Digital Commons Network^™

Srtsim: Spatial Pattern Preserving Simulations For Spatially Resolved Transcriptomics, Jiaqiang Zhu, Lulu Shang, Xiang Zhou

Faculty, Staff and Student Publications

Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic. Single-cell simulators are not directly applicable for SRT simulation as they cannot incorporate spatial information. We present SRTsim, an SRT-specific simulator for scalable, reproducible, and realistic SRT simulations. SRTsim not only maintains various expression characteristics of SRT data but also preserves spatial patterns. We illustrate the benefits of SRTsim in benchmarking methods for spatial clustering, spatial expression pattern detection, and cell-cell communication identification.

Umbilical Cord Blood Transplantation: Connecting Its Origin To Its Future, Gabriela Sanchez-Petitto, Katayoun Rezvani, May Daher, Hind Rafei, Partow Kebriaei, Elizabeth J Shpall, Amanda Olson

Faculty, Staff and Student Publications

Transplantation of umbilical cord blood (UCB) is an attractive alternative source of hematopoietic stem cells (HSCs). The unique properties of cord blood and its distinct immune tolerance and engraftment kinetics compared to bone marrow (BM) and peripheral blood progenitor cells, permit a wider disparity in human leukocyte antigen levels between a cord blood donor and recipient after an unrelated umbilical cord blood transplant (UCBT). In addition, it is readily available and has a lowered risk of graft-versus-host disease (GvHD), with similar long-term clinical outcomes, compared to BM transplants. However, the relatively low number of cells administered by UCB units, as …

Understanding Lived Experiences Of Stigma For People Living With Hiv: A Community Based Participatory Research Study, Brent Oliver Dr., Catherine Pearl, Egbert S. Felix – John, Deborah Norris, Folasade J. Elizabeth Olaniyan, Kim Samson, Aniela Dela Cruz, Gabriel Aseselin, Kate Berezowski, Celeste Hayward, Becky Vam Tassel, Floyd Visser

The Qualitative Report

The goal of this project was to better understand the experiences and impacts of HIV stigma and discrimination on people living with HIV and to co-create knowledge that has the potential to challenge existing stigma within the healthcare, social services, and public policy sectors in the province of Alberta, Canada. We employed community-based participatory research and a mixed methods design (survey methods and qualitative interviews) to address these questions. An online survey was completed by 148 people living with HIV and semi-structured interviews were conducted with an additional 20 participants. The research findings have been conceptualized within a social ecological …

Isomerization Of Galactose To Tagatose: Recent Advances In Non-Enzymatic Isomerization, Jikai Zhao, Zhuo Wang, Qing Jin, Danyi Feng, Juhee Lee

School of Earth, Environmental, & Marine Sciences Faculty Publications

The valorization of galactose derived from acid whey to low-calorie tagatose has gained increasing attention. Enzymatic isomerization is of great interest but faces several challenges, such as poor thermal stability of enzymes and a long processing time. In this work, non-enzymatic (supercritical fluids, triethylamine, arginine, boronate affinity, hydrotalcite, Sn-β zeolite, and calcium hydroxide) pathways for galactose to tagatose isomerization were critically discussed. Unfortunately, most of these chemicals showed poor tagatose yields (70%). The latter is able to form a tagatose–calcium hydroxide–water complex, which stimulates the equilibrium toward tagatose and prevents sugar degradation. Nevertheless, the excessive use of calcium hydroxide may …

Anchoring Lifeline Criminal Jurisprudence: Making The Leap From Theory To Critical Race-Inspired Jurisprudence, Danardo S. Jones

Dalhousie Law Journal

This article takes as a starting point the claim that anti-Black racism permeates Canadian society and finds expression in our institutions, most notably the criminal justice system. Indeed, anti-Black racism in criminal justice and its impact on Black lives are not credibly in dispute. Thus, what should concern legal scholars is the staying power or permanence of racism. In other words, should Canadian legal scholars ‘get real’ about the intractability of race? Or can anti-Black racism be effectively confronted by developing legal and evidentiary tools designed to fix, rather than dismantle, the current system? Put another way, this article aims …

Description Of A New Species Of Crossidius Leconte (Coleoptera: Cerambycidae: Cerambycinae: Trachyderini) From Texas, Frederick W. Skillman Jr.

Insecta Mundi

Crossidius wappesi Skillman, new species (Coleoptera: Cerambycidae) is described from Presidio County, Texas, USA.

