Digital Commons Network^™

Neural Bases Of Phonological And Semantic Processing In Early Childhood, Avantika Mathur, Douglas H. Schultz, Yingying Wang Dr.

Center for Brain, Biology, and Behavior: Faculty Publications

During the early period of reading development, children gain phonological (letter-to-sound mapping) and semantic knowledge (storage and retrieval of word meaning). Their reading ability changes rapidly, accompanied by learning-induced brain plasticity as they learn to read. This study aims at identifying the neural bases of phonological and semantic processing in early childhood by using a combination of univariate and multivariate pattern analysis. Nineteen typically developing children between the age of five and seven performed visual word-level phonological (rhyming) and semantic (related meaning) judgment tasks during functional magnetic resonance imaging scans. Our multivariate analysis showed that young children with good reading …

Influence Of Conformational Restriction On The Antibacterial Activity And Ribosomal Selectivity Of Aminoglycoside Antibiotics, Michael Gabriel Pirrone

Wayne State University Dissertations

The ever-increasing threat posed by multidrug-resistant infectious bacteria necessitates

the development of novel antibiotics. Aminoglycoside antibiotics are growing in interest due to

their broad spectrum of activity, lack of known drug related allergies, low manufacturing cost,

and their well-studied mechanism of action. The simplification of rational drug design due to the

well-studied mechanism of action is the key to overcoming the issues presented by these drugs,

namely ototoxicity and nephrotoxicity.

A study of the effect of the conformation of the aminoglycoside ring I side chain is

described wherein it was discovered that an increase in a particular conformation augments the …

Semantic Segmentation Of Sorghum Using Hyperspectral Data Identifies Genetic Associations, Chenyong Miao, Alejandro Pages, Zheng Xu, Eric Rodene, Jinliang Yang, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

This study describes the evaluation of a range of approaches to semantic segmentation of hyperspectral images of sorghum plants, classifying each pixel as either nonplant or belonging to one of the three organ types (leaf, stalk, panicle). While many current methods for segmentation focus on separating plant pixels from background, organ-specific segmentation makes it feasible to measure a wider range of plant properties. Manually scored training data for a set of hyperspectral images collected from a sorghum association population was used to train and evaluate a set of supervised classification models. Many algorithms show acceptable accuracy for this classification task. …

Isoseq Transcriptome Assembly Of C3 Panicoid Grasses Provides Tools To Study Evolutionary Change In The Panicoideae, Daniel S. Carvalho, Aime V. Nishimwe, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses—Poaceae—have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C₄ photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C₃ panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and …

Oxidosqualene Cyclases Involved In The Biosynthesis Of Triterpenoids In Quercus Suber Cork, Lucas Busta, Olga Serra, Ok Tae Kim, Marisa Molinas, Irene Peré-Fossoul, Mercè Figueras, Reinhard Jetter

Center for Plant Science Innovation: Faculty Publications

Cork is a water-impermeable, suberin-based material harboring lignin, (hemi)cellulose, and extractable small molecules (primarily triterpenoids). Extractables strongly influence the properties of suberin-based materials. Though these previous findings suggest a key role for triterpenoids in cork material quality, directly testing this idea is hindered in part because it is not known which genes control cork triterpenoid biosynthesis. Here, we used gas chromatography and mass spectrometry to determine that the majority (>85%) of non-polar extractables from cork were pentacyclic triterpenoids, primarily betulinic acid, friedelin, and hydroxy-friedelin. In other plants, triterpenoids are generated by oxidosqualene cyclases (OSCs). Accordingly, we mined Quercus suber …

Plant Segmentation By Supervised Machine Learning Methods, Jason Adams, Yumou Qiu, Yuhang Xu, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping systems provide abundant data for statistical analysis through plant imaging. Before usable data can be obtained, image processing must take place. In this study, we used supervised learning methods to segment plants from the background in such images and compared them with commonly used thresholding methods. Because obtaining accurate training data is a major obstacle to using supervised learning methods for segmentation, a novel approach to producing accurate labels was developed. We demonstrated that, with careful selection of training data through such an approach, supervised learning methods, and neural networks in particular, can outperform thresholding methods at segmentation.

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil Kumar Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is referred to as phenotyping (Singh et al., 2016). While the use of phenotyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genetics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent of inexpensive genotyping …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS …

Methods And Compositions For Obtaining Useful Plant Traits, Sally Mackenzie, Michael Fromm, Kamaldeep Viridi, Yashitola Wamboldt

Center for Plant Science Innovation: Faculty Publications

The present invention provides methods for obtaining plants that exhibit useful traits by perturbation of plastid function in plant rootstocks and grafting the rootstocks to scions. Methods for identifying genetic loci that provide for useful traits in plants and plants produced with those loci are also provided. In addition, plants that exhibit the useful traits, parts of the plants including seeds, and products of the plants are provided as well as methods of using the plants. Recombinant DNA vectors and transgenic plants comprising those vectors that provide for plastid perturbation are also provided.

