studies are conducted to investigate the effect of tube slenderness ratio (b/t or D/t), material strength ratio (Fy/f&rsquo;c), axial load ratio (P/Pn) and member length-to-depth ratio (L/B or L/D) on the behavior of noncompact and slender rectangular and circular CFT beam-columns. Updated P-M interaction equations were developed using results from these parametric studies, as discussed in detail by Lai (2014). The updated P-M interaction equations were verified by using them to calculate the P-M interaction curves of 197 beam-columns included in the database.The resulting comparisons of the updated interaction curves (with solid lines) obtained using these equations with interaction curves (with dashed lines) from the parametric studies are included in this database. In the research by Lai (2014), effective stress-strain curves were developed for the steel tube and concrete infill for noncompact and slender CFT members. The validation of these curves are also included in this database. This analytical database also presents the results from comprehensive parametric studies conducted using  benchmarked finite element method (FEM) models developed by the author (Lai, 2014). These parametric studies are conducted to develop effective stress-strain curve for the steel tube and concrete infill for noncompact and slender CFT members. The parameters evaluated in these studies include the effect of tube slenderness ratio (b/t or D/t), steel yield strength (Fy), and concrete compressive strength (f&#39;c). The developed stress-strain curves were discussed in detail by Lai (2014).&lt;/p&gt;
description: This analytical database presents the results from comprehensive parametric studies (conducted using FEM models) on noncompact and slender CFT members.
DOI: 10.4231/r7kk98pg
title: A Non-parametric Bayesian Model for Joint Cell Clustering and Cluster Matching: Identification of Anomalous Sample Phenotypes with Random Effects.

description: &lt;p&gt;Background: Flow cytometry (FC)-based computer-aided diagnostics is an emerging technique utilizing modern multiparametric cytometry systems.The major difficulty in using machine-learning approaches for classification of FC data arises from limited access to a wide variety of anomalous samples for training. In consequence, any learning with an abundance of normal cases and a limited set of specific anomalous cases is biased towards the types of anomalies represented in the training set. Such models do not accurately identify anomalies, whether previously known or unknown, that may exist in future samples tested. Although one-class classifiers trained using only normal cases would avoid such a bias, robust sample characterization is critical for a generalizable model. Owing to sample heterogeneity and instrumental variability, arbitrary characterization of samples by feature extraction algorithms usually introduces feature noise that may lead to poor predictive performance. Herein, we present a non-parametric Bayesian algorithm called ASPIRE (anomalous sample phenotype identification with random effects) that identifies phenotypic differences across a batch of samples in the presence of random effects. Our approach involves simultaneous clustering of cellular measurements in individual samples and matching of discovered clusters across all samples in order to recover global clusters using probabilistic sampling techniques in a systematic way.  Results: We demonstrate the performance of the proposed method in identifying anomalous samples in two different FC data sets, one of which represents a set of samples including acute myeloid leukemia (AML) cases, and the other a generic 5-parameter peripheral-blood immunophenotyping. Results are evaluated in terms of the area under the receiver operating characteristics curve (AUC). ASPIRE achieved AUCs of 0.99 and 1.0 on the AML and generic blood immunophenotyping data sets, respectively. Conclusions: These results demonstrate that anomalous samples can be identified by ASPIRE with almost perfect accuracy without {it a priori} access to samples of anomalous subtypes in the training set. The ASPIRE approach is unique in its ability to form generalizations regarding normal and anomalous states given only very weak assumptions regarding sample characteristics and origin. Thus, ASPIRE could become highly instrumental in providing unique insights about observed biological phenomena in the absence of full information about the investigated samples.&lt;/p&gt;
description: The manuscript presents a non-parametric Bayesian algorithm called ASPIRE (Anomalous Sample Phenotype Identification with Random Effects) able to identify phenotypic differences across batches of cytometry samples in the presence of random effects
DOI: 10.4231/r7ft8hzr
title: 1 Mark (Mahoney, Berea College)

description: &lt;p&gt;Prompted to recollect the story of his department&#39;s recent curriculum revision, Mark talks about multiple topics, including: The renaming of Berea College&#39;s &quot;Industrial Arts&quot; program to its current name of &quot;Technology and Applied Design&quot; The self-study and curriculum revision process that led to the emphasis on &quot;design thinking&quot; The need for a common definition of the word &quot;design,&quot; and his personal take on the concept The difference between personal trust (visiting a sick neighbor, letting a friend borrow your car) and professional trust (allowing a colleague to visit your classroom and critique your teaching), and why the latter is more difficult How he developed a &quot;thick skin&quot; for criticism on his teaching, and the need for others to develop similarly &quot;think skins&quot; so they can improve their courses for the sake of their students&lt;/p&gt;
description: The first narrative from Mark Mahoney of Berea College, collected on Feb. 21, 2014.