Life Sciences Commons^™

A Single-Cell Gene Expression Atlas Of Human Follicular Aspirates: Identification Of Leukocyte Subpopulations And Their Paracrine Factors, Yohan Choi, Hayce Jeon, Mats Brännström, James W. Akin, Thomas E. Curry, Misung Jo

UK CARES Faculty Publications

Leukocytes are in situ regulators critical for ovarian function. However, little is known about leukocyte subpopulations and their interaction with follicular cells in ovulatory follicles, especially in humans. Single-cell RNA sequencing (scRNA- seq) was performed using follicular aspirates obtained from four IVF patients and identified 13 cell groups: one granulosa cell group, one thecal cell group, 10 subsets of leukocytes, and one group of RBC/platelet. RNA velocity analyses on five granulosa cell populations predicted developmental dynamics denoting two projections of differentiation states. The cell type-specific transcriptomic profiling analyses revealed the presence of a diverse array of leukocyte-derived factors that can …

Effect Of Lifestyle-Based Lipid Lowering Interventions On The Relationship Between Circulating Levels Of Per-And Polyfluoroalkyl Substances And Serum Cholesterol, Stephanie Morgan, M. Abdul Mottaleb, Maria P. Kraemer, Debra K. Moser, Jessica Worley, Andrew J. Morris, Michael C. Petriello

UK CARES Faculty Publications

Exposure to certain per-and polyfluoroalkyl substances (PFAS) has been shown to be positively associated with total and/or low-density lipoprotein cholesterol. Examining this association in lipid lowering interventions may provide additional evidence linking PFAS to cardiovascular risk. We examined the relationship of 6 PFAS with cholesterol in a 6-month lifestyle-based intervention. We quantitated PFAS in 350 individuals at baseline and post intervention and examined associations of PFAS with cholesterol before and after intervention. Food frequency questionnaires and GIS analyses were used to investigate PFAS hotspots and possible exposure routes. Cholesterol significantly decreased following intervention and in parallel, PFOS, PFOA, PFHxS, and …

Genomics Of Secondarily Temperate Adaptation In The Only Non-Antarctic Icefish, Angel G. Rivera-Colón, Niraj Rayamajhi, Bushra Fazal Minhas, Giovanni Madrigal, Kevin T. Bilyk, Veronica Yoon, Mathias Hüne, Susan Gregory, C. H.Christina Cheng, Julian M. Catchen

Department of Biology Faculty Scholarship and Creative Works

White-blooded Antarctic icefishes, a family within the adaptive radiation of Antarctic notothenioid fishes, are an example of extreme biological specialization to both the chronic cold of the Southern Ocean and life without hemoglobin. As a result, icefishes display derived physiology that limits them to the cold and highly oxygenated Antarctic waters. Against these constraints, remarkably one species, the pike icefish Champsocephalus esox, successfully colonized temperate South American waters. To study the genetic mechanisms underlying secondarily temperate adaptation in icefishes, we generated chromosome-level genome assemblies of both C. esox and its Antarctic sister species, Champsocephalus gunnari. The C. esox genome is …

Cafuncapa: A Knowledgebase For Systematic Functional Annotations Of Apa Events In Human Cancers, Kexin Huang, Sijia Wu, Xiaotong Yang, Tiangang Wang, Xi Liu, Xiaobo Zhou, Liyu Huang

Faculty, Staff and Student Publications

Alternative polyadenylation (APA) is a widespread posttranscriptional regulation process. APA generates diverse mRNA isoforms with different 3' UTR lengths, affecting mRNA expression, miRNA binding regulation and alternative splicing events. Previous studies have demonstrated the important roles of APA in tumorigenesis and cancer progression through diverse aspects. Thus, a comprehensive functional landscape of diverse APA events would aid in a better understanding of the underlying mechanisms related to APA in human cancers. Here, we built CAFuncAPA (https://relab.xidian.edu.cn/CAFuncAPA/) to systematically annotate the functions of 15478 APA events in human pan-cancers. Specifically, we first identified APA events associated with cancer survival and tumor …

