Digital Commons Network^™

The Khmer Software Package: Enabling Efficient Nucleotide Sequence Analysis, Michael R. Crusoe, Hussien F. Alameldin, Sherine Awad, Elmar Boucher, Adam Caldwell, Reed Cartwright, Amanda Charbonneau, Bede Constantinides, Greg Edvenson, Scott Fay, Jacob Fenton, Thomas Fenzl, Jordan Fish, Leonor Garcia-Gutierrez, Phillip Garland, Jonathan Gluck, Iván González, Sarah Guermond, Jiarong Guo, Aditi Gupta, Joshua R. Herr, Adina Howe, Alex Hyer, Andreas Härpfer, Luiz Irber, Rhys Kidd, David Lin, Justin Lippi, Tamer Mansour, Pamela Mca'nulty, Eric Mcdonald, Jessica Mizzi, Kevin D. Murray, Joshua R. Nahum, Kaben Nanlohy, Alexander Johan Nederbragt, Humberto Ortiz-Zuazaga, Jeramia Ory, Jason Pell, Charles Pepe-Ranney, Zachary N. Russ, Camille Scott, Josiah Seaman, Scott Sievert 38, Jared Simpson, Connor T. Skennerton, James Spencer, Ramakrishnan Srinivasan, Daniel Standage, James A. Stapleton, Susan R. Steinman, Joe Stein, Benjamin Taylor, Will Trimble, Heather L. Wiencko, Michael Wright, Brian Wyss, Qingpeng Zhang, En Zyme, C. Titus Brown, Erich Schwarz

Department of Plant Pathology: Faculty Publications

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer.

The Trial Of Calcium And Vitamin D For The Prevention Of Colorectal Adenomas, John A. Baron, Elizabeth L. Barry, Leila A. Mott, Judy R. Rees

Dartmouth Scholarship

BACKGROUND Epidemiologic and preclinical data suggest that higher intake and serum levels of vitamin D and higher intake of calcium reduce the risk of colorectal neoplasia. To further study the chemopreventive potential of these nutrients, we conducted a randomized, double-blind, placebo-controlled trial of supplementation with vitamin D, calcium, or both for the prevention of colorectal adenomas. METHODS We recruited patients with recently diagnosed adenomas and no known colorectal polyps remaining after complete colonoscopy. We randomly assigned 2259 participants to receive daily vitamin D3 (1000 IU), calcium as carbonate (1200 mg), both, or neither in a partial 2Å~2 factorial design. Women …

Emoji, Emoji, What For Art Thou?, Lisa Lebduska

Harlot: A Revealing Look at the Arts of Persuasion

This essay provides a history and context for emoji as a way of re-materializing composing while simultaneously arguing that emoji do not threaten alphabetic literacy and instead provide a means of creative graphic expression. The essay acknowledges that n some instances emoji do help to clarify the intent or tone of alphabetic writing, but it notes that emoji, like alphabetic writing, is culturally and contextually bound. Emoji expand expression and doing so open themselves to re-appropriation, intepretation and even misinterpretation, along with the affirming possibilities of artistic creation.

Time/Depth Dependent Diffusion-Covection Model Of Chloride With Transportation In Concrete Structures With Chloride-Binding Isotherms, Wen-Hu Tsao, Ming-Te Liang

Journal of Marine Science and Technology–Taiwan

Ion transport through a hydrated cement system often becomes a principal factor to degrade concrete in a chlorideladen environments. Based on the transport mechanism of chloride ion, an analytical solution of mathematical model for predicting chloride penetration into concrete structures was herein derived. The model consists of both the diffusion of chloride due to concentration gradient and the convection of chloride due to moisture transport. The model also depends on temperature, age, relative humidity, and chloride binding. Based on both the diffusion coefficient and the mean velocity with time/depth dependence, an analytical solution of the mathematical model developed by previous …

Investigation On Intermittent Microwave-Assisted Extraction Of Sulfated Polysaccharides From Porphyra Dentata, Shao-Chi Wu, Yeu-Pyng Lin

Journal of Marine Science and Technology–Taiwan

This study investigated the intermittent microwave-assisted extraction (MAE) of sulfated polysaccharides from Porphyra (P.) dentata Kjellman, 1897. The experiment consisted of adjusting 10% to 90% ethanol solutions (v/v) used as extraction solvents, and then applied intermittent MAE to extract P. dentata solutions. These different extract solutions were then further evaluated for their sulfated polysaccharides contents (μg/mL). The optimal conditions of the sulfated polysaccharides content using intermittent MAE with 3, 4, and 5 cycle treatment were studied using response surface methodology. This study was performed using a three-level, threefactor design and aimed to determine the optimal combination of ethanol concentration (10~90%, …

The Montclarion, October 15, 2015, The Montclarion

The Montclarion

Student Newspaper of Montclair State University

Library Publishing Directory 2016, Library Publishing Coalition

Library Publishing Directory

No abstract provided.