Interspecific Analysis Of Diurnal Gene Regulation In Panicoid Grasses Identifies Known And Novel Regulatory Motifs, Xianjun Lai, Claire Bendix, Lang Yan, Yang Zhang, James C. Schnable, Frank G. Harmon

Center for Plant Science Innovation: Faculty Publications

Background: The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum.

Results: Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in …

Voxel Carving-Based 3d Reconstruction Of Sorghum Identifies Genetic Determinants Of Light Interception Efficiency, Mathieu Gaillard, Chenyong Miao, James C. Schnable, Bedrich Benes

Center for Plant Science Innovation: Faculty Publications

Changes in canopy architecture traits have been shown to contribute to yield in- creases. Optimizing both light interception and light interception efficiency of agri- cultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identifi- cation logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving …

Compounds For Increasing Lipid Synthesis And Storage, Concetta Dirusso, Nishikant Wase

Center for Plant Science Innovation: Faculty Publications

This invention relates to methods for increasing lipid accumulation and lipid production in cells. Methods of producing biofuel from cells and preparing nutraceuticals comprising lipids produced according to a method provided herein are also provided.

Non-Homology-Based Prediction Of Gene Functions In Maize (Zea Mays Ssp. Mays), Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C. Schnable, Pinghua Li

Center for Plant Science Innovation: Faculty Publications

Advances in genome sequencing and annotation have eased the difficulty of identifying new gene sequences. Predicting the functions of these newly identified genes remains challenging. Genes descended from a common ancestral sequence are likely to have common functions. As a result, homology is widely used for gene function pre- diction. This means functional annotation errors also propagate from one species to another. Several approaches based on machine learning classification algorithms were evaluated for their ability to accurately predict gene function from non-homology gene features. Among the eight supervised classification algorithms evaluated, random- forest-based prediction consistently provided the most accurate gene …

A High-Throughput Phenotyping Pipeline For Image Processing And Functional Growth Curve Analysis, Ronghao Wang, Yumuo Qiu, Yuzhen Zhou, Zhikai Liang, James Schnable

Center for Plant Science Innovation: Faculty Publications

High-throughput phenotyping system has become more and more popular in plant science research. The data analysis for such a system typically involves two steps: plant feature extraction through image processing and statistical analysis for the extracted features. The current approach is to perform those two steps on different platforms. We develop the package “implant” in R for both robust feature extraction and functional data analysis. For image processing, the “implant” package provides methods including thresholding, hidden Markov random field model, and morphological operations. For statistical analysis, this package can produce nonparametric curve fitting with its confidence region for plant growth. …

Leaf Angle Extractor: A High-Throughput Image Processing Framework For Leaf Angle Measurements In Maize And Sorghum, Sunil Kumar Kenchanmane Raju, Miles Adkins, Alex Enersen, Daniel Santana De Carvalho, Anthony J. Studer, Baskar Ganapathysubramanian, Patrick Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

PREMISE: Maize yields have significantly increased over the past half-century owing to advances in breeding and agronomic practices. Plants have been grown in increasingly higher densities due to changes in plant architecture resulting in plants with more upright leaves, which allows more efficient light interception for photosynthesis. Natural variation for leaf angle has been identified in maize and sorghum using multiple mapping populations. However, conventional phenotyping techniques for leaf angle are low throughput and labor intensive, and therefore hinder a mechanistic understanding of how the leaf angle of individual leaves changes over time in response to the environment.

METHODS: High-throughput …

Advances In Plant Phenomics: From Data And Algorithms To Biological Insights, Sunil K. Kenchanmane Raju, Addie M. Thompson, James Schnable

Center for Plant Science Innovation: Faculty Publications

The measurement of the characteristics of living organisms is re- ferred to as phenotyping (Singh et al., 2016). While the use of phe- notyping in plant biology and genetics can be traced back at least to Gregor Mendel sorting and counting peas by shape and pod color 160 years ago, addressing current questions in plant biology, genet- ics, and breeding often requires increasingly precise phenotyping of a wide range of traits. Accurate phenotyping has played a role in both novel discoveries about the fundamental biology of plants and the development of improved crop varieties around the world. With the advent …

Metabolic Profiles Of Six African Cultivars Of Cassava (Manihot Esculenta Crantz) Highlight Bottlenecks Of Root Yield, Toshihiro Obata, Patrick A.W. Klemens, Laise Rosado-Souza, Armin Schlereth, Andreas Gisel, Livia Stavolone, Wolfgang Zierer, Nicolas Morales, Lukas A. Mueller, Samuel C. Zeeman, Frank Ludewig, Mark State, Uwe Sonnewald, H. Ekkehard Neuhaus, Alisdair R. Femie