I discovered a new species of Crossidius LeConte (Cerambycinae) in the fall of 2018 while collecting with Jim Wappes in Presidio County, Texas. Additional specimens were collected at the same location in 2019 by Jim Wappes and Kenneth Kuckartz.

This large, predominately western trachyderine genus presently contains 17 species and 37 subspecies (Bezark 2022). It should be noted that in the study of the genus by Linsley and Chemsak (1961), numerous popu­lations, known from short series, were mentioned, given short descriptions and left nameless. It is …

A New Species Of Cymatodera Gray (Coleoptera: Cleridae) From Honduras, Jacques Rifkind

Insecta Mundi

Cymatodera batleth new species (Coleoptera: Cleridae) is described from Honduras. It appears to belong to a group of Central American congeners that share similar facies and coloration, deeply emarginate elytral apices and elaborately modified male pygidia.

Heretofore ten species of Cymatodera Gray have been recorded from Honduras: C. conflagrata (Klug), C. depau­perata Gorham, C. guatemalensis Schenkling, C. prolixa (Klug), C. sallei Thomson, C. sinuosa Burke, C. rileyi Rifkind, C. crassa Burke and Sole, C. nigrofasciata Burke and Sole, and C. parva Burke which have distributions extending into neighboring Central American countries (Burke 2013; Burke et al. 2017). The known Honduran …

Predicting The Impact Of Climate Change On The Distribution Of Rhipicephalus Sanguineus In The Americas, Marcos Sánchez Pérez, Teresa Patricia Feria-Arroyo, Crystian Sadiel Venegas Barrera, Carolina Sosa-Gutiérrez, Javier Torres, Katherine A. Brown, Guadalupe Gordillo Pérez

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Biology)

Climate change may influence the incidence of infectious diseases including those transmitted by ticks. Rhipicephalus sanguineus complex has a worldwide distribution and transmits Rickettsial infections that could cause high mortality rates if untreated. We assessed the potential effects of climate change on the distribution of R. sanguineus in the Americas in 2050 and 2070 using the general circulation model CanESM5 and two shared socioeconomic pathways (SSPs), SSP2-4.5 (moderate emissions) and SSP2-8.5 (high emissions). A total of 355 occurrence points of R. sanguineus and eight uncorrelated bioclimatic variables were entered into a maximum entropy algorithm (MaxEnt) to produce 50 replicates per …

Behavioural Defences Against Parasites Across Host Social Structures, Sebastian Stockmeier, Yuko Ulrich, Gregory F. Albery, Sylvia Cremer, Patricia C. Lopes

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

1. Animals exhibit a variety of behavioural defences against socially transmitted parasites. These defences evolved to increase host fitness by avoiding, resisting or tolerating infection.
2. Because they can occur in both infected individuals and their uninfected social partners, these defences often have important consequences for the social group.
3. Here, we discuss the evolution and ecology of anti-parasite behavioural defences across a taxonomically wide social spectrum, considering colonial groups, stable groups, transitional groups and solitary animals.
4. We discuss avoidance, resistance and tolerance behaviours across these social group structures, identifying how social complexity, group composition and interdependent social relationships may contribute to the …

Rhythmic Eating Pattern Preserves Fruit Fly Muscle Function Under Obese Conditions, Public Relations

Browse All News

No abstract provided.

Results Of Duet: A Web-Based Weight Loss Randomized Controlled Feasibility Trial Among Cancer Survivors And Their Chosen Partners, Wendy Demark-Wahnefried, Robert A Oster, Tracy E Crane, Laura Q Rogers, W Walker Cole, Harleen Kaur, David Farrell, Kelsey B Parrish, Hoda J Badr, Kathleen Y Wolin, Dori W Pekmezi

Faculty, Staff and Students Publications

Simple Summary

Effective and scalable diet, exercise, and weight management interventions are needed for primary cancer prevention in the general public, as well as for cancer control and tertiary prevention among the growing population of cancer survivors. A 6-month online intervention, entitled “Daughters, dUdes, mothErs, and others Together” (DUET), was designed to promote weight loss, a healthful diet, and increased physical activity among cancer survivors and their chosen partners. Fifty-six cancer survivor-partner dyads (n = 112 participants in total) were recruited into a randomized controlled trial that compared DUET to a waitlist control. The trial surpassed all feasibility endpoints …

