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Iowa State University

Selected Works

2014

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Articles 1 - 15 of 15

Full-Text Articles in Physical Sciences and Mathematics

The North American Carbon Program Multi-Scale Synthesis And Terrestrial Model Intercomparison Project – Part 2: Environmental Driver Data, Y. Wei, S. Liu, D. N. Huntzinger, A. M. Michalak, N. Viovy, W. M. Post, C. R. Schwalm, K. Schaefer, A. R. Jacobson, Chaoqun (Crystal) Lu, Hanqin Tian, D. M. Ricciuto, R. B. Cook, J. Mao, X. Shi Dec 2014

The North American Carbon Program Multi-Scale Synthesis And Terrestrial Model Intercomparison Project – Part 2: Environmental Driver Data, Y. Wei, S. Liu, D. N. Huntzinger, A. M. Michalak, N. Viovy, W. M. Post, C. R. Schwalm, K. Schaefer, A. R. Jacobson, Chaoqun (Crystal) Lu, Hanqin Tian, D. M. Ricciuto, R. B. Cook, J. Mao, X. Shi

Chaoqun (Crystal) Lu

Ecosystems are important and dynamic components of the global carbon cycle, and terrestrial biospheric models (TBMs) are crucial tools in further understanding of how terrestrial carbon is stored and exchanged with the atmosphere across a variety of spatial and temporal scales. Improving TBM skills, and quantifying and reducing their estimation uncertainties, pose significant challenges. The Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal multi-scale and multi-model intercomparison effort set up to tackle these challenges. The MsTMIP protocol prescribes standardized environmental driver data that are shared among model teams to facilitate model–model and model–observation comparisons. This paper describes …

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Differential Effects Of Canopy Trimming And Litter Deposition On Litterfall And Nutrient Dynamics In A Wet Subtropical Forest, Steven J. Hall, Whendee L. Silver, Grizelle González Nov 2014

Differential Effects Of Canopy Trimming And Litter Deposition On Litterfall And Nutrient Dynamics In A Wet Subtropical Forest, Steven J. Hall, Whendee L. Silver, Grizelle González

Steven J. Hall

Humid tropical forests have the highest rates of litterfall production globally, which fuels rapid nutrient recycling and high net ecosystem production. Severe storm events significantly alter patterns in litterfall mass and nutrient dynamics through a combination of canopy disturbance and litter deposition. In this study, we used a large-scale long-term manipulation experiment to explore the separate and combined effects of canopy trimming and litter deposition on litterfall rates and litter nutrient concentrations and content. The deposition of fine litter associated with the treatments was equivalent to more than two times the annual fine litterfall mass and nutrient content in control …

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Complex Spatiotemporal Responses Of Global Terrestrial Primary Production To Climate Change And Increasing Atmospheric Co2 In The 21st Century, Shufen Pan, Hanqin Tian, Shree R. S. Dangal, Chi Zhang, Jia Yang, Bo Tao, Zhiyun Ouyang, Xiaoke Wang, Chaoqun (Crystal) Lu, Wei Ren, Kamaljit Banger, Qichun Yang, Bowen Zhang, Xia Li Nov 2014

Complex Spatiotemporal Responses Of Global Terrestrial Primary Production To Climate Change And Increasing Atmospheric Co2 In The 21st Century, Shufen Pan, Hanqin Tian, Shree R. S. Dangal, Chi Zhang, Jia Yang, Bo Tao, Zhiyun Ouyang, Xiaoke Wang, Chaoqun (Crystal) Lu, Wei Ren, Kamaljit Banger, Qichun Yang, Bowen Zhang, Xia Li

Chaoqun (Crystal) Lu

Quantitative information on the response of global terrestrial net primary production (NPP) to climate change and increasing atmospheric CO2 is essential for climate change adaptation and mitigation in the 21st century. Using a process-based ecosystem model (the Dynamic Land Ecosystem Model, DLEM), we quantified the magnitude and spatiotemporal variations of contemporary (2000s) global NPP, and projected its potential responses to climate and CO2 changes in the 21st century under the Special Report on Emission Scenarios (SRES) A2 and B1 of Intergovernmental Panel on Climate Change (IPCC). We estimated a global terrestrial NPP of 54.6 (52.8–56.4) PgC yr−1 as a result …

