Other Life Sciences Commons^™

Climate Change-Associated Declines In Water Clarity Impair Feeding By Common Loons, Walter H. Piper, Max R. Glines, Kevin C. Rose

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Climate change has myriad impacts on ecosystems, but the mechanisms by which it affects individual species can be difficult to pinpoint. One strategy to discover such mechanisms is to identify a specific ecological factor related to survival or reproduction and determine how that factor is affected by climate. Here we used Landsat imagery to calculate water clarity for 127 lakes in northern Wisconsin from 1995 to 2021 and thus investigate the effect of clarity on the body condition of an aquatic visual predator, the common loon (Gavia immer). In addition, we examined rainfall and temperature as potential predictors …

Variables Affecting The Extraction Of Antioxidants In Cold And Hot Brew Coffee: A Review, Brian Yust, Frank Wilkinson, Niny Rao

College of Life Sciences Faculty Papers

Coffee beans are a readily available, abundant source of antioxidants used worldwide. With the increasing interest in and consumption of coffee beverages globally, research into the production, preparation, and chemical profile of coffee has also increased in recent years. A wide range of variables such as roasting temperature, coffee grind size, brewing temperature, and brewing duration can have a significant impact on the extractable antioxidant content of coffee products. While there is no single standard method for measuring all of the antioxidants found in coffee, multiple methods which introduce the coffee product to a target molecule or reagent can be …

Ecological Protection Alone Is Not Enough To Conserve Ecosystem Carbon Storage: Evidence From Guangdong, China, Lihan Cui, Wenwen Tang, Sheng Zheng, Ramesh P. Singh

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The increase in atmospheric CO₂ caused by land use and land cover change (LUCC) is one of the drivers of the global climate. As one of the most typical high-urbanization areas, the ecological conflicts occurring in Guangdong Province warrant urgent attention. A growing body of evidence suggests LUCC could guide the future ecosystem carbon storage, but most LUCC simulations are simply based on model results without full consistency with the actual situation. Fully combined with the territorial spatial planning project and based on the land use pattern in 2010 and 2020, we have used the Markov and Patch-generating Land …

Open Source Solutions In Experimental Design: An Introduction To The Symposium, Richelle L. Tanner, Kirt L. Onthank

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The Open Science movement has increased dramatically in popularity with deserved calls to action around transparency, access to resources, and inclusion in our field. However, its practical applications within experimental design have been slow to uptake, with researchers unsure where to even start with the dizzying array of open source hardware and software solutions available. The perceived time investment and unknown cost, especially in implementing open source hardware, has stagnated the implementation of inexpensive experimental solutions, but we sought to increase awareness to lower the barrier to participation in this space. While there are countless technical and financial advantages to …

Tissue Decay Tested In Modern Metasequoia Leaves: Implications For Early Diagenesis Of Leaves In Fossil Lagerstätten, Caitlyn R. Witkowski, Qin Leng, Christopher W. Reid, Liang Feng, Hong Yang

Science and Technology Department Faculty Journal Articles

Sedimentary deposits yielding extraordinarily-preserved fossils (known as Lagerstätten) may provide significant insights into the physiology and environments of ancient plants, particularly when the fossils represent their original characteristics with limited diagenetic modifications. To better understand molecular, isotopic, and morphological changes during the early stages of diagenesis, degradation experiments were conducted in two time series: 1) a laboratory decay series using fungi on leaves over the course of a month and 2) a natural decay series with leaves collected from different stages of leaf senescence and early diagenesis. Both experiments used modern leaves of the dawn redwood Metasequoia glyptostroboides …

Virtual Expeditions Facilitated By Open Source Solutions Broaden Student Participation In Natural History Research, Richelle L. Tanner, Talia Y. Moore

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

From its genesis in the Victorian era as an activity for the elite to today's emphasis on “Big Data” and continuous monitoring, natural history has a prominent role in scientific discoveries for many fields. However, participation in field expeditions is limited by funding, space, accessibility, and safety constraints. Others have detailed the active exclusion of minoritized groups from field expeditions and harm/discrimination faced by the few who do participate, but we provide one solution to broaden opportunities for participation in natural history: Virtual Expeditions. Virtual Expeditions are broadly defined as open source, web-facilitated research activities designed to analyze bulk-collected digital …