Center for Plant Science Innovation: Faculty Publications

Cassava is an important staple crop in sub-Saharan Africa, due to its high productivity even on nutrient poor soils. The metabolic characteristics underlying this high productivity are poorly understood including the mode of photosynthesis, reasons for the high rate of photosynthesis, the extent of source/sink limitation, the impact of environment, and the extent of variation between cultivars. Six commercial African cassava cultivars were grown in a greenhouse in Erlangen, Germany, and in the field in Ibadan, Nigeria. Source leaves, sink leaves, stems and storage roots were harvested during storage root bulking and analyzed for sugars, organic acids, amino acids, phosphorylated …

Increased Power And Accuracy Of Causal Locus Identification In Time Series Genome-Wide Association In Sorghum1[Open], Chenyong Miao, Yuhang Xu, Sanzhen Liu, Patrick S. Schnable, James C. Schnable

Center for Plant Science Innovation: Faculty Publications

The phenotypes of plants develop over time and change in response to the environment. New engineering and computer vision technologies track these phenotypic changes. Identifying the genetic loci regulating differences in the pattern of phenotypic change remains challenging. This study used functional principal component analysis (FPCA) to achieve this aim. Time series phenotype data were collected from a sorghum (Sorghum bicolor) diversity panel using a number of technologies including conventional color photography and hyperspectral imaging. This imaging lasted for 37 d and centered on reproductive transition. A new higher density marker set was generated for the same population. Several genes …

Rab39 And Klp98a Are Required For Furrow Formation During Early Drosophila Embryogenesis, Megan R. Millage

Electronic Theses and Dissertations

The formation of a plasma membrane furrow is an essential process during development. Furrow formation is necessary for successful cell division and cytokinesis in addition to the ability to create multicellular tissues. Here, I will explore the role of the Golgi-associated Rab protein Rab39 in furrow formation during early Drosophila embryogenesis. Rab39 is one of eight Rab proteins that has been shown to localize to discrete puncta by live imaging in early Drosophila embryos, but its function and pathway have not been well characterized. In this thesis will I show that Rab39 forms dynamic, tubular structures that colocalize with trans-Golgi …

Single Mothers Empowerment: A Program For Increasing Income For Single Mothers In Rwanda, Francine Ngoga Nduwayo

Regis University Student Publications (comprehensive collection)

In Rwanda, 47% of pregnancies are unintended every year (Basinga et al., 2012). These pregnancies lead to problems such as children growing without fathers, single mothers, girls dropping out of school, stigmatisation in the community and consequently a cycle of poverty. My literature review revealed that single mothers become mothers in their teen years, while they are exercising experimental sex. In many cases, their partners are children themselves which might explain their lack of involvement in the child’s life. However, there are other cases where girls and women are raped or involved in transactional sex for survival. I conducted a …

Early Conservation Benefits Of A De Facto Marine Protected Area At San Clemente Island, California, Michael W. Esgro, James Lindholm, Kerry J. Nickols, Jessica Bredvik

Marine Science Faculty Publications and Presentations

De facto marine protected areas (DFMPAs) are regions of the ocean where human activity is restricted for reasons other than conservation. Although DFMPAs are widespread globally, their potential role in the protection of marine habitats, species, and ecosystems has not been well studied. In 2012 and 2013, we conducted remotely operated vehicle (ROV) surveys of marine communities at a military DFMPA closed to all civilian access since 2010 and an adjacent fished reference site at San Clemente Island, the southernmost of California’s Channel Islands. We used data extracted from ROV imagery to compare density and biomass of focal species, as …

A Tutorial Of Bland Altman Analysis In A Bayesian Framework, Krissina M. Alari, Steven B. Kim, Jeffrey O. Wand

Mathematics and Statistics Faculty Publications and Presentations

There are two schools of thought in statistical analysis, frequentist, and Bayesian. Though the two approaches produce similar estimations and predictions in large-sample studies, their interpretations are different. Bland Altman analysis is a statistical method that is widely used for comparing two methods of measurement. It was originally proposed under a frequentist framework, and it has not been used under a Bayesian framework despite the growing popularity of Bayesian analysis. It seems that the mathematical and computational complexity narrows access to Bayesian Bland Altman analysis. In this article, we provide a tutorial of Bayesian Bland Altman analysis. One approach we …

Using Strontium Coated Clay Nanoparticles For Bone Regeneration And Other Biomedical Applications, Anusha Elumalai

Doctoral Dissertations

The aim of this project is to coat halloysite nanotubes (HNTs) with strontium in an ecofriendly, simple, and non-expensive process. These particles, when doped in calcium phosphate cements (CPC), are predicted to increase the osteoconductive and antibacterial properties of three dimensional (3D) printed bone scaffolds.

