Life Sciences Commons^™

Models Of Pasture Production To Aid On-Farm Decision Making In New Zealand, J A. Baars, M D. Rollo

IGC Proceedings (1993-2023)

Two microcomputer-based predictive pasture models, for use in decision making by agricultural consultants and industry, are described. The first model (GRASS) was developed to understand the interactions between environment and management. The second model supplies pasture growth rates for current or predicted weather conditions by adjustment of stored actual average fortnightly pasture growth rates for a wide range of measurement sites. Ways are described in which the models are being used in transfer of technology.

Micro-Computer Version Of The Database On Feed Commodities Derived From Pastures And Green Crops, H T. Ostrowski-Meissner

IGC Proceedings (1993-2023)

The subunit of the national feed database devoted specifically to feeds derived from grasslands and green crops is presented. This collection of chemical and nutritional data is the result of 20 years of data collection from analyses conducted from 62 laboratories Australia-wide, The data entries are classified according to each Australian state and laboratory which provided the analytical and nutritional characteristics of fodder. Each entry is classified according to the International Feed Numbering (IFN) system as maintained by the International Network of Feed Information Centres (INFIC), The data in the collection as presented in the paper are an integral part …

Plant List Of Accepted Nomenclature, Taxonomy And Symbols, J S. Peterson

IGC Proceedings (1993-2023)

The Plant List of Accepted Nomenclature, Taxonomy & Symbols (PLANTS) is a dynamic database providing scientific and vernacular names, distributional, growth form, origin, symbols and bibliographic standardised botanical data to US federal agencies. PLANTS encompasses the vascular plant, moss, lichen and liverwort flora of North America, north of the Mexico border, including US states and territories.

The Development Of A Web-Based Tool To Facilitate Epidemiological Research In Toxoplasma Gondii, Gabrielle N. Russell

Masters Theses

The apicomplexan parasite Toxoplasma gondii (T. gondii) is a global zoonotic pathogen that endangers animals and humans alike. In the past two decades, genetic tools have been used to identify thousands of T. gondii samples from a variety of hosts, providing a grand view of its population structure. However, the detailed genotyping data are scattered in literature, making it difficult to grasp the full picture. From polymorphic virulence factors to still poorly understood host pathogen relationships, there are many things to be gained from knowing the genotype distribution of T. gondii. There are many static maps presenting …

The Plants Database: Providing Basic Plant Information, J S. Peterson, J F. Henson, W Oaks, J T. Kartesz

IGC Proceedings (1993-2023)

The PLANTS database provides basic plant information to the United States Department of Agriculture (USDA), Natural Resources Conservation Service (NRCS), its clients, cooperators, and the general public via the World Wide Web (Fig. 1). The foundation of PLANTS is a taxonomic backbone (checklist) of the vascular and nonvascular plants of North America (north of Mexico) and United States territories in the Caribbean and Pacific regions. Attribute data are appended to this backbone pertaining to distribution, vegetative specifications, nativity, federal and state status, crop data, growth form, growth parameters, species abstracts, and images.

Forage Data Hub – A Platform For Sharing Valuable Datasets For Resilience, Amanda J. Ashworth, L. Marshall, J. J. Volenec, M. Berti, E. Van Santen, C. Williams, V. Gopakumar, J. Foster, V. Picasso, J. Su

IGC Proceedings (1993-2023)

In accord with the necessity to enhance ecosystem services and productivity in food systems, is the increase of data availability at multiple scales and over time. To help meet this need, we discuss the development of a National Forage Data Hub which will act as a platform to curate, share, and analyze data pertaining to forage systems. This centralized hub will leverage existing datasets by bridging multiple sources including forage crop—soil, water, and nutrient availability—yield (animal and crop) potential (and gaps)— climate—management systems at high spatial and temporal resolution enabling system interaction assessments through next-generation analytics. This novel approach to …

Creation Of A Digital Storage System For Genome Sequencing Metadata, Jacquelin W. Olexa

Undergraduate Theses, Professional Papers, and Capstone Artifacts

As the field of computational genomics continues to expand in both potential and application, it is now more imperative than ever to ensure that massive genetic sequencing datasets are properly stored in an accessible manner. This project sought to establish a practical, user-friendly, secure system for a genomics research lab (the Good Lab; thegoodlab.org) at the University of Montana. A MySQL database and connected web application was ruled the best configuration to maximize utility and accessibility for the lab’s researchers. Building the logical framework for the database, creating the server, and sourcing data occurred over several months. The dataset ranged …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

Compilation Of A Database Of Research Information On Legume Based Grazing Systems; A Part Of The Leggraze Research Project, J. J. Rochon, G. Molle, A. Hopkins, J. M. Greef

IGC Proceedings (1993-2023)

The establishment of a publicly accessible web-resident database of published and current European research on agronomy, animal production and environmental impact of legume based grazing systems is reported. This database facilitates the sharing of information among the partners of the "Low input animal production based on forage legumes for grazing systems" (Leggraze), a research project funded by the UE (QL K5 CT-2001-02328). It also forms an important tool for transferring the results of the project to the wider research community and to end users in the agricultural sector and to policy makers at national and community level.