The Utilization Of Volatile Organic Compounds And Human Leukocyte Antigen Genes For Ethnic-Specific Differentiation Within Target Populations, Alice Breia Boone

FIU Electronic Theses and Dissertations

Human scent has been previously defined as a complex mixture of volatile organic compounds (VOCs) detected in the headspace above a scent sample. Humans generate odor from several areas of the body including hair, mouth, hand, axillae, and foot. Due to the novelty of human scent research, human scent evidence has been undervalued in the court of law. However, this type of evidence has significant value when physical evidence is not available at crime scenes. To increase the individualization and differentiation power of human scent evidence, this study aimed to further investigate the identification of chemical signatures within axillae of …

A Push For Inclusive Data Collection In Stem Organizations, Nicholas P. Burnett, Alyssa M. Hernandez, Emily E. King, Richelle L. Tanner, Kathryn Wilsterman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Professional organizations in STEM (science, technology, engineering, and mathematics) can use demographic data to quantify recruitment and retention (R&R) of underrepresented groups within their memberships. However, variation in the types of demographic data collected can influence the targeting and perceived impacts of R&R efforts - e.g., giving false signals of R&R for some groups. We obtained demographic surveys from 73 U.S.-affiliated STEM organizations, collectively representing 712,000 members and conference-attendees. We found large differences in the demographic categories surveyed (e.g., disability status, sexual orientation) and the available response options. These discrepancies indicate a lack of consensus regarding the demographic groups that …

Emory-Tibet Science Initiative: Changes In Monastic Science Learning Motivation And Engagement During A Six-Year Curriculum, Kelsey M. Gray, Cindy Achat-Mendes, Ann Cale Kruger, Tashi Lhamo, Rinchen Wangyal, Gelek Gyatso, Carol M. Worthman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Led by His Holiness the Dalai Lama, the initiative taken by the Tibetan Buddhist monastic community to connect with western science and scientists presents a unique opportunity to understand the motivations and engagement behaviors that contribute to monastic science learning. In this study, we draw on quantitative data from two distinct surveys that track motivations and engagement behaviors related to science education among monastic students. The first survey was administered at one monastic university in 2018, and the second follow-up survey was completed by students at two monastic universities in 2019. These surveys assessed the reception of science education related …

Fish And Invertebrate Use Of Restored Vs. Natural Oyster Reefs In A Shallow Temperate Latitude Estuary, Jonathan H. Grabowski, Christopher J. Baillie, Adam Baukus, Rachael Carlyle, F. Joel Fodrie, Rachel K. Gittman, A. Randall Hughes, David L. Kimbro, Juhyung Lee, Hunter S. Lenihan, Sean P. Powers, Kevin Sullivan

University Faculty and Staff Publications

Coastal marine habitats continue to be degraded, thereby compelling largescale restoration in many parts of the world. Whether restored habitats function similarly to natural habitats and fully recover lost ecosystem services is unclear. In estuaries, oyster reefs have been degraded by multiple anthropogenic activities including destructive fishing practices and reduced water quality, motivating restoration to maintain oyster fisheries and other ecosystem services, often at relatively high cost. We compared fish and invertebrate communities on recently restored (0–1 year post-restoration), older restored (3–4 years post-restoration), and natural oyster reefs to determine if and when restored reefs support functionally similar faunal communities. …

Introduction To Neutrosophic Genetics, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

Neutrosophic Genetics is the study of genetics using neutrosophic logic, set, probability, statistics, measure and other neutrosophic tools and procedures. In this paper, based on the Neutrosophic Theory of Evolution (that includes degrees of Evolution, Neutrality (or Indeterminacy), and Involution) – as extension of Darwin’s Theory of Evolution, we show the applicability of neutrosophy in genetics, and we present within the frame of neutrosophic genetics the following concepts: neutrosophic mutation, neutrosophic speciation, and neutrosophic coevolution.

