Digital Commons Network^™

Acoustic Space Occupancy: Combining Ecoacoustics And Lidar To Model Biodiversity Variation And Detection Bias Across Heterogeneous Landscapes, Danielle I. Rappaport, J. Andrew Royle, Douglas C. Morton

United States Geological Survey: Staff Publications

There is global interest in quantifying changing biodiversity in human-modified landscapes. Ecoacoustics may offer a promising pathway for supporting multi-taxa monitoring, but its scalability has been hampered by the sonic complexity of biodiverse ecosystems and the imperfect detectability of animal-generated sounds. The acoustic signature of a habitat, or soundscape, contains information about multiple taxa and may circumvent species identification, but robust statistical technology for characterizing community-level attributes is lacking. Here, we present the Acoustic Space Occupancy Model, a flexible hierarchical framework designed to account for detection artifacts from acoustic surveys in order to model biologically relevant variation in acoustic space …

Human-Associated Species Dominate Passerine Communities Across The United States, Helen R. Sofaer, Curtis H. Flather, Catherine S. Jarnevich, Kristin P. Davis, Liba Pejchar

United States Geological Survey: Staff Publications

Aim: Human development and agriculture can have transformative and homogenizing effects on natural systems, shifting the composition of ecological communities towards non-native and native species that tolerate or thrive under human-dominated conditions. These impacts cannot be fully captured by summarizing species presence, as they include dramatic changes to patterns of species abundance. However, how human land use patterns and species invasions intersect to shape patterns of abundance and dominance within ecological communities is poorly understood even in well-known taxa.

Location: Conterminous United States.

Time period: 2010–2012.

Major taxa studied: Passeriformes.

Methods: We analyse continental-scale monitoring data to study the proportional …

Ecosystem Processes, Land Cover, Climate, And Human Settlement Shape Dynamic Distributions For Golden Eagle Across The Western Us, J.D. Tack, Barry R. Noon, Zachary Bowen, Brad C. Fedy

United States Geological Survey: Staff Publications

Species–environment relationships for highly mobile species outside of the breeding season are often highly dynamic in response to the collective effects of everchanging climatic conditions, food resources, and anthropogenic disturbance. Capturing dynamic space-use patterns in a model-based framework is critical as model inference often drives place-based conservation planning. We applied dynamic occupancy models to broad-scale golden eagle Aquila chrysaetos survey data collected annually from 2006 to 2012 during the late summer post-fledging period in the western US. We defined survey sites as 10 km transect segments with a 1 km buffer on either transect side (n = 3540). Derived estimates …

Human-Associated Species Dominate Passerine Communities Across The United States, Helen R. Sofaer, Curtis H. Flather, Catherine S. Jarnevich, Kristin P. Davis

United States Geological Survey: Staff Publications

Aim: Human development and agriculture can have transformative and homogenizing effects on natural systems, shifting the composition of ecological communities towards non-native and native species that tolerate or thrive under human-dominated conditions. These impacts cannot be fully captured by summarizing species presence, as they include dramatic changes to patterns of species abundance. However, how human land use patterns and species invasions intersect to shape patterns of abundance and dominance within ecological communities is poorly understood even in well-known taxa.

Location: Conterminous United States.

Time period: 2010–2012.

Major taxa studied: Passeriformes.

Methods: We analyse continental-scale monitoring data to study the proportional …

Acoustic Space Occupancy: Combining Ecoacoustics And Lidar To Model Biodiversity Variation And Detection Bias Across Heterogeneous Landscapes, Danielle I. Rappaport, J. Andrew Royle, Douglas C. Morton

United States Geological Survey: Staff Publications

There is global interest in quantifying changing biodiversity in human-modified landscapes. Ecoacoustics may offer a promising pathway for supporting multi-taxa monitoring, but its scalability has been hampered by the sonic complexity of biodiverse ecosystems and the imperfect detectability of animal-generated sounds. The acoustic signature of a habitat, or soundscape, contains information about multiple taxa and may circumvent species identification, but robust statistical technology for characterizing community-level attributes is lacking. Here, we present the Acoustic Space Occupancy Model, a flexible hierarchical framework designed to account for detection artifacts from acoustic surveys in order to model biologically relevant variation in acoustic space …

Characterization Of Pallid Sturgeon (Scaphirhynchus Albus) Spawning Habitat In The Lower Missouri River, Caroline M. Elliott, Aaron J. Delonay, Kimberly Chojnacki, Robert B. Jacobson