Timolol As A Migraine Acute Attack Therapy: Randomized, Otcs Control Study, Shimaa Elgamal, Hossam Egila, Ibrahim Kabbash, Hussien El-Ansarey, Mohamed Elshafie, Osama Elshafei

Mansoura Medical Journal

Background: Migraine is manifested by recurrent headache attacks, with variable characteristics and associated symptoms. Oral beta blockers are widely used to prevent and reduce the frequency these attacks. However, the use of topical beta blockers for acute treatment is still controversial. Aims: In this randomized double – armed study, we aim to compare the efficacy of Timolol 0.5% eyedrops compared to other over-the-counter (OTC) medications used for acute treatment of migraine. Methods: Fifty-seven patients were randomly allocated to group A (treatment group: Timolol 0.5% eyedrops), and group B (control group: OTC drugs including Non-steroidal anti-inflammatory drugs (NSAIDs), caffeine, aspirin, and …

Mining For Equitable Health: Assessing The Impact Of Missing Data In Electronic Health Records, Emily Getzen, Lyle Ungar, Danielle Mowery, Xiaoqian Jiang, Qi Long

Faculty, Staff and Student Publications

Electronic health records (EHR) are collected as a routine part of healthcare delivery, and have great potential to be utilized to improve patient health outcomes. They contain multiple years of health information to be leveraged for risk prediction, disease detection, and treatment evaluation. However, they do not have a consistent, standardized format across institutions, particularly in the United States, and can present significant analytical challenges- they contain multi-scale data from heterogeneous domains and include both structured and unstructured data. Data for individual patients are collected at irregular time intervals and with varying frequencies. In addition to the analytical challenges, EHR …

Automated Ct Pancreas Segmentation For Acute Pancreatitis Patients By Combining A Novel Object Detection Approach And U-Net, Yang Deng, Lan Lan, Lei You, Kai Chen, Li Peng, Weiling Zhao, Bin Song, Yi Wang, Zhiwei Ji, Xiaobo Zhou

Faculty, Staff and Student Publications

Acute pancreatitis is an inflammatory disorder of the pancreas. Medical imaging, such as computed tomography (CT), has been widely used to detect volume changes in the pancreas for acute pancreatitis diagnosis. Many pancreas segmentation methods have been proposed but no methods for pancreas segmentation from acute pancreatitis patients. The segmentation of an inflamed pancreas is more challenging than the normal pancreas due to the following two reasons. 1) The inflamed pancreas invades surrounding organs and causes blurry boundaries. 2) The inflamed pancreas has higher shape, size, and location variability than the normal pancreas. To overcome these challenges, we propose an …

Editorial: Structure And Function Of Chloroplasts, Volume Iii, Hongbo Gao, Alistair J. Mccormick, Rebecca Roston, Yan Lu

Department of Biochemistry: Faculty Publications

Chloroplasts are endosymbiotic organelles derived from cyanobacteria. They have a double envelope membrane, including the outer envelope and the inner envelope. A complex membrane system, thylakoids, exists inside the chloroplast. It is the site of the light-dependent reactions of photosynthesis. The stroma is the main site of the carbon fixation reactions. Although photosynthesis is a very complicated process with many proteins involved, there are many other important processes that occur in chloroplasts, including the regulation of photosynthesis, the biogenesis and maintenance of the structures, carbohydrate, lipid, tetrapyrrole, amino acid, and isoprenoid metabolism, production of some phytohormones, production of specialized metabolites, …

Joint 2022 European Society Of Thoracic Surgeons And The American Association For Thoracic Surgery Guidelines For The Prevention Of Cancer-Associated Venous Thromboembolism In Thoracic Surgery, Yaron Shargall, Wojtek Wiercioch, Alessandro Brunelli, Sudish Murthy, Wayne Hofstetter, Jules Lin, Hui Li, Lori-Ann Linkins, Marc Crowther, Roger Davis, Gaetano Rocco, Gian Paolo Morgano, Finn Schünemann, Giovanna Muti-Schünemann, James Douketis, Holger J Schünemann, Virginia R Litle

Faculty, Staff and Student Publications

Background: Venous thromboembolism (VTE), which includes deep vein thrombosis and pulmonary embolism, is a potentially fatal but preventable postoperative complication. Thoracic oncology patients undergoing surgical resection, often after multimodality induction therapy, represent among the highest risk groups for postoperative VTE. Currently there are no VTE prophylaxis guidelines specific to these thoracic surgery patients. Evidenced-based recommendations will help clinicians manage and mitigate risk of VTE in the postoperative period and inform best practice.