Agate Fossil Beds National Monument, Paleontological Resources Management Plan (Public Version), Scott Kottkamp, Vincent L. Santucci, Justin S. Tweet, Jessica De Smet, Ellen Stark

United States National Park Service: Publications

Executive Summary

Since Agate Springs Ranch was founded by James H. Cook in 1887, exquisite examples of transitional Miocene mammalian fauna have been found along this stretch of the Niobrara River valley. Collectively these paleontological discoveries, along with the existing archeological and historical Native American collection, were the basis for establishing Agate Fossil Beds National Monument (AGFO) as a unit of the National Park System (NPS). The fossil remains from the Harrison and Anderson Ranch formations span a short, but important, time period within the Miocene Epoch. AGFO has provided science with an intimate look into North American mammalian evolution …

A Neutrosophic Clinical Decision-Making System For Cardiovascular Diseases Risk Analysis, Florentin Smarandache, Shaista Habib, Wardat-Us- Salam, M. Arif Butt, Muhammad Akram

Branch Mathematics and Statistics Faculty and Staff Publications

Cardiovascular diseases are the leading cause of death worldwide. Early diagnosis of heart disease can reduce this large number of deaths so that treatment can be carried out. Many decision-making systems have been developed, but they are too complex for medical professionals. To target these objectives, we develop an explainable neutrosophic clinical decision-making system for the timely diagnose of cardiovascular disease risk. We make our system transparent and easy to understand with the help of explainable artificial intelligence techniques so that medical professionals can easily adopt this system. Our system is taking thirtyfive symptoms as input parameters, which are, gender, …

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Master of Science in Forensic Science Directed Research Projects

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample …

Comparison Of Periglacial Block Fields And Talus Slopes In South-Central Pennsylvania And Northern Maryland, Ilana B. Sobel, Abigail F. Rec, Sarah M. Principato

Environmental Studies Faculty Publications

Relict periglacial boulder fields, or block fields, are scattered across south-central Pennsylvania and northern Maryland (e.g. Potter and Moss, 1968; Denn et al 2018). This pilot study uses a combination of digital analyses using Google Earth Pro and fieldwork to investigate block fields at different scales. Fieldwork focused on two block fields, which were compared with fieldwork conducted on two talus slopes. The block fields studied were Raven Rock Hollow in Maryland and River of Rocks at Hawk Mountain in Pennsylvania, and the talus slopes were located at Catoctin Mountain, Maryland and Waggoner’s Gap, Pennsylvania. The importance of geomorphic processes …

Seasonal Origins Of Soil Water Used By Trees, Scott T. Allen, James W. Kirchner, Sabine Braun, Rolf T. W. Siegwolf, Gregory R. Goldsmith

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Rain recharges soil water storages and either percolates downward into aquifers and streams or is returned to the atmosphere through evapotranspiration. Although it is commonly assumed that summer rainfall recharges plant-available water during the growing season, the seasonal origins of water used by plants have not been systematically explored. We characterize the seasonal origins of waters in soils and trees by comparing their midsummer isotopic signatures (δ2H) to seasonal isotopic cycles in precipitation, using a new seasonal origin index. Across 182 Swiss forest sites, xylem water isotopic signatures show that summer rain was not the predominant water source …

Ecological Response Of Phytoplankton To The Oil Spills In The Oceans, Danling Tang, Jing Sun, Li Zhou, Sufen Wang, Ramesh P. Singh, Gang Pan

Mathematics, Physics, and Computer Science Faculty Articles and Research

Oil spills in oceans have substantial influence on marine ecosystems. This study investigates 21 oil spills in the world. Analyzing Chlorophyll-a (Chl-a) from Moderate Resolution Imaging Spectroradiomerer (MODIS) data after Penglai oil spills on 4 June 2011, found a bloom with peak value of Chl-a (13.66 mg m⁻³) spread over an area of 800 km² during 18–25 June 2011, and a pronounced increase in the monthly Chl-a concentration (6.40 mg m⁻³) on June 2012 in the Bohai Sea. Out of the 21 oil spills, 14 blooms were observed, while 11 …

Assessment Of The Effects Of Climate Change On Evapotranspiration With An Improved Elasticity Method In A Nonhumid Area, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Climatic elasticity is a crucial metric to assess the hydrological influence of climate change. Based on the Budyko equation, this study performed an analytical derivation of the climatic elasticity of evapotranspiration (ET). With this derived elasticity, it is possible to quantitatively separate the impacts of precipitation, air temperature, net radiation, relative humidity, and wind speed on ET in a watershed. This method was applied in the Wuding River Watershed (WRW), located in the center of the Yellow River Watershed of China. The estimated rate of change in ET caused by climatic variables is −10.69 mm/decade, which is close to the …