Raman Spectroscopy - An Analytical Tool For Biologics, Cindy Mayorga, Shreya Milind Athalye, Mohit Verma

Graduate Industrial Research Symposium

Raman Spectroscopy (RS) is a non-invasive technique that analyses biomolecules qualitatively and quantitatively. Raman spectroscopy measures the inelastic scattering of light due to molecular vibrations. It can be applied to liquid, solid, or semi-solid forms of the biological sample reducing the sample preparation measures. The minimal sample preparation and non-invasive nature of Raman Spectroscopy can be applied in developing a Process analytical technology (PAT) tool and as a diagnostic tool. We demonstrated qualitative and quantitative measurements of biologics with Raman spectroscopy through our previous studies. Our results indicate that RS distinguishes various Gram-positive and Gram-negative bacteria, fungi, and a mixture …

Yield Stress And Flow Behavior Of Enzyme Liquiefied Slurries From Corn Cobs And Corn Stover Pellets, Diana Milena Ramiez Gutierrez

Graduate Industrial Research Symposium

With the increase in population, the world will depend on renewable sources to meet the increasing energy needs. The use of lignocellulosic biomass as a renewable source has been proven efficient for conversion to cellulosic ethanol and capable of contributing to thresholds for energy demand while reducing greenhouse gases by 90% when compared with fossil fuels. However, feeding and flow of biomass within biorefineries represent a constant challenge and needs to be addressed.

The purpose of this research is to understand the yield stress and flow behavior of enzyme liquefied slurries from Corn Cobs and Corn Stover Pellets and explore …

Design Of A Virtual Lab For Plate Heat Exchanger Sterilization System, Daniel N. Hauersperger

Graduate Industrial Research Symposium

Online learning has become a staple in contemporary education, requiring new ways to display and promote experiences. Virtual labs can be used to give learners a way to enter a lab environment without the need for expensive equipment or materials. One example is to give students a “hands-on” experience using a sterilization process to preserve biological materials. Sterilization systems incorporate heat exchangers to bring product up to temperature and then cool product down quickly to prevent excess degradation of nutrients. Data generated from virtual labs will allow learners to use the system responses and build their understanding of how the …

Identifying Essential Genes For The Assembly And Function Of Tails In Novel Myoviridae Bacteriophages, Harry Ashbaugh, Kari Clase

Graduate Industrial Research Symposium

A bacteriophage is a virus that infects bacterial hosts. They are typically composed of a head, a tail, and fibers on the tail that allow it to attach to the bacterial membrane. Myoviridae are a family of bacteriophage that are distinct for their short, contractile tails that undergo conformational changes when they attach to bacteria, which are essential to inject its genetic material into the cell. The purpose of this research is to utilize genetic sequencing and comparative genomics to identify the genes that allow for the tail structure, conformation change, and attachment in novel Myoviridae bacteriophages. In characterizing these …

Sea-Phages Course-Based Undergraduate Research Experience For Creating A Biotechnology Workforce Development Pipeline, Daphne Fauber, Kari Clase, Carol Weaver

Graduate Industrial Research Symposium

Purdue University has been a member of the SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) program since 2011. This program, created in conjunction with the Howard Hughes Medical Institute (HHMI), facilitates undergraduate curriculum for the authentic discovery of novel bacteriophages within the classroom. Since joining the program, undergraduates at Purdue have harnessed wet lab and bioinformatics principles to contribute over 200 previously uncharacterized bacteriophages and 25 novel genomes to the wider scientific literature. The SEA-PHAGES classes at Purdue have resulted in tangible professional deliverables for students through conference presentations and publications. Student outcomes also include transferable skills …

Nucleic Acid Detection Of Live Pathogens On Contaminated Foods, Simerdeep Kaur, Mohit Verma

Graduate Industrial Research Symposium

The goal is to develop a point-of-care biosensor for the detection of live pathogens contaminating beef products. Biosensing of live pathogens is based on isothermal amplification of nucleic acid on a paper-based device. A colorimetric dye is employed as an indicator of the amplification product for visual result. The assay incorporates a compound Propidium monoazide (PMA) that makes the DNA from dead cells inaccessible for amplification. This approach is especially applicable for pathogens that can enter a viable but non-culturable state (VBNC).