Transforming Institutions: Undergraduate Stem Education For The 21st Century, Gabriela C. Weaver, Wilella D. Burgess, Amy L. Childress, Linda Slakey

Purdue University Press Books

Higher education is coming under increasing scrutiny, both publically and within academia, with respect to its ability to appropriately prepare students for the careers that will make them competitive in the 21^st-century workplace. At the same time, there is a growing awareness that many global issues will require creative and critical thinking deeply rooted in the technical STEM (science, technology, engineering, and mathematics) disciplines. However, the existing and ingrained structures of higher education, particularly in the STEM fields, are not set up to provide students with extensive skill development in communication, teamwork, and divergent thinking, which is needed …

A Quantitative And Qualitative Multi-Criteria Evaluating Approach To Identify Priority For Location Developing Multimodal Logistic Modes, Kuo-Liang Lee

Journal of Marine Science and Technology–Taiwan

The main purpose of this paper is to empirically study the selection for developing multimodal logistic mode (M-LM) locations in Taiwan using the quantitative and qualitative multicriteria decision-making approach. Multinational corporations in the logistics arena were surveyed to collect factors and the priorities for location development for each type of M-LM using the fuzzy multiple criteria Q-analysis (MCQA) approach. It is suggested that each location has different competitive elements that support different types of M-LM. The findings show proposed locations for developing M-LM in Taiwan.

Rainfall-Induced Slope Landslide Pontential And Landslide Distribution Characteristics Assessment, Yung-Sheng Chue, Jing-Wan Chen, Yie-Ruey Chen

Journal of Marine Science and Technology–Taiwan

According to observations over the few years before and after typhoon and extreme rainfall events in the Laonong catchment of Kaohsiung, Southern Taiwan, this study combined a genetic adaptive neural network architecture, image texture analysis, and a geographic information system (GIS) in satellite image interpretation and land use change analysis to obtain disaster records and surface information. A multivariate hazards evaluation method was applied to quantitatively analyze the weights of various natural environmental and slope development hazard factors. Furthermore, this study established a slope landslide potential assessment model and depicted a slope landslide potential diagram by using the GIS platform. …

Quantification Of Statistical Uncertainties In Performing The Peak Over Threshold Method, Yi Zhang, Yingyi Cao, Jian Dai

Journal of Marine Science and Technology–Taiwan

Peak over threshold (POT) method is frequently used in the modeling of extreme values in offshore engineering. In this paper, the POT method is examined in terms of epistemic uncertainties in practical usage. Real observed ocean data with specific considerations to extreme events are analyzed. In particular, the procedures including the use of de-clustering and threshold in POT method are addressed. A key element in the application of probability and statistical theories is the estimation of model parameters. The performance of these estimation methods is tested in the context of epistemic uncertainty. This is done through a numerical simulation study …

Analytical Model Of Ultrasonic Pulse Velocity Of Waste Lcd Glass Concrete, Chien-Chih Wang, Her-Yung Wang, Shyh-Haur Chen, Chi Huang

Journal of Marine Science and Technology–Taiwan

The purpose of this study is to establish a prediction model for the ultrasonic pulse velocity (UPV) of waste LCD glass concrete and then analyze the results obtained from a series of laboratory tests. The power function is used to perform the nonlinear-multivariate regression analysis of the UPV prediction model, with parameters such as water-binder ratio (w/b), curing age (t) and waste glass content (G). According to the relative regression analysis, the UPV prediction model is developed. The calculated results are in accord with the laboratory-measured data, which are the concrete UPV of various mix proportions. The regression analysis results …

Applying The Rasch Model To Construct The Shipping Industry Employability Indicators, Tzeu-Chen Han, Ti-Huei Li

Journal of Marine Science and Technology–Taiwan

In recent years, with the increase of the unemployment rate, employability has become a popular issue for different industries, as it can enhance the employment rate for industries and project industrial growth. This study examines shipping-related industries using the Rasch model, to construct scientific evaluation items in relation to the professional techniques and skills of the shipping-related industries. It further validates whether the generalized employability in the shipping-related industries is needed. Research findings are reorganized as employability indicators of the shipping-related industries. The findings are expected to serve as references for the shipping industry to evaluate new employees and for …

Vista: October 15, 2015, University Of San Diego

USD Vista (1965-)

No abstract provided.