Quantifying The Impact Of Climate Change And Human Activities On Streamflow In A Semi-Arid Watershed With The Budyko Equation Incorporating Dynamic Vegetation Information, Lei Tian, Jiming Jin, Pute Wu, Guo-Yue Niu

Watershed Sciences Faculty Publications

Understanding hydrological responses to climate change and land use and land cover change (LULCC) is important for water resource planning and management, especially for water-limited areas. The annual streamflow of the Wuding River Watershed (WRW), the largest sediment source of the Yellow River in China, has decreased significantly over the past 50 years at a rate of 5.2 mm/decade. Using the Budyko equation, this study investigated this decrease with the contributions from climate change and LULCC caused by human activities, which have intensified since 1999 due to China’s Grain for Green Project (GFGP). The Budyko parameter that represents watershed characteristics …

Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO^® ChromaTOF^® software and facilitates selection of analytes of interest based on peak area …

Mental Models And Neutrosophic Cognitive Maps (Modelos Mentales Y Mapas Cognitivos Neutrosóficos), Maykel Leyva-Vazquez, Rebeca Escobar-Jara, Florentin Smarandache

Branch Mathematics and Statistics Faculty and Staff Publications

In this work, elements related to mental models elicitation and analysis are addressed through causal models. Issues related to the need to include indeterminacy in causal relationships through neutrophic cognitive maps are discussed. A proposal for static analysis in neutrosophic cognitive maps is presented. The following activities are included in the proposal: Calculate, measures of centrality, Classify nodes, De-neutrosification, and Ranking nodes. As future works, the incorporation of new metrics of centrality in neutrosophic cognitive maps is proposed. The inclusion of scenario analysis to the proposal is another area of future work.

Atomistic Simulations And Network-Based Modeling Of The Hsp90-Cdc37 Chaperone Binding With Cdk4 Client Protein: A Mechanism Of Chaperoning Kinase Clients By Exploiting Weak Spots Of Intrinsically Dynamic Kinase Domains, John Czemeres, Kurt Buse, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37- Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic …

Virtual Reality As A Training Tool To Treat Physical Inactivity In Children, Adam W. Kiefer, David Pincus, Michael J. Richardson, Gregory D. Myer

Psychology Faculty Articles and Research

Lack of adequate physical activity in children is an epidemic that can result in obesity and other poor health outcomes across the lifespan. Physical activity interventions focused on motor skill competence continue to be developed, but some interventions, such as neuromuscular training (NMT), may be limited in how early they can be implemented due to dependence on the child’s level of cognitive and perceptual-motor development. Early implementation of motor-rich activities that support motor skill development in children is critical for the development of healthy levels of physical activity that carry through into adulthood. Virtual reality (VR) training may be beneficial …

No Evidence For Trace Metal Limitation On Anaerobic Carbon Mineralization In Three Peatland Soils, Jason K. Keller, Jillian Wade

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands store roughly one-third of the terrestrial soil carbon and release the potent greenhouse gas methane (CH₄) to the atmosphere, making these wetlands among the most important ecosystems in the global carbon cycle. Despite their importance, the controls of anaerobic decomposition of organic matter to carbon dioxide (CO₂) and CH₄ within peatlands are not well understood. It is known, however, that the enzymes responsible for CH₄ production require cobalt, iron and nickel, and there is a growing appreciation for the potential role of trace metal limitation in anaerobic decomposition. To explore the possibility of …

T-Time: A Data Repository Of T Cell And Calcium Release-Activated Calcium Channel Activation Imagery, Cody Arbuckle, Milton L. Greenberg, Adrienne Bergh, Rene German, Nick Sirago, Erik J. Linstead

Mathematics, Physics, and Computer Science Faculty Articles and Research

BACKGROUND: A fundamental understanding of live-cell dynamics is necessary in order to advance scientific techniques and personalized medicine. For this understanding to be possible, image processing techniques, probes, tracking algorithms and many other methodologies must be improved. Currently there are no large open-source datasets containing live-cell imaging to act as a standard for the community. As a result, researchers cannot evaluate their methodologies on an independent benchmark or leverage such a dataset to formulate scientific questions.