Comprehensive Microenvironment Monitoring For The Productivity And Welfare Of Sows And Piglets, Jun Ho Kim

Graduate Industrial Research Symposium

The world is facing increasing food demand and climate change. To improve piglet survivability and sow welfare through microenvironment management using precision technology, a USDA sponsored research project started in 2021 and is ongoing. A comprehensive yet low-cost system was designed and developed for continuous and real-time microenvironment monitoring in three rooms of Farrowing Building #1 at the Animal Sciences Research and Education Center, Purdue University. The system consists of two gas analyzers and 103 different sensors, including sensors in a weather station. The first trial of the project was conducted from Jan. 13 to Feb. 8, 2023, when the …

Identifying Non-Traditional Slippery Sequences Associated With Translational Frameshifts, Aaron J. Gin, Kari Lynn Clase

Graduate Industrial Research Symposium

Genetic frameshifts are a mutation in which
a nucleotide skip leads to a shift in the
reading frame. In viruses, these frameshifts
can be programmed using a slippery
sequence to bypass the stop codon
associated with the initial protein. This
allows for variable control of protein
expression. In bacteriophages, translational
frameshifts have been identified but only a
few have been proven experimentally. Using
experimental data and comparative
genomics, non-traditional slippery
sequences can be identified as assisting in
controlling the protein coding throughout
viruses. Novel slippery sequences can aid in
the understanding of protein expression in
biological environments and further the …

The Next-Gen Crop Nutrient Stress Identification With High-Precision Sensing Technology In Digital Agriculture, Zhihang Song, Ziling Chen, Xing Wei, Jian Jin

Graduate Industrial Research Symposium

Crop yields are facing significant losses from nutrient deficiencies. Over-fertilizing also has negative economic and environmental impacts. It is challenging to optimize fertilizing without an accurate diagnosis. Recently, plant phenotyping has demonstrated outstanding capabilities in estimating crop traits. As one of the leading technologies, LeafSpec, provides high-quality crop image data for improving phenotyping quality. In this study, novel algorithms are developed for LeafSpec to identify crop nutrient deficiencies more accurately. Combined with UAV system, this technology will bring growers a robust solution for fertilizing diagnosis and scientific crop management.

The Pursuit Of Peak Athletic Performance, Trevor Short

Topics in Exercise Science and Kinesiology

Topics in Exercise Science and Kinesiology Volume 4: Issue 1, Article 3, 2023. Achieving peak performance in sports is a multifactorial phenomenon that spans several scientific disciplines. The optimization of human performance requires a comprehensive and systematic assessment that identifies potential performance-inhibiting factors. The result of such analysis allows for more individualized and accurate evaluation, athlete monitoring, and training interventions. Thus, there is a need for a multidisciplinary model of peak performance to guide practitioners when conducting a comprehensive analysis. The purpose of this manuscript is to provide a brief but practical vade mecum for practitioners to consider in the …

An Intervention To Promote Growth Mindset And Stem Self-Efficacy Of High School Students: Exploring The Complexity Of Beliefs, Amy Kramer, Emily Dringenberg, Carter Morris, Darcy Mccarthy

Journal of Pre-College Engineering Education Research (J-PEER)

The marginalization of women in engineering is a persistent problem. The overall goal of our collaborative project was to promote interest and participation in science, technology, engineering, and mathematics (STEM), particularly for high school girls. We took an action research approach with a local high school science teacher to develop, implement, and research the impact of a classroom-based intervention designed to encourage growth mindset and STEM self-efficacy beliefs using mixed methods. We analyzed pre- and postsurvey data collected using a control-treatment design to determine the impact of the intervention on high school boys’ and girls’ self-efficacy and mindset beliefs. We …

Additional Curricular Changes Proposed For 2023-2025 Morris Catalog Pt. 3, Curriculum Committee

Curriculum Committee Reports

No abstract provided.

Is God A Magician Or Scientist?, Sarah Palmer, Josh Oliver, Jessica Abele, Jamie Jensen Ph.D

Library/Life Sciences Undergraduate Poster Competition 2023

There is a body of evidence in biology education indicating that most American undergraduate students believe evolution acceptance to be an aesthetic position (1). Introductory biology professors at Brigham Young University have gathered essays written by students entering the class on their experiences with evolution since about 1980. Because BYU is a religious college, most of these students wrote about how their understanding of God impacts their acceptance of evolution. To learn whether student perceptions of God have changed in the past 30 years, we qualitatively analyzed these essays from a cohort of students in 1992 and another cohort of …

Heart Breaking: Rapid Discovery Of Novel Heart Development Genes In Zebrafish, Bryce Johnson, Andrew Jenkins, Ryan Halls, Cayden Bro, Jonathon T. Hill

Library/Life Sciences Undergraduate Poster Competition 2023

Congenital heart defects (CHD) impact approximately 1% with BioRender.com of the U.S. population. Identifying the genes and pathways involved in embryonic heart development is essential to better diagnose and treat CHD. Previous genetic screens were nonspecific and inefficient at finding novel genes To find genes associated with CHD, we ran a novel rapid genetic screening method on zebrafish, an established model for studying human heart development.