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The Historical Role Of Base Maps In Soil Geography, Bradley A. Miller, R. J. Schaetzl Oct 2014

The Historical Role Of Base Maps In Soil Geography, Bradley A. Miller, R. J. Schaetzl

Bradley A Miller

Soil mapping is a major goal of soil science. Soil maps rely upon accurate base maps, both for positional reference and to provide environmental data that can assist in the prediction of soil properties. This paper reviews the historical development of base maps used for soil mapping, and evaluates the dependence of soil mapping on base maps. The availability of geographic technology for producing base maps has both constrained and directed the geographic study of soil. The lack of accurate methods for determining location limited early geographic descriptions of soils to narratives, or to listings of attributes for property-based map …

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Outage Constrained Robust Secure Transmission For Miso Wiretap Channels, Shuai Ma, Mingyi Hong, Engin Song, Xiangfeng Wang, Dechun Sun Oct 2014

Outage Constrained Robust Secure Transmission For Miso Wiretap Channels, Shuai Ma, Mingyi Hong, Engin Song, Xiangfeng Wang, Dechun Sun

Mingyi Hong

In this paper, we consider the robust secure beam-former design for multiple-input-single-output wiretap channels. Assuming that the eavesdroppers' channels are only partially available at the transmitter, we seek to maximize the secrecy rate under the transmit power and the secrecy rate outage probability constraint. The outage probability constraint requires that the secrecy rate exceed certain thresholds with high probability. Therefore, including such constraint in the design naturally ensures the desired robustness. Unfortunately, the presence of the probabilistic constraints makes the problem nonconvex and, hence, difficult to solve. In this paper, we investigate the outage probability constrained secrecy rate maximization problem …

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These Are Not The K-Mers You Are Looking For: Efficient Online K-Mer Counting Using A Probabilistic Data Structure, Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown Jul 2014

These Are Not The K-Mers You Are Looking For: Efficient Online K-Mer Counting Using A Probabilistic Data Structure, Qingpeng Zhang, Jason Pell, Rosangela Canino-Koning, Adina Chuang Howe, C. Titus Brown

Adina Howe

K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for fast and memory efficient online counting of k-mers in sequencing data sets. Unlike previous methods based on data structures such as hash tables, suffix arrays, and trie structures, khmer relies entirely on a simple probabilistic data structure, a Count-Min Sketch. The Count-Min Sketch permits online updating and retrieval of k-mer counts in memory which is necessary to support online k-mer analysis algorithms. On sparse data sets this …

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Evaluation Of Trophic Niche Overlap Between Native Fishes And Young-Of-The-Year Common Carp, Michael J. Weber, Jessica M. Howell, Michael L. Rown Jul 2014

Evaluation Of Trophic Niche Overlap Between Native Fishes And Young-Of-The-Year Common Carp, Michael J. Weber, Jessica M. Howell, Michael L. Rown

Michael J Weber Dr

Common carp Cyprinus carpio is a ubiquitous invasive species that commonly imposes negative effects on aquatic ecosystems. However, research evaluating the effects of carp on native fishes is limited. Carp are highly fecund and larvae and juveniles can be abundant. If age-0 carp use similar prey resources as native fishes, they may compete if food becomes limited. We used traditional diet analysis for samples during Jul. and Aug. 2008 in Brant Lake. Stable sotopes were used for samples collected during Aug. and Sep. 2009 in Brant Lake and Lake Sinai to examine prey resource use by age-0 carp and four …

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Impact Of Large-Scale Climate Extremes On Biospheric Carbon Fluxes: An Intercomparison Based On Mstmip Data, Jakov Zscheischler, Anna M. Michalak, Christopher Schwalm, Miguel D. Mahecha, Deborah N. Huntzinger, Markus Reichstein, Gwenaëlle Berthier, Philippe Ciais, Robert B. Cook, Bassil El-Masri, Maoyi Huang, Akihiko Ito, Atul Jain, Anthony King, Huimin Lei, Chaoqun (Crystal) Lu, Jiafu Mao, Shushi Peng, Benjamin Poulter, Daniel Ricciuto, Xiaoying Shi, Bo Tao, Hanqin Tian, Nicolas Viovy, Weile Wang, Yaxing Wei, Jia Yang, Ning Zeng Jun 2014