Lanthorn, Vol. 50, No. 15, October 15, 2015, Grand Valley State University

Volume 50, July 13, 2015 - June 6, 2016

Lanthorn is Grand Valley State's student newspaper, published from 1968 to the present.

Bis(Spirolactam) 1,3-Double-Armed Calix[4]Arene Compounds And Their Application As Extractants For The Determination Of Heavy Metal Ions, Fintan Kelleher, Mary Deasy, James Ward, Li Li, Fiona Regan

Articles

A number of double-armed calix[4]arene compounds, with proline-derived spirolactam ligating groups on the lower rim, have been synthesised and investigated as extractants of toxic heavy metal ions from aqueous solution. Pedersen’s extraction technique was employed to determine the capability of these new 1,3-distal derived calix[4]arene spiroalactams to extract selected heavy metal ions (e.g. Pb²⁺, Cd²⁺, Zn²⁺, Cu²⁺, Ni²⁺, Co²⁺) from an aqueous phase into an organic phase. The percentage extraction was calculated using UV-vis spectroscopy. All of the compounds synthesised demonstrated good selectivity for the heavy metals selected …

7 Things To Know For The Week, Traci Bratton

Browse All News

No abstract provided.

Revival Or Revolution: U.S. Trust's Role In The Contracts Clause Circuit Split, Michael Cataldo

St. John's Law Review

(Excerpt)

This Note argues that U.S. Trust's Contracts Clause test created ambiguities that have spawned varying and conflicting approaches in the circuits. This Note also argues that U.S. Trust's failure to advance the Framers' original intent and departure from precedent has created the doctrinal disagreement that feeds the circuit split. Part I presents the history of the Contracts Clause from the Constitutional Convention up to the decision in U.S. Trust. Part II emphasizes the negative consequences of U.S. Trust's novel approach by detailing the varying approaches the circuits have taken in applying the ambiguous dual standards set out in …

A Collective Good: Disability Diversity As A Value In Public Sector Collective Bargaining Agreements, Carrie Griffin Basas

St. John's Law Review

(Excerpt)

Part I of this Article explains why disability is a helpful lens and reviews the theoretical underpinnings of the roles of contracts, such as CBAs, in setting workplace dynamics and generating "informal laws." Part II describes the methodology used in this study of CBAs. Part III is a taxonomy of the models of disability-framing and workplace dynamics that the CBAs reflect. Part IV presents a new framework for envisioning how the corrective, civil rights vision of the Idealist model might transform workplaces for all workers-marginalized or empowered, public or private-and, therefore, transform labor and employment law. In other words, …

Weekly News Digest 10/14/2015, Jenna Ray

Weekly Bulletin Archive

In This Issue:

● This Week Marks End of First-Half Term Classes

● Roger Rose Becomes Center for Small Towns Director

● Morris Is a Top Choice for American Indian Students

● Bjorklund ’09 Reflects on Early Days at Morris

An Azide-Functionalized Nitronyl Nitroxide Radical: Synthesis, Characterization And Staudinger-Bertozzi Ligation Reactivity, Stephanie M. Barbon, Pierangelo Gobbo, Wilson Luo, Jacquelyn T. Price, Mark C. Biesenger, Mark S. Workentin, Joe Gilroy

Chemistry Publications

An azide-functionalized nitronyl nitroxide was successfully synthesized and its reactivity towards the Staudinger-Bertozzi ligation was explored. While a model reaction in solution showed the conversion of the nitronyl nitroxide to an imino nitroxide radical, the same reaction at the interface of gold nanoparticles allowed for successful covalent incorporation of the nitronyl nitroxide radical onto the nanoparticles.

Research‐Driven Facilitation Of Systems Thinking With Computational Models In Life Sciences Education, Heather E. Bergan-Roller, Nicholas Galt, Tomáš Helikar, Joseph T. Dauer

Discipline-Based Education Research Group Speaker Series

Systems thinking, computational modeling, and simulating systems are examples of important skills stressed in life sciences education by Vision and Change. In response to these calls, we have designed a computational modeling and simulation‐driven intervention to supplement current instruction in the life sciences curriculum. As part of our pre‐intervention assessment we evaluated students on their systems thinking in the context of cellular respiration. For this assessment, we had students create conceptual models. We found that students with lecture instruction are able to recall more components associated with the cellular respiration process but are not better able to integrate these components …

Free Energies And Minimal States For Scalar Linear Viscoelasticity, Giovambattista Amendola, Mauro Fabrizio, John Murrough Golden

Articles

The concept of a minimal state was introduced in recent decades, based on earlier work by Noll. The property that a given quantity is a functional of the minimal state is of central interest in the present work. Using a standard representation of a free energy associated with a linear memory constitutive relation, a new condition, involving linear functionals, is derived which, if satisfied, ensures that the free energy is a functional of the minimal state. Using this result and recent work on constructing free energy functionals, it is shown that if the kernel of the rate of dissipation functional …