The Effect Of Menstruation Duration On The Achilles Tendon Cross-Sectional Area In Female Ballet Dancers, Li Kaitong, Aaron W. Johnson, Steven Allen, Shayla Bott, Chris Dillon, Joshua K. Sponbeck, Camille Nguyen Jones, Annie Allen

Library/Life Sciences Undergraduate Poster Competition 2023

Females are more likely to suffer Achilles tendon injury that consequently leads to more complications including pain or tendon rupture, and experiencing fewer benefits from therapeutic interventions. There is a lack of knowledge on how estrogen, which may limit collagen synthesis, can affect tendon health and growth. The duration and cross-sectional area (CSA) of the Acobjective of this study is to examine the relationship between menstruation hilles tendon over a 5-month period of intensive dance training.

Reconversion Of Parahydrogen Gas In Surfactant-Coated Glass Nmr Tubes, Robert V. Chimenti, James Daley, James Sack, Jennifer Necsutu, Nicholas Whiting

College of Science & Mathematics Departmental Research

The application of parahydrogen gas to enhance the magnetic resonance signals of a diversity of chemical species has increased substantially in the last decade. Parahydrogen is prepared by lowering the temperature of hydrogen gas in the presence of a catalyst; this enriches the para spin isomer beyond its normal abundance of 25% at thermal equilibrium. Indeed, parahydrogen fractions that approach unity can be attained at sufficiently low temperatures. Once enriched, the gas will revert to its normal isomeric ratio over the course of hours or days, depending on the surface chemistry of the storage container. Although parahydrogen enjoys long lifetimes …

Anterior And Posterior Tongue Regions And Taste Papillae: Distinct Roles And Regulatory Mechanisms With An Emphasis On Hedgehog Signaling And Antagonism., Archana Kumari, Charlotte M. Mistretta

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Sensory receptors across the entire tongue are engaged during eating. However, the tongue has distinctive regions with taste (fungiform and circumvallate) and non-taste (filiform) organs that are composed of specialized epithelia, connective tissues, and innervation. The tissue regions and papillae are adapted in form and function for taste and somatosensation associated with eating. It follows that homeostasis and regeneration of distinctive papillae and taste buds with particular functional roles require tailored molecular pathways. Nonetheless, in the chemosensory field, generalizations are often made between mechanisms that regulate anterior tongue fungiform and posterior circumvallate taste papillae, without a clear distinction that highlights …

The Need For Fathers As Role Models To Aid Family And Social Cohesion In Resource-Constrained Contexts, Tolulope Victoria Balogun, Leoba Nyathi, Kezia October, Athandiwe Skhuni, Nicolette V. Roman

Journal of Family Strengths

The impact of parents on their children, especially in the developmental years, must not be undermined. Each parent influences a child separately and in different ways, which may have long-lasting effects on adulthood. Paternal involvement in children’s lives plays a different but crucial role that leads to improved behavioural and psychosocial outcomes. This study identifies and explores the need for fathers as role models to aid family and social cohesion in resource-constrained contexts. Individuals older than 18 years were interviewed from four different communities in the Western Cape Province of South Africa. Interviews were conducted in English, Afrikaans, and IsiXhosa …

Mystifying Mimics: The Influence Of Distribution On Mimicry, Taylor Probst, Dallin Kohler, Alison Whiting, Jacob Searcy

Library/Life Sciences Undergraduate Poster Competition 2023

Many animals display bright colors or patterns to advertise or warn predators that they are dangerous. Coral snakes effectively use bright red and yellow bands to warn of their venom. There are also many harmless snakes which try to copy or mimic the color patterns of the coral snakes to gain that same protection from predators without the venom. This is known as Batesian mimicry. It has long been thought that for mimicry to be effective, both the dangerous animals and their mimics need to be found in the same geographic area. This study focuses on two species of kingsnake, …