Systematic Evaluation Of Database Builds In Metaproteomics For The Advancement Of Microbiome Research, Katherine E. Ostrouchov

Masters Theses

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host …

18s-Nemabase: Curated 18s Rrna Database Of Nematode Sequences, Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval- Ruiz, Abigail Borgemeier, J. Parr Mcqueen, Rachel M. Shepherd, Dieter Slos, Tom Powers, Dorota L. Porazinska

Department of Plant Pathology: Faculty Publications

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant …

18s-Nemabase: Curated 18s Rrna Database Of Nematode Sequences, Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval- Ruiz, Abigail Borgemeier, J. Parr Mcqueen, Rachel M. Shepherd, Dieter Slos, Tom Powers, Dorota L. Porazinska

Department of Plant Pathology: Faculty Publications

Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant …

A Review Of Host Plants For The Tortricid Tribe Grapholitini, With A Synopsis Of Host Utilization By Genus (Lepidoptera: Tortricidae), John W. Brown

Insecta Mundi

A database of larval host plants for the tortricid tribe Grapholitini (Lepidoptera: Tortricidae: Ole­threutinae) is presented, and larval hosts are summarized for each genus. Food plants have been reported for over 400 of the approximately 1,644 described species of Grapholitini. Of the 81 genera currently as­signed to the tribe, at least one larval host has been reported for 51. Ninety-seven different plant families have been reported at least once for a species of Grapholitini, with the greatest number of grapholitines recorded from Fabaceae (168 species), followed by Fagaceae (43 species), Pinaceae (43), Sapindaceae (36), Rosaceae (30), Asteraceae (30), Euphorbiaceae (15), …

The Development Of A Global Shoreland Information Database May Help Determine The Appropriate Bacteria And Nutrient Technology Needed To Remediate Oil Contaminated Shorelands, Tiffany Ann Veeder

Honors Projects

The use of oil and its derivative products is well known world-wide. The benefits of oil are many and its products, for example, range from gasoline used in our automobiles to its use in plastics, building products, and medical supplies. Oil spill hazards associated with oil extraction, production, and transportation can have devastating impacts on the environment and local economies. When oil spills happen in the water, for instance, major shorelands are placed at risk of significant harm. As oil contaminates shorelands, the impacts can range from killing sea creatures and seabirds to destroying entire ecosystems. To help mitigate the …

Trophish: Building A Global Database Of Freshwater Trophic Interactions, Jacob M. Ridgway

Honors Thesis

Freshwater management and research frequently use the trophic data of freshwater fishes. Despite this fact, it is difficult to perform a simple search of dietary information for any one fish species. FishBase represents, to our knowledge, the largest compilation of freshwater dietary information to date. However, it excludes a large portion of the ecological literature due to its development taking place prior to the creation of most modern scientific search engines. Our project (TroPhish) is building upon FishBase by digitizing approximately 130 years of data from the fish predation literature. Data from the primary and grey (e.g. theses, dissertations, reports) …

Maud Gordon Holmes Arboretum List Of Tree Species, Chloe Mokadam

Maud Gordon Holmes Arboretum List of Tree Species

A database of tree species that links to descriptions/profiles for over 90 tree species.

The database is also available here: Maud Gordon Holmes Arboretum

Cbp60-Db: An Alphafold-Predicted Plant Kingdom-Wide Database Of The Calmodulin-Binding Protein 60 (Cbp60) Protein Family With A Novel Structural Clustering Algorithm, Keaun Amani, Vanessa Shivnauth, Christian Castroverde

Biology Faculty Publications

Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CAM-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation and diversification in most species remain unclear. Here we have created CBP60-DB, a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs …

Irreproducibility In Searches Of Scientific Literature: A Comparative Analysis, Gábor Pozsgai, Gábor L. Lövei, Liette Vasseur, Geoff Gurr, Péter Batáry, János Korponai, Nick A. Littlewood, Jian Liu, Arnold Móra, John J. Obrycki, Olivia Reynolds, Jenni A. Stockan, Heather Vanvolkenburg, Jie Zhang, Wenwu Zhou, Minsheng You