Objective: These joint evidence-based guidelines from The American Association for Thoracic Surgery and the European Society of Thoracic Surgeons aim to inform clinicians and patients in decisions about …

The Use Of Open Data Kit (Odk) In Characterizing The Cacao Industry Sites In Panay Island, Rhea J. Subong-Espina, Reynold D. Tan, Christine Mae D. Hernando

The Philippine Agricultural Scientist

Cacao is one of the world's most valuable export commodities and cash crops. Western Visayas, along with the other regions in the Philippines, has committed to participate in national efforts to strengthen the production capacity of the cacao industry and address prospects and opportunities for the industry growth and development. This paper presents the results of a region-wide study that mapped out and assessed key cacao-producing areas in Western Visayas, specifically Aklan, Antique, Capiz, and Iloilo. The study sought their current production levels, important agricultural properties of farming areas, production densities, and growth potentials. Geospatial data was generated, analyzed, and …

Impact Of The Dimethyl Sulfoxide Reductase Superfamily On The Evolution Of Biogeochemical Cycles, Michael Wells, Minjae Kim, Denise M. Akob, Partha Basu, John F. Stolz

UK CARES Faculty Publications

The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not …

The Nebraska Bird Review: A Magazine Of Ornithology Of The Nebraska Region. Volume 91, Number 1. March 2023, Nebraska Ornithologists’ Union

Nebraska Bird Review

Winter Field Report, Dec. 2022 - Feb. 2023 by W. Ross Silcock

Annual Color Photo Section

Annual Treasurer's Report for 2022 by Jan Johnson

Subscription and Organization Information

2022-2023 Christmas Bird Counts, Don Paseka

Nebraska Bird Review

Sixteen counts were run in the 2022-2023 CBC season. Because of weather and rescheduling issues, the Crawford, Harrison, and Harlan County counts were cancelled. Eight of the counts were completed during the first week of the count period and the other eight were scattered throughout the remainder of the count period. An early December cold snap seemed to drive many of the birds south, but the weather on actual count days was fairly benign: mostly dry with an average high of 34˚F and an average low of 19˚F and with three circles reporting light snow. The total number of species …

The Nebraska Bird Review Annual Color Photo Section

Nebraska Bird Review

Virginia Rail and chick, Washboard Road, North Platte, Lincoln Co., 28 June 2023. Photo by Boni Edwards.

American Coot, Eagle Scout Lake, Hall Co., April 2020. Photo by Colleen Childers.

Hudsonian Godwit, Marsh Wren Community Wetlands, Lancaster Co., 21 May 2022. Photo by Kirill Belashchenko.

American Avocet, N.P. Dodge Park, Omaha, Douglas Co., 2 May 2023. Photo by Thane Dinsdale

Female Cape May Warbler, photographer's backyard, Bellevue, Sarpy Co., 10 May 2022. Photo by Loren Padelford.

Male Cape May Warbler, Ft. Niobrara NWR, Cherry Co., 13 May 2022. Photo by Gordon Warrick.

Tennessee Warbler, Fontenelle Forest Wetlands, Sarpy Co., 24 …

Forage News [2023-03], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

No abstract provided.

Polymer Coated Urea: Microplastics In The Urban Landscape, C. J. Seely, B. T. Geary, Bryan G. Hopkins

Library/Life Sciences Undergraduate Poster Competition 2023

Polymer Coated Urea (PCU) is an effective fertilizer.

Microplastics, from a wide range of waste materials, pollute water bodies.

One potential source of microplastics are from PCU fertilizers if the coatings are transported overland into water bodies.

Various urban landscape systems vary in the potential for surface runoff.