Impact Of Large-Scale Climate Extremes On Biospheric Carbon Fluxes: An Intercomparison Based On Mstmip Data, Jakov Zscheischler, Anna M. Michalak, Christopher Schwalm, Miguel D. Mahecha, Deborah N. Huntzinger, Markus Reichstein, Gwenaëlle Berthier, Philippe Ciais, Robert B. Cook, Bassil El-Masri, Maoyi Huang, Akihiko Ito, Atul Jain, Anthony King, Huimin Lei, Chaoqun (Crystal) Lu, Jiafu Mao, Shushi Peng, Benjamin Poulter, Daniel Ricciuto, Xiaoying Shi, Bo Tao, Hanqin Tian, Nicolas Viovy, Weile Wang, Yaxing Wei, Jia Yang, Ning Zeng

Chaoqun (Crystal) Lu

Understanding the role of climate extremes and their impact on the carbon (C) cycle is increasingly a focus of Earth system science. Climate extremes such as droughts, heat waves, or heavy precipitation events can cause substantial changes in terrestrial C fluxes. On the other hand, extreme changes in C fluxes are often, but not always, driven by extreme climate conditions. Here we present an analysis of how extremes in temperature and precipitation, and extreme changes in terrestrial C fluxes are related to each other in 10 state-of-the-art terrestrial carbon models, all driven by the same climate forcing. We use model …

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Influence Of Environment On The Measurement Of Rates Of Charge Transport Across Agts/Sam//Ga2o3/Egain Junctions, Jabulani R. Barber, Hyo Jae Yoon, Carleen M. Bowers, Martin M. Thuo, Benjamin Breiten, Diana M. Gooding, George M. Whitesides Jun 2014

Influence Of Environment On The Measurement Of Rates Of Charge Transport Across Agts/Sam//Ga2o3/Egain Junctions, Jabulani R. Barber, Hyo Jae Yoon, Carleen M. Bowers, Martin M. Thuo, Benjamin Breiten, Diana M. Gooding, George M. Whitesides

Martin M. Thuo

This paper investigates the influence of the atmosphere used in the fabrication of top electrodes from the liquid eutectic of gallium and indium (EGaIn) (the so-called “EGaIn” electrodes), and in measurements of current density, J(V) (A/cm2), across self-assembled monolayers (SAMs) incorporated into Ag/SR//Ga2O3/EGaIn junctions, on values of J(V) obtained using these electrodes. A gas-tight measurement chamber was used to control the atmosphere in which the electrodes were formed, and also to control the environment in which the electrodes were used to measure current densities across SAM-based junctions. Seven different atmospheres—air, oxygen, nitrogen, argon, and ammonia, as well as air containing …

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Fabrication Of Low-Cost Paper-Based Microfluidic Devices By Embossing Or Cut-And-Stack Methods, Martin M. Thuo, Ramses V. Martinez, Wen-Jie Lan, Xinyu Liu, Jabulani Barber, Manza B. Atkinson, Dineth Bandarage, Jean-Francis Bloch, George M. Whitesides Jun 2014

Fabrication Of Low-Cost Paper-Based Microfluidic Devices By Embossing Or Cut-And-Stack Methods, Martin M. Thuo, Ramses V. Martinez, Wen-Jie Lan, Xinyu Liu, Jabulani Barber, Manza B. Atkinson, Dineth Bandarage, Jean-Francis Bloch, George M. Whitesides

Martin M. Thuo

This article describes the use of embossing and “cut-and-stack” methods of assembly, to generate microfluidic devices from omniphobic paper and demonstrates that fluid flowing through these devices behaves similarly to fluid in an open-channel microfluidic device. The porosity of the paper to gases allows processes not possible in devices made using PDMS or other nonporous materials. Droplet generators and phase separators, for example, could be made by embossing “T”-shaped channels on paper. Vertical stacking of embossed or cut layers of omniphobic paper generated three-dimensional systems of microchannels. The gas permeability of the paper allowed fluid in the microchannel to contact …

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Climate And Land Use Controls On Soil Organic Carbon In The Loess Plateau Region Of China, Yaai Dang, Wei Ren, Bo Tao, Guangsheng Chen, Chaoqun (Crystal) Lu, Jia Yang, Shufen Pan, Guodong Wang, Shiqing Li, Hanqin Tian May 2014