United States Geological Survey: Staff Publications

Acipenseriformes (sturgeons and paddlefish) globally have declined throughout their range due to river fragmentation, habitat loss, overfishing, and degradation of water quality. In North America, pallid sturgeon (Scaphirhynchus albus) populations have experienced poor to no recruitment, or substantial levels of hybridization with the closely related shovelnose sturgeon (S. platorynchus). The Lower Missouri River is the only portion of the species’ range where successful reproduction and recruitment of genetically pure pallid sturgeon have been documented. This paper documents spawning habitat and behavior on the Lower Missouri River, which comprises over 1,300 km of unfragmented river habitat. The …

Late Quaternary Sea-Level History Of Saipan, Commonwealth Of The Northern Mariana Islands, Usa: A Test Of Tectonic Uplift And Glacial Isostatic Adjustment Models, Daniel R. Muhs, Eugene S. Schweig, Kathleen R. Simmons

United States Geological Survey: Staff Publications

In 1979, S. Uyeda and H. Kanamori proposed a tectonic model with two end members of a subduction-boundary continuum: the “Chilean” type (shallow dip of the subducting plate, great thrust events, compression, and uplift of the overriding plate) and a “Mariana” type (steep dip of the subducting plate, no great thrust events, tension, and no uplift). This concept has been used to explain variable rates of Quaternary uplift around the Pacific Rim, yet no uplift rates have been determined for the Mariana Islands themselves, one of the end members in this model. We studied the late Quaternary Tanapag Limestone, which …

Simultaneous Cognate Epitope Recognition By Bovine Cd4 And Cd8 T Cells Is Essential For Primary Expansion Of Antigen-Specific Cytotoxic T-Cells Following Ex Vivo Stimulation With A Candidate Mycobacterium Avium Subsp. Paratuberculosis Peptide Vaccine, Gaber S. Abdellrazeq, Lindsay M. Fry, Mahmoud M. Elnaggar, J. P. Bannantine, David A. Schneider, William M. Chamberlin, Asmaa H.A. Mahmoud, Kun-Taek Park, Victoria Hulubei, William C. Davis

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Studies in cattle show CD8 cytotoxic T cells (CTL), with the ability to kill intracellular bacteria, develop following stimulation of monocyte-depleted peripheral blood mononuclear cells (mdPBMC) with antigen-presenting cells (APC, i.e. conventional dendritic cells [cDC] and monocyte-derived DC [MoDC]) pulsed with MMP, a membrane protein from Mycobacterium avium subsp. paratuberculosis (Map) encoded byMAP2121c. CTL activity was diminished if CD4 T cells were depleted from mdPBMC before antigen (Ag) presentation by APC, suggesting simultaneous cognate recognition of MMP epitopes presented by MHC I and MHC II molecules to CD4 and CD8 T cells is essential for development of CTL activity. To …

Allelic Variation In Rice Fertilization Independent Endosperm 1 Contributes To Grain Width Under High Night Temperature Stress, Balpreet K. Dhatt, Puneet Paul, Jaspreet Sandhu, Waseem Hussain, Larissa Irvin, Feiyu Zhu, Maria Arlene Adviento-Borbe, Argelia Lorence, Paul Staswick, Hongfeng Yu, Gota Morota, Harkamal Walia

Department of Agronomy and Horticulture: Faculty Publications

A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored.

We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions.

A novel locus contributing to grain width under HNT …

Leveraging Genome-Enabled Growth Models To Study Shoot Growth Responses To Water Deficit In Rice, Malachy T. Campbell, Alexandre Grondin, Harkamal Walia, Gota Morota

Department of Agronomy and Horticulture: Faculty Publications

lucidating genotype-by-environment interactions and partitioning its contribution to phenotypic variation remains a challenge for plant scientists. We propose a framework that utilizes genome-wide markers to model genotype-specific shoot growth trajectories as a function of time and soil water availability. A rice diversity panel was phenotyped daily for 21 d using an automated, high-throughput image-based, phenotyping platform that enabled estimation of daily shoot biomass and soil water content. Using these data, we modeled shoot growth as a function of time and soil water content, and were able to determine the time point where an inflection in the growth trajectory occurred. We …

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

Department of Agronomy and Horticulture: Faculty Publications

Changes in canopy architecture traits have been shown to contribute to yield increases. Optimizing both light interception and light interception efficiency of agricultural 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 identification 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 algorithm to allow …