Topological Data Analysis For Discovery In Preclinical Spinal Cord Injury And Traumatic Brain Injury, Jessica L. Nielson, Jesse Paquette, Aiwen W. Liu, Cristian F. Guandique, C. Amy Tovar, Tomoo Inoue, Karen-Amanda Irvine, John C. Gensel, Jennifer Kloke, Tanya C. Petrossian, Pek Y. Lum, Gunnar E. Carlsson, Geoffrey T. Manley, Wise Young, Michael S. Beattie, Jacqueline C. Bresnahan, Adam R. Ferguson

Physiology Faculty Publications

Data-driven discovery in complex neurological disorders has potential to extract meaningful syndromic knowledge from large, heterogeneous data sets to enhance potential for precision medicine. Here we describe the application of topological data analysis (TDA) for data-driven discovery in preclinical traumatic brain injury (TBI) and spinal cord injury (SCI) data sets mined from the Visualized Syndromic Information and Outcomes for Neurotrauma-SCI (VISION-SCI) repository. Through direct visualization of inter-related histopathological, functional and health outcomes, TDA detected novel patterns across the syndromic network, uncovering interactions between SCI and co-occurring TBI, as well as detrimental drug effects in unpublished multicentre preclinical drug trial data …

Information Security Newsletter

Offices & Divisions: Division of Information Technology Services (Archived)

No abstract provided.

Volume 53, Number 9: October 14, 2015, University Of North Dakota

University Letter Archive

No abstract provided.

A Fast Algorithm For Simulating Multiphase Flows Through Periodic Geometries Of Arbitrary Shape, Gary R. Marple, Alex Barnett, Adrianna Gillman, Shravan Veerapaneni

Dartmouth Scholarship

This paper presents a new boundary integral equation (BIE) method for simulating particulate and mul- tiphase flows through periodic channels of arbitrary smooth shape in two dimensions. The authors consider a particular system—multiple vesicles suspended in a periodic channel of arbitrary shape—to describe the numerical method and test its performance. Rather than relying on the periodic Green’s function as classical BIE methods do, the method combines the free-space Green’s function with a small auxiliary basis, and imposes periodicity as an extra linear condition. As a result, we can exploit existing free-space solver libraries, quadratures, and fast algorithms, and handle a …

Invariant Characteristics Of Carcinogenesis., Simon Sherman, Nirosha Rathnayake, Tengiz Mdzinarishvili

Journal Articles: Eppley Institute

Carcinogenic modeling is aimed at mathematical descriptions of cancer development in aging. In this work, we assumed that a small fraction of individuals in the population is susceptible to cancer, while the rest of the population is resistant to cancer. For individuals susceptible to cancer we adopted methods of conditional survival analyses. We performed computational experiments using data on pancreatic, stomach, gallbladder, colon and rectum, liver, and esophagus cancers from the gastrointestinal system collected for men and women in the SEER registries during 1975-2009. In these experiments, we estimated the time period effects, the birth cohort effects, the age effects …

Management Options For Water-Repellent Soils In Australian Dryland Agriculture, M. M. Roper, S. L. Davies, P. S. Blackwell, D. J. M. Hall, D. Bakker, R. Jongepier, P. R. Ward

Natural Resources Research Articles

Water-repellent (‘non-wetting’) soils are a major constraint to agricultural production in southern and south-west Australia, affecting >10 Mha of arable sandy soils. The major symptom is dry patches of surface soil, even after substantial rainfall, directly affecting agricultural production through uneven crop and pasture germination, and reduced nutrient availability. In addition, staggered weed germination impedes effective weed control, and delayed crop and pasture germination increases the risk of wind erosion. Water repellency is caused by waxy organic compounds derived from the breakdown of organic matter mostly of plant origin. It is more prevalent in soils with a sandy surface texture; …

The Role Of Community Participation In Water Production And Management: Lessons From Sustainable Aid In Africa International Sponsored Water Schemes In Kisumu, Kenya, Erick Oniango Ananga

USF Tampa Graduate Theses and Dissertations

Few studies have attempted to determine the tenability of Community Participation (CP) theory is explicating Water Production and Management dynamics in Urban Informal Settlements. Consequently, several gaps exist in knowledge of the value of this important theory for efforts to improve water service delivery in such settlements. The main purpose of this study is to contribute to efforts addressed to filling these gaps. Four water schemes established by Sustainable Aid in Africa International in partnership with different communities in the informal neighborhoods of Kisumu Kenya are used as empirical referent. The study is guided by the following three Research Questions; …