Entomology Faculty Publications

1. Repeatability is the cornerstone of science, and it is particularly important for systematic reviews. However, little is known on how researchers’ choice of database, and search platform influence the repeatability of systematic reviews. Here, we aim to unveil how the computer environment and the location where the search was initiated from influence hit results.
2. We present a comparative analysis of time-synchronized searches at different institutional locations in the world and evaluate the consistency of hits obtained within each of the search terms using different search platforms.
3. We revealed a large variation among search platforms and showed that PubMed and Scopus …

Alfanet: A Database Of Alfalfa-Bacterial Stem Blight Protein–Protein Interactions Revealing The Molecular Features Of The Disease-Causing Bacteria, Raghav Kataria, Rakesh Kaundal

Plants, Soils and Climate Student Research

Alfalfa has emerged as one of the most important forage crops, owing to its wide adaptation and high biomass production worldwide. In the last decade, the emergence of bacterial stem blight (caused by Pseudomonas syringae pv. syringae ALF3) in alfalfa has caused around 50% yield losses in the United States. Studies are being conducted to decipher the roles of the key genes and pathways regulating the disease, but due to the sparse knowledge about the infection mechanisms of Pseudomonas, the development of resistant cultivars is hampered. The database alfaNET is an attempt to assist researchers by providing comprehensive Pseudomonas proteome …

Calibration Chain Transformation Improves The Comparability Of Organic Hydrogen And Oxygen Stable Isotope Data, Sarah Magozzi, Clement P. Bataille, Keith A. Hobson, Michael B. Wunder, John D. Howa, Andrea Contina, Hannah B. Vander Zanden, Gabriel J. Bowen

School of Integrative Biological and Chemical Sciences Faculty Publications and Presentations

1. Stable hydrogen and oxygen isotopic compositions (δ2H and δ18O, respectively) of animal tissues have been used to infer geographical origin or mobility based on the premise that the isotopic composition of tissue is systematically related to that of local water sources. Isotopic data for known-origin samples are required to quantify these tissue–environment relationships. Although many of such data have been published and could be reused by researchers, differences in the standards used for calibration and analytical procedures for different datasets limit the comparability of these data.
2. We develop an algorithm that uses results from comparative analysis of secondary standards to …

Current Mutatome Of Sars-Cov-2 In Turkey Reveals Mutations Of Interest, Doğa Eski̇er, Evren Akalp, Özlem Dalan, Gökhan Karakülah, Yavuz Oktay

Turkish Journal of Biology

As the underlying pathogen for the COVID-19 pandemic that has affected tens of millions of lives worldwide, SARS-CoV-2 and its mutations are among the most urgent research topics worldwide. Mutations in the virus genome can complicate attempts at accurate testing or developing a working treatment for the disease. Furthermore, because the virus uses its own proteins to replicate its genome, rather than host proteins, mutations in the replication proteins can have cascading effects on the mutation load of the virus genome. Due to the global, rapidly developing nature of the COVID-19 pandemic, local demographics of the virus can be difficult …

Development Of Computational Tools To Target Microrna, Luo Song

Dissertations & Theses (Open Access)

MicroRNAs (a.k.a, miRNAs) play an important role in disease development. However, few of their structures have been determined and structure-based computational methods remain challenging in accurately predicting their interactions with small molecules. To address this issue, my thesis is to develop integrated approaches to screening for novel inhibitors by targeting specific structure motifs in miRNAs. The project starts with implementing a tool to find potential miRNA targets with desired motifs. I combined both sequence information of miRNAs and known RNA structure data from Protein Data Bank (PDB) to predict the miRNA structure and identify the motif to target, then I …

Challenging The Wallacean Shortfall: A Total Assessment Of Insect Diversity On Guadeloupe (French West Indies), A Checklist And Bibliography, François Meurgey, Thibault Ramage

Insecta Mundi

This work is the first attempt to integrate into one list and quantify all the known species of Guade­loupean insects. It includes all the species known to us to be reported for the island of Guadeloupe until the 31^st of December 2019. A total of 3097 valid species are listed, of which the largest component is the beetles (1447 species). Preliminarily, 632 species (20%) are considered to be strictly endemic to Guadeloupe, and 250 species are recognized as adventive or introduced. The bibliography complements the taxonomic information and includes over 350 titles. Brief annotations are also given on the …

The Fire And Tree Mortality Database, For Empirical Modeling Of Individual Tree Mortality After Fire, C. Alina Cansler, Sharon M. Hood, J. Morgan Varner, Phillip J. Van Mantgem, Michelle C. Agne, Robert A. Andrus, Matthew P. Ayres, Bruce D. Ayres, Jonathan D. Bakker, Michael A. Battaglia, Barbara J. Bentz, Carolyn R. Breece, James K. Brown, Daniel R. Cluck, Tom W. Coleman, R. Gregory Corace Iii, W. Wallace Covington, Douglas S. Cram, James B. Cronan, Joseph E. Crouse, Adrian J. Das, Ryan S. Davis, Et Al.