Valproic Acid Affects Neuronal Specification And Differentiation During Early Optic Tectum Development Of Zebrafish, Sierra C. Dixon, Bailey J. Calder, Shane M. Lilya, Brandon M. Davies, Annalie Martin, Maggie Peterson, Jason M. Hansen, Arminda Suli

Library/Life Sciences Undergraduate Poster Competition 2023

The mammalian superior colliculus and its non-mammalian homolog, the optic tectum (OT), are midbrain structures that integrate multimodal sensory inputs and guide non-voluntary movements in response to prevalent stimuli. Recent studies have implicated this structure as a possible site affected in Autism Spectrum Disorder (ASD). Interestingly, fetal exposure to valproic acid (VPA) has also been associated with an increased risk of ASD in humans and animal models. Therefore, we took the approach of determining the effects of VPA treatment on zebrafish OT development as a first step in identifying the mechanisms that allow its formation. We describe the normal OT …

Understanding The Factors Affecting The Quantity And Composition Of Street Litter: Implication For Management Practices, Alessandra Rossi, Meiyin Wu, Bernabas T. Wolde, Kevin W. Zerbe, Tsung Ta David Hsu, Ariane Giudicelli, Rosana Da Silva

Department of Biology Faculty Scholarship and Creative Works

Some urban areas have more litter than others. Understanding the reason for this is important not only for dealing with urban littering but also for marine water quality because approximately 80% of the world's marine litter originates on land. This study aimed to better understand the quality and quantity of litter on sidewalks along with the sampling site's socio-economic attributes to better discern why some areas have more/different litter than others and what, if any, are the implications for a more tailored waste management strategy. We surveyed twice each of the 35 sites we selected from the Lower Passaic River …

Dredged Sediments Contain Potentially Beneficial Microorganisms For Agriculture And Little Harmful Cyanobacteria, Megan A. Rúa, Ashley N. Julian, Louise Stevenson

Biological Sciences Faculty Publications

Abstract Introduction Soils worldwide are degrading, raising concerns about our ability to feed the growing global population. Soil amendments that can alleviate degradation are gaining attention. The application of sediments dredged from waterways to agricultural fields has increasing promise as a means for improving degraded soils. However, herbaceous plant species may have difficulty establishing on dredged material because of low nutrient availability, inhibitory levels of toxins, unsuitable moisture conditions and lack of microorganisms capable of ameliorating these characteristics. To counteract these issues, we sought to understand if the use of a cover crop would increase the abundance, diversity and function …

Associations Between Preweaning Calf Feeding Behaviors With Age At First Calving And Lactational Performance Using An Automatic Calf Feeder, Turner H. Swartz, Christina Petersson-Wolfe

Dairy Science and Food Science Faculty Publications: 2022 to Present

The objective of this retrospective observational study was to determine whether preweaning calf behaviors and milk replacer (MR) intake from an automatic calf feeder were associated with age at first calving and first-lactation performance. Calves were housed in groups with access to an automatic calf feeder for 7 wk with a maximum milk allowance of 1,800 g/d of MR (12 L/d). Outcomes of interest included age at first calving (n = 137), first-lactation mature-equivalent 305-d (ME305) milk yield (n = 132), and first-lactation ME305 energy-corrected milk (ECM) yield (n = 132). Linear models included the fixed effects of the daily …

Encoding Permanent Records Of Transcription In The Genome, Francesco Ettore Emiliani

Dartmouth College Ph.D Dissertations

Current approaches to study cellular transcriptional states offer only a single frame in the life of a cell, often in a destructive fashion. This means that our state snapshot neither has the context of the past, nor the ability to be traced into the future. To overcome this, we present a technology that can permanently encode gene expression for later recovery. Our technology uses transcriptional responses to guide CRISPR/AsCas12a to ‘write’ information into the cell’s own genome, creating a permanent and heritable record of this response. By placing a set of AsCas12a guides under the control of a Wnt-responsive TCF/LEF …

Lichens Of Ultramafic Rocks: A Multidisciplinary Approach To Understanding The Ecology Of An Understudied Organism In A Well-Studied System, Michael Mulroy

Master's Theses

Lichens are among the most prominent and successful life forms of metal-rich habitats, including ultramafic rocks and soils; however, research on lichens of ultramafic habitats is limited, especially on the North American continent. A review of the published literature on lichens of ultramafic substrates in North America yielded a total of 437 lichen species reported from ultramafic rocks and soils. Lichen assemblages of ultramafic substrates vary in composition and are dominated by acidophytic (low pH preferring) taxa with a minor, but consistent, basiphytic (high pH preferring) component. Species lists from ultramafic habitats in different geographic regions varied widely, suggesting that …

Fenclorim Rice Safening And Weed Control With Fall-Applied Acetochlor And Pyroxasulfone, Tristen H. Avent, Jason K. Norsworthy, Thomas R. Butts, Trenton Roberts, Nicholas R. Bateman

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Applications of very long-chained fatty acid elongase (VLCFA)-inhibiting herbicides are currently not labeled within U.S. rice (Oryza sativa L.) production but have been used in Asian rice production to suppress weedy rice and control other annual grasses and small-seeded broadleaves. Therefore, separate experiments were initiated in the fall of 2019 and 2020 to evaluate rice tolerance and weedy rice (O. sativa L.) control with acetochlor and pyroxasulfone in the following spring. A three-factor experiment within a randomized complete block design was implemented with the factors being (1) herbicide choice (acetochlor or pyroxasulfone), (2) a low or high herbicide …

Comorbid Mental Illness In Adults Correspond With Certain Demographics And Higher Rates Of Injuries And Poisoning, Mckay A. Ashton, Ray M. Merrill

Library/Life Sciences Undergraduate Poster Competition 2023

• Mental illness is a common problem among adults aged 18 years and older in the United States, with approximately 21% (15.8% men and 25.8% women) of the population living with a mental, behavioral, or emotional disorder.
• Comorbidity is the presence of at least one other mental health disorder in relation to the index disorder, and has been found to be present in 45% to 54% of those with a mental health disorder
• Although it is well understood that the prevalence of comorbid mental health disorders is common, there is less known about which conditions most commonly occur together and how …

Capturing Of Organic Carbon And Nitrogen In Eelgrass Sediments Of Southern Scandinavia, Carmen Leiva-Dueñas, Anna Elizabeth Løvgren Graversen, Gary T. Banta, Marianne Holmer, Pere Masque, Peter Anton Upadhyay Stæhr, Dorte Krause-Jensen

Research outputs 2022 to 2026

The ability of seagrass meadows to filter nutrients and capture and store CO₂ and nutrients in the form of organic carbon (OC) and nitrogen (N) in their sediments may help to mitigate local eutrophication as well as climate change via meadow restoration and protection. This study assesses OC and N sediment stocks (top 50 cm) and sequestration rates within Danish eelgrass meadows. At four locations, eelgrass-vegetated and nearby unvegetated plots were studied in protected and exposed areas. The average OC and N sediment 50 cm stocks were 2.6 ± 0.3 kg OC m ^{− 2} and 0.23 ± 0.01 …

Predicting Fecal Indicator Bacteria Using Spatial Stream Network Models In A Mixed-Land-Use Suburban Watershed In New Jersey, Usa, Tsung Ta David Hsu, Danlin Yu, Meiyin Wu

Department of Biology Faculty Scholarship and Creative Works

Good water quality safeguards public health and provides economic benefits through recreational opportunities for people in urban and suburban environments. However, expanding impervious areas and poorly managed sanitary infrastructures result in elevated concentrations of fecal indicator bacteria and waterborne pathogens in adjacent waterways and increased waterborne illness risk. Watershed characteristics, such as urban land, are often associated with impaired microbial water quality. Within the proximity of the New York–New Jersey–Pennsylvania metropolitan area, the Musconetcong River has been listed in the Clean Water Act’s 303 (d) List of Water Quality-Limited Waters due to high concentrations of fecal indicator bacteria (FIB). In …

A Draft Of The Genome Of The Gulf Coast Tick, Amblyomma Maculatum, Jose M.C. Ribeiro, Natalia J. Bayona-Vásquez, Khemraj Budachetri, Deepak Kumar, Julia Catherine Frederick, Faizan Tahir, Brant C