Climate And Land Use Controls On Soil Organic Carbon In The Loess Plateau Region Of China, Yaai Dang, Wei Ren, Bo Tao, Guangsheng Chen, Chaoqun (Crystal) Lu, Jia Yang, Shufen Pan, Guodong Wang, Shiqing Li, Hanqin Tian

Chaoqun (Crystal) Lu

The Loess Plateau of China has the highest soil erosion rate in the world where billion tons of soil is annually washed into Yellow River. In recent decades this region has experienced significant climate change and policy-driven land conversion. However, it has not yet been well investigated how these changes in climate and land use have affected soil organic carbon (SOC) storage on the Loess Plateau. By using the Dynamic Land Ecosystem Model (DLEM), we quantified the effects of climate and land use on SOC storage on the Loess Plateau in the context of multiple environmental factors during the period …

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Revealing The Bacterial Butyrate Synthesis Pathways By Analyzing (Meta)Genomic Data, Marius Vital, Adina Chuang Howe, James M. Tiedje Apr 2014

Revealing The Bacterial Butyrate Synthesis Pathways By Analyzing (Meta)Genomic Data, Marius Vital, Adina Chuang Howe, James M. Tiedje

Adina Howe

Butyrate-producing bacteria have recently gained attention, since they are important for a healthy colon and when altered contribute to emerging diseases, such as ulcerative colitis and type II diabetes. This guild is polyphyletic and cannot be accurately detected by 16S rRNA gene sequencing. Consequently, approaches targeting the terminal genes of the main butyrate-producing pathway have been developed. However, since additional pathways exist and alternative, newly recognized enzymes catalyzing the terminal reaction have been described, previous investigations are often incomplete. We undertook a broad analysis of butyrate-producing pathways and individual genes by screening 3,184 sequenced bacterial genomes from the Integrated Microbial …

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Tuning The Selectivity Of Ionic Liquid Stationary Phases For Enhanced Separation Of Nonpolar Analytes In Kerosene Using Multidimensional Gas Chromatography, Leandro W. Hantao, Ali Najafi, Cheng Zhang, Fabio Augusto, Jared L. Anderson Mar 2014

Tuning The Selectivity Of Ionic Liquid Stationary Phases For Enhanced Separation Of Nonpolar Analytes In Kerosene Using Multidimensional Gas Chromatography, Leandro W. Hantao, Ali Najafi, Cheng Zhang, Fabio Augusto, Jared L. Anderson

Jared L. Anderson

In this study, a series of ionic liquids (ILs) are evaluated as stationary phases in comprehensive two-dimensional gas chromatography (GC × GC) for the separation of aliphatic hydrocarbons from kerosene. IL-based stationary phases were carefully designed to evaluate the role of cavity formation/dispersive interaction on the chromatographic retention of nonpolar analytes by GC × GC. The maximum allowable operating temperature (MAOT) of the IL-based columns was compared to that of commercial IL-based columns. Evaluation of the solvation characteristics of GC columns guided the selection of the best performing IL-based stationary phases for the resolution of aliphatic hydrocarbons, namely, trihexyl(tetradecyl)phosphonium tetrachloroferrate …

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Semantic Calibration Of Digital Terrain Analysis Scale, Bradley A. Miller Feb 2014

Semantic Calibration Of Digital Terrain Analysis Scale, Bradley A. Miller

Bradley A Miller

Digital terrain analysis (DTA) provides efficient, repeatable, and quantified metrics of landscape characteristics that are important to the Earth sciences, particularly for detailed soil mapping applications. However, DTA has not been field tested to the extent that traditional field metrics of topography have been. Human assessment of topography synthesizes multiple parameters at multiple scales to characterize a landscape, based on field experience. In order to capture the analysis scale used by field scientists, this study introduces a method for calibrating the analysis scale of DTA to field assessments. This method is used to calibrate land-surface derivatives of relative elevation, profile …

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A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore Jan 2014

A Nmr Experiment For Simultaneous Correlations Of Valine And Leucine/Isoleucine Methyls With Carbonyl Chemical Shifts In Proteins, Vitali Tugarinov, Vincenzo Venditti, G. Marius Clore

Vincenzo Venditti

A methyl-detected ‘out-and-back’ NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ileδ1, Leuδ and Valγ (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of 13Cα, 13Cβ and 13CO are known from prior NMR studies and where some losses in …

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