Biology Faculty Publications

Wildland fires have a multitude of ecological effects in forests, woodlands, and savannas across the globe. A major focus of past research has been on tree mortality from fire, as trees provide a vast range of biological services. We assembled a database of individual-tree records from prescribed fires and wildfires in the United States. The Fire and Tree Mortality (FTM) database includes records from 164,293 individual trees with records of fire injury (crown scorch, bole char, etc.), tree diameter, and either mortality or top-kill up to ten years post-fire. Data span 142 species and 62 genera, from 409 fires occurring …

Multisector Water Consumption Database: Surkhandarya Region Of The Republic Of Uzbekistan, М. Ikramova, С. Batishev, О. Ikramov, H. Kabilov, D. Nazaraliev, А. Khodjiev, I. Akhmedkhodjaeva

Irrigation and Melioration

The available water resources in the country are used by the different sectors of economy as industry, agriculture, energy, communal service and etc. In this case the water distribution within the river basin requires perfect information service and data exchange facilities. In the paper the developed unified multi-sector on-line database is presented aimed to monitor the water distribution among sectors of economy, database structure, and data exchange tools. The software works at operative mood, allows evaluating the combined water use efficiency by water users.

Creating And Associating Tables In Access Program, Nazokat Sayfullaevna Sayidova, Shakhlo Erkin Qizi Rakhmatova, Sarvinoz Mamadradjabovna Berdieva

Scientific reports of Bukhara State University

In this article, the sequence of creating tables and linking them with each other is developed in the Access program. The creation of any database begins with the creation of its project. The main task of the database designer is to choose the objects and the parameters that characterize them, establish links between the data. The file, which is stored in the data itself and managed under the database management system, is known before-called motlar Bank, and later began to be referred to as the database dab.

Functional Responses Are Maximized At Intermediate Temperatures, Stella F. Uiterwaal, John Delong

School of Biological Sciences: Faculty Publications

Functional responses describe how consumer foraging rates change with resource density. Despite extensive research looking at the factors underlying foraging interactions, there remains ongoing controversy about how temperature and body size control the functional response parameters space clearance (or attack) rate and handling time. Here, we investigate the effects of temperature, consumer mass, and resource mass using the largest compilation of functional responses yet assembled. This compilation contains 2,083 functional response curves covering a wide range of foragers and prey types, environmental conditions, and habitats. After accounting for experimental arena size, dimensionality of the foraging interaction, and consumer taxon, we …

Assess The Changing Role Of Database Technology Within Geographic Information System Over The Past 45 Years, Ashna Bdulrahman Kareem

Polytechnic Journal

Spatial data stored in databases have been become progressively crucial in the geographic information system (GIS) field within recent years. Spatial data are increasingly being noted for its significance in representing for real-life relationships. The value of spatial databases cannot be underestimated since it has been established to be an efficient and flexible means of handling enormous spatial datasets. This paper shows the different methods, in which spatial data are integrated by major database vendors and database within GIS. The current report has also examined the new technologies and advancements by database and GIS vendors in relational database management systems …

Assess The Changing Role Of Database Technology Within Geographic Information System Over The Past 45 Years, Ashna Bdulrahman Kareem

Polytechnic Journal

Spatial data stored in databases have been become progressively crucial in the geographic information system (GIS) field within recent years. Spatial data are increasingly being noted for its significance in representing for real-life relationships. The value of spatial databases cannot be underestimated since it has been established to be an efficient and flexible means of handling enormous spatial datasets. This paper shows the different methods, in which spatial data are integrated by major database vendors and database within GIS. The current report has also examined the new technologies and advancements by database and GIS vendors in relational database management systems …

Assess The Changing Role Of Database Technology Within Geographic Information System Over The Past 45 Years, Ashna Bdulrahman Kareem

Polytechnic Journal

Spatial data stored in databases have been become progressively crucial in the geographic information system (GIS) field within recent years. Spatial data are increasingly being noted for its significance in representing for real-life relationships. The value of spatial databases cannot be underestimated since it has been established to be an efficient and flexible means of handling enormous spatial datasets. This paper shows the different methods, in which spatial data are integrated by major database vendors and database within GIS. The current report has also examined the new technologies and advancements by database and GIS vendors in relational database management systems …