Genome-Wide Identification And Analysis Of Heterotic Loci In Three Maize Hybrids, Hongjun Liu, Qin Wang, Mengjiao Chen, Yahui Ding, Xuerong Yang, Jie Liu, Xiaohan Li, Congcong Zhou, Qilin Tian, Yiqi Lu, Danlin Fan, Junpeng Shi, Lin Zhang, Congbin Kang, Mingfei Mingfei Sun, Fangyuan Li, Yujian Wu, Yongzhong Zhang, Baoshen Liu, Xiang Yu Zhao, Qi Feng, Jinliang Yang, Bin Han, Jinsheng Lai, Xian Sheng Zhang, Xuehui Huang

Department of Agronomy and Horticulture: Faculty Publications

Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the …

Induction Of Seed Coat Darkening In Common Beans (Phaseolus Vulgaris L.) And The Association With Cooking Time After Storage, Renata C. Alvares, Helton S. Pereira, Leonardo C. Melo, Phillip N. Miklas, Patrícia G.S. Melo

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Carioca is the most important edible dry bean (Phaseolus vulgaris L.) grown in Brazil. It represents the largest dry bean market class in the world. The seed coat of carioca beans will darken under adverse harvest conditions and with the increasing of storage time. In general, darkened seeds are associated with older seeds that suffer from prolonged cooking times. A relatively new ‘slow darkening’ trait is available in carioca that delays seed coat darkening under storage. However, its effect on cooking time is unknown. The objective of this work was to evaluate two induction methods of seed coat darkening and …

Cropping System And Landscape Characteristics Influence Long-Term Grain Crop Profitability, L. S. Conway, M. A. Yost, Newell Kitchen, K. A. Sudduth, R. E. Massey, E. J. Sadler

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Converting from standard tillage or no-tillage cropping systems to more conservation-based cropping systems that include no-tillage, cover crops, and reduced agrichemical inputs must be profitable for large-scale adoption. Therefore, research was conducted at the central Mississippi River Basin site of the USDA Long-Term Agroecosystem Research Network from 1996 to 2009 to determine how cropping systems, landscape position, and depth to claypan affected net economic return. Treatments consisted of three cropping systems {mulch-till corn (Zea mays L.)–soybean [Glycine max (L.) Merr.], MTCS; no-till corn–soybean, NTCS; no-till corn–soybean–wheat (Triticum aestivum L.) (NTCSW)–cover crop} and three landscape positions (summit, backslope, and footslope). Within …

Achieving An Equitable Transition To Open Access For Researchers In Lower And Middle-Income Countries, Andrea Powell, Rob Johnson, Rachel Herbert

Copyright, Fair Use, Scholarly Communication, etc.

Introduction

The origins of this White Paper can be traced to a discussion started in mid-2019 between a number of scholarly publishers and the Publisher Coordinator for Research4Life (a role that is supported financially by the STM Association). These interlocutors voiced concern that while the publishing and research communities in the developed world were making steady and positive progress towards universal Open Access based on a ‘pay to publish’ model, those same communities in the less developed lower and middle-income countries (often referred to as the “Global South”) were being excluded from these discussions. Following discussions at the STM Board …

The Trust Principles For Digital Repositories, Dawei Lin, Jonathan Crabtree, Ingrid Dillo, Robert R. Downs, Rorie Edmunds, David Giaretta, Marisa De Giusti, Hervé L'Hours, Wim Hugo, Reyna Jenkyns, Varsha Khodiyar, Maryann E. Martone, Mustapha Mokrane, Vivek Navale, Jonathan Petters, Barbara Sierman, Dina V. Sokolova, Martina Stockhause, John Westbrook

Copyright, Fair Use, Scholarly Communication, etc.

As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold.

Following a year-long public discussion and building on existing community consensus , several stakeholders, representing various segments of the digital repository community, have collaboratively developed and endorsed a set of guiding principles to demonstrate digital repository trustworthiness. Transparency, Responsibility, User focus, …

Who’S Writing Open Access (Oa) Articles? Characteristics Of Oa Authors At Ph.D.-Granting Institutions In The United States, Anthony J. Olejniczak, Molly J. Wilson

Copyright, Fair Use, Scholarly Communication, etc.

The open access (OA) publication movement aims to present research literature to the public at no cost and with no restrictions. While the democratization of access to scholarly literature is a primary focus of the movement, it remains unclear whether OA has uniformly democratized the corpus of freely available research, or whether authors who choose to publish in OA venues represent a particular subset of scholars—those with access to resources enabling them to afford article processing charges (APCs). We investigated the number of OA articles with article processing charges (APC OA) authored by 182,320 scholars with known demographic and institutional …

Small Mammal Communities In Grasslands At The Grand Forks Air Force Base, North Dakota, Usa, Lynda R. Lafond, Elizabeth H. Rave, Kathryn A. Yurkonis

The Prairie Naturalist

Small mammals are important in grasslands but are often overlooked in management and reconstruction efforts. We sampled small mammals in three sites on the Grand Forks Air Force Base (GFAFB) located in central Grand Forks County, North Dakota, USA. The study sites varied in their management history and represented the three major types of grasslands (reconstructed prairie, old field, and hay field) within Grand Forks County. We captured 463 individuals of six species with Sherman live traps in summer (June, July, August) 2014 and 2015. We captured the most individuals and species (295 individuals of 5 species), including all shrews …

Wood Frogs (Rana Sylvatica) In Southwestern Roberts County And Western Grant County, South Dakota, Dennis R. Skadsen, Drew R. Davis

The Prairie Naturalist

Historically, only six records of Wood Frogs (Rana sylvatica) existed from South Dakota, all represented by museum specimens. A single specimen was collected from Hartford Beach on Big Stone Lake, Roberts County in 1922 (National Museum of Natural History, Smithsonian Institution [USNM] 65452) and five Wood Frogs were collected near the outlet of Blue Dog Lake, Day County in 1929 (USNM 312618– 312622; Fig. 1). After the 1920s, no other Wood Frogs were reported in South Dakota for the next six decades, and the species was presumed extirpated. Over (1923, 1943) reported the species was common in the …

Trends In A Greater Prairie Chicken Population Established By Translocation In North Dakota, Gary Huschle, John E. Toepfer

The Prairie Naturalist

In 1992, an effort was undertaken by the North Dakota Game and Fish Department (NDGFD), U.S. Fish and Wildlife Service, and North Dakota Chapter of the Wildlife Society to reestablish a viable population of greater prairie chickens (Tympanuchus cupido pinnatus; hereafter prairie chickens) in northeast North Dakota. The release area was centered on the Prairie Chicken Wildlife Management Area located 22.5 km northwest of Grand Forks, North Dakota, in the northern part of Grand Forks County. Topography consists of poorly drained, saline flats and swells separated by poorly drained swales and sloughs in the Red River Valley (Beringer 1995). Permanent …

Patterns And Potential Causes Of Changing Winter Bird Distributions In South Dakota, David L. Swanson, Reza Goljani Amirkhiz, Mark D. Dixon

The Prairie Naturalist

Average winter temperatures in the north-central United States have been increasing since the 1970s, and this warming might influence winter distributions of birds in the region. Species potentially influenced by such winter warming include short-distance migrants for which the northern boundary of the winter range is influenced by temperature, such as hermit thrush (Catharus guttatus), yellow-rumped warbler (Setophaga coronata), and fox sparrow (Passerella iliaca). We examined winter records during 1974–2017 from a citizen-science bird observation database for South Dakota to determine recent trends in winter records for these three species. We compared their occurrence patterns with those for three benchmark …

Local Control Of Resource Allocation Is Sufficient To Model Optimal Dynamics In Syntrophic Systems, Glenn Ledder, Sabrina E. Russo, Erik B. Muller, Angela Peace, Roger M. Nisbet

School of Biological Sciences: Faculty Publications

Syntrophic systems are common in nature and include forms of obligate mutualisms in which each participating organism or component of an organism obtains from the other an essential nutrient or metabolic product that it cannot provide for itself. Models of how these complementary resources are allocated between partners often assume optimal behavior, but whether mechanisms enabling global control exist in syntrophic systems, and what form they might take, is unknown. Recognizing that growth of plant organs that supply complementary resources, like roots and shoots, can occur autonomously, we present a theory of plant growth in which rootshoot allocation is determined …

Predator-Dependent Functional Responses Alter The Coexistence And Indirect Effects Among Prey That Share A Predator, Kyle E. Coblentz, John P. Delong

School of Biological Sciences: Faculty Publications

Predator functional responses describe predator feeding rates as a function of prey abundance and are central to pred-ator–prey theory. Despite ample evidence that functional responses also depend on predator abundance, theory incor-porating predator-dependent functional responses has focused almost exclusively on specialist predator–prey pairs or linear food chains. This leaves a large gap in our knowledge as many predators feed on multiple prey, and in so doing, generate indirect effects among prey that can alter their coexistence. Here we investigate how predator-dependent functional responses in a one predator–two prey model alter the coexistence among prey and their net effects on one …

Adaptations Of Interferon Regulatory Factor 3 With Transition From Terrestrial To Aquatic Life, Monica Angeletti, Wan-Ling Nicole Hsu, Nashaat Majo, Hideaki Moriyama, Etsuko Moriyama, Luwen Zhang

School of Biological Sciences: Faculty Publications

Interferon regulatory factor 3 (IRF3) and IRF7 are closely related IRF members and the major factors for the induction of interferons, a key component in vertebrate innate immunity. However, there is limited knowledge regarding the evolution and adaptation of those IRFs to the environments. Two unique motifs in IRF3 and 7 were identified. One motif, GASSL, is highly conserved throughout the evolution of IRF3 and 7 and located in the signal response domain. Another motif, DPHK, is in the DNA-binding domain. The ancestral protein of IRF3 and 7 seemed to possess the DPHK motif. In the ray-finned fish lineage, while …

Presence Of Fruits Decreases Probability Of Retaining Flowers In A Sequentially Flowering Plant, Shivani Jadeja, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Both intrinsic and extrinsic plant processes affect the fate of flowers along an inflorescence in sequen- tially flowering plants. We investigated whether the intrinsic process of competition for limited resource between fruits and flowers owing to resource preemption or sink strength of basal fruits, or architectural effects due to posi- tional differences in the probability of retaining flowers, explains a lower probability of retaining distal flowers inYucca glauca. Further, we investigated how the extrinsic process of seed herbivory interacts with the plant’s intrinsic processes of flower retention. We carried out a field experiment to compare flower retention among nine combi- …

Peer Review Of Teaching Portfolio For Hort 306: Greenhouse Operations & Management, Stacy Adams

UNL Faculty Course Portfolios

A Greenhouse Operations and Management course designed specifically to serve the needs of horticulture students at an institution of higher learning has transitioned teaching philospophy to additionally serve any student with a potential use of a greenhouse in instruction, community outreach, research, extension, early childhood development, and thearapy. Through the Peer Review of Teaching Project, the course is explored, analyzed and redeveloped with intentional purpose.

Fdst 880p: Food Proteins - A Peer Review Of Teaching Project, Benchmark Portfolio, Kaustav Majumder

UNL Faculty Course Portfolios

FDST 880P: Food Proteins, is a course designed only for the graduate students for the department of food science and technology. The course work provides the opportunity to dwell deep into the fundamental chemistry, protein structures and functions to understand the physiochemical and biochemicals factors that govern the functionality and biological activity of the food proteins and proteins-derived peptides. For each of the course objectives, I describe how and why I organize the course, as well as how my pedagogical choices encourage the student learning and engagement. Collect and analyze the data on students' performance and progress during the semester …

Peer Review Of Teaching Benchmark Portfolio - Nres/Wats/Bio 459/859: Limnology, Jessica Corman

UNL Faculty Course Portfolios

Limnology (NRES/BIO/WATS 459/859) is an upper-division course taken primarily by Fisheries and Wildlife and Water Science majors in the College of Agricultural Sciences and Natural Resources (CASNR) at the University of Nebraska-Lincoln. Although the course enrollment is open to graduate students, none were enrolled in the year in which this portfolio was written. Learning outcomes focus on understanding the interdisciplinarity of limnological sciences, assessing anthropogenic impacts on lake ecosystems, learning basic limnological field techniques, and investigating and critically evaluating relevant, publicly available datasets. The course satisfies the “ACE 10” requirement for undergraduate students; students meet this requirement by completing a …

An Exploration Of Student Engagement And Learning Within A Newly Online Version Of Teac 861: Teaching In A Pluralistic Society - A Peer Review Of Teaching Benchmark Portfolio, Amanda R. Morales

UNL Faculty Course Portfolios

Given the current racial, economic, and socio-political tensions in K-12 education, the work of teacher preparation arguably has never been more important or difficult. This benchmark portfolio targets a core required course aimed at increased teachers’ cultural competence and equity literacy, 861: Teaching in a Pluralistic Society. In this portfolio, I focus primarily on methods and mechanisms I used to increase student engagement in and critical reflection on a social justice-oriented curriculum in a new online format. I describe the context for the course, my initial anxieties around teaching the course online for the first time, student demographics, my redesigned …

Russ391: Russian Culture And Civilization Through Film - A Peer Review Of Teaching Portfolio, Olha Tytarenko

UNL Faculty Course Portfolios

The Benchmark Portfolio traces the process of revamping my survey course RUSS391 “Russian Culture and Civilization Through Film” taught for the second time in Spring 2020. In addition to The primary goal of the course was to acquaint students with major developments in the cultural and political life of twentieth and twenty-first-century Russia examined through the prism of cinema. In addition to main course objectives, my teaching goal was to engage students in the subject, incite their intellectual curiosity, and create a productive learning experience conducive to the development of critical thinking. In this course portfolio, I discuss my teaching …