The purpose of the 3D printed bone scaffolds is to assume the same function as the bones they are replacing but with several additional functionalities. These biomaterials will have the ability to be resorbed as new bone is formed. Due to inherent osteogenic factors and antibiotics released from doped HNTs during the reparative process, it …

Meat Consumption, Cooking Practices, And Blood Harmane Concentrations In Essential Tremor: A Population-Based, Environmental Study In The Faroe Islands, Monica Ferrer Socorro

Yale Medicine Thesis Digital Library

Background: Essential tremor (ET) is among the most prevalent neurological disease, yet potential modifiable environmental factors contributing to its etiology are poorly understood. Harmane [1-methyl-9H-pyrido(3,4-b)indole], is a potent neurotoxin, of which elevated levels may be linked to ET. Possible etiologies for this elevation include increased dietary consumption, impaired metabolism, or increased endogenous production. Harmane is particularly abundant in meats and long cooking times can increase its concentrations. One previous study provided preliminary data of a dietary difference between male ET cases and controls. To clarify the relationship between ET and harmane we conducted a population-based, case-control study, in the Faroe …

Using Climate To Explain And Predict West Nile Virus Risk In Nebraska, Kelly Smith, Andrew Tyre, Jeff Hamik, Michael Hayes, Yuzhen Zhou, Li Dai

National Drought Mitigation Center: Faculty Publications

We used monthly precipitation and temperature data to give early warning of years with higher West Nile Virus (WNV) risk in Nebraska. We used generalized additive models with a negative binomial distribution and smoothing curves to identify combinations of extremes and timing that had the most influence, experimenting with all combinations of temperature and drought data, lagged by 12, 18, 24, 30, and 36 months. We fit models on data from 2002 through 2011, used Akaike's Information Criterion (AIC) to select the best‐fitting model, and used 2012 as out‐of‐sample data for prediction, and repeated this process for each successive year, …

The Feeding Pattern Of C57bl/6j Mice, Yakshkumar Dilipbhai Rathod

Browse all Theses and Dissertations

The feeding pattern and control of energy intake in social mice are poorly understood. Here, we determined and quantify the normal nocturnal feeding pattern of group-housed male and female mice of the C57BL/6J genetic background fed a chow diet. Mice at 10 and 20weeks of age showed the expected age-dependent increase in lean and fat mass being them more pronounced in males. Under ad libitum conditions, male and female mice ate comparable amounts of food per unit of body weight irrespective of gender. The analysis of the feeding microstructure revealed that energy intake in females is the result of significantly …

Recommendations On Alaskan Arctic Coast Port Access Route Study

United States Marine Mammal Commission

No abstract provided.

Maker Fridays: Engaging Rural And Underrepresented High School Students In Pre-Engineering Design And Creativity, Michelle Howell-Smith, Kirstie Bash

Nebraska Center for Research on Children, Youth, Families, and Schools: Faculty Publications

The engineering field struggles to develop sufficient interest and sustained participation across underrepresented demographic groups including women and individuals from rural, Hispanic, or Native American origin. It is critical to foster interest in engineering during formative years when students are deciding career paths. Northeast Community College (Northeast) addressed the shortage of diverse students entering into engineering fields by developing a course to engage rural and underrepresented high school students in maker design and creativity and to determine best practices that attract and retain these students. The Maker Fridays pre-engineering course was part of the Fridays@Northeast program that targets high school …

01 Guide To Student Work In Fire And Ice, Christopher F. Bauer

Student Work Products

WELCOME to WINDOWS on the INQUIRY CLASSROOM!

You have landed on a piece of a National Science Foundation Project (DUE 1245730) directed by Professor Chris Bauer, Chemistry Department, University of New Hampshire. This is one part of a completely documented inquiry-based university science course called “Fire & Ice” which explores the nature of heat and temperature. There are multiple video perspectives and commentary from instructors and students, and documents of all course materials (agenda, instructions, student work). It’s too complicated to explain here. Take a look at the user orientation document at this link.

Syllabus, Christopher F. Bauer

Structure

WELCOME to WINDOWS on the INQUIRY CLASSROOM!

You have landed on a piece of a National Science Foundation Project (DUE 1245730) directed by Professor Chris Bauer, Chemistry Department, University of New Hampshire. This is one part of a completely documented inquiry-based university science course called “Fire & Ice” which explores the nature of heat and temperature. There are multiple video perspectives and commentary from instructors and students, and documents of all course materials (agenda, instructions, student work). It’s too complicated to explain here. Take a look at the user orientation document at this link.