FINDINGS: Here we present T-Time, the largest free and publicly available data set of T cell phase contrast imagery designed with the …

Associated Dataset: Climate Change Impacts On Southern Ross Sea Phytoplankton Composition, Productivity And Export, Daniel E. Kaufman, Marjorie A.M. Friedrichs, Walker O. Smith Jr., Eileen E. Hofmann, Michael S. Dinniman, John C.P. Hemmings

Data

This dataset includes data used in the publication Kaufman et al., 2017, JGR-Oceans, which investigates how these climatic changes in the Ross Sea, Antarctica, may alter phytoplankton composition, primary productivity and export. A one-dimensional version of the Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification was adapted for use in the Ross Sea (MEDUSA-RS). Glider measurements were used to force MEDUSA-RS, which includes diatoms and both solitary and colonial forms of Phaeocystis antarctica. Model performance was evaluated with glider observations, and experiments were conducted using projections of physical drivers for mid- and late-21st century. Additional scenarios examined the …

Chapman University 2016 Environmental Audit: Residence Life Dining Services Equipment, Alexandra Fw Sidun, Devon T. Bloss

Student Scholar Symposium Abstracts and Posters

Chapman University accommodates over 1700 student meal plans per day through the on-campus dining services provided by Sodexo Restaurant Services. The commercial-grade kitchens found in the Randall Dining Commons (RDC) of Sandhu Conference Center are frequently used to prepare food for students for every meal, seven days a week. The RDC kitchen facility has staff working around the clock and high consumption electrical, water, and gas appliances constantly running to parallel the high demand. The frequent use of commercial kitchen appliances results in an enormous consumption of energy and water resources leading to comparably high utility bills. Measuring the energy …

The Women Of Helamb: Life After The 2015 Earthquake, Emma Squier

Independent Study Project (ISP) Collection

Disasters exacerbate inequalities that are already present in the society, put particular groups of individuals at risk, specifically women. The vulnerabilities of women shape the way they experience disasters as well as their ability to recover from them. Although it has now been over a year since the earthquake that occurred in Nepal on April 25, 2015, the recovery has been slow, and the destruction that it has caused is still greatly visible. For this project, women in the Helambu region of Nepla were interviewed to learn about how their lives were affected by the earthquake and the challenges that …

Success Stories And Emerging Themes In Conservation Physiology, Christine L. Madliger, Steven J. Cooke, Erica J. Crespi, Jennifer L. Funk, Kevin R. Hultine, Kathleen E. Hunt, Jason R. Rohr, Brent J. Sinclair, Cory D. Suski, Craig K. R. Willis, Oliver P. Love

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The potential benefits of physiology for conservation are well established and include greater specificity of management techniques, determination of cause–effect relationships, increased sensitivity of health and disturbance monitoring and greater capacity for predicting future change. While descriptions of the specific avenues in which conservation and physiology can be integrated are readily available and important to the continuing expansion of the discipline of ‘conservation physiology’, to date there has been no assessment of how the field has specifically contributed to conservation success. However, the goal of conservation physiology is to foster conservation solutions and it is therefore important to assess whether …

Report On The Workshop For Life Detection In Samples From Mars, Gerhard Kminek, Catherine Conley, Carlton C. Allen, Douglas H. Bartlett, David W. Beaty, Liane G. Benning, Rohit Bhatia, Penelope J. Boston, Caroline Duchaine, Jack D. Farmer, George J. Flynn, Daniel P. Glavin, Yuri Gorby, John E. Hallsworth, Rakesh Mogul, Duane Moser, P. Buford Price, Ruediger Pukall, David Fernandez-Remolar, Caroline L. Smith, Kenneth M. Stedman, Andrew Steele, Ramunas Stepanauskas, Henry Sun, Jorge L. Vago, Mary A. Voytek, Paul S. Weiss, Frances Westfall

Biology Faculty Publications and Presentations

The question of whether there is or was life on Mars has been one of the most pivotal since Schiaparellis’ telescopic observations of the red planet. With the advent of the space age, this question can be addressed directly by exploring the surface of Mars and by bringing samples to Earth for analysis. The latter, however, is not free of problems. Life can be found virtually everywhere on Earth. Hence the potential for contaminating the Mars samples and compromising their scientific integrity is not negligible. Conversely, if life is present in samples from Mars, this may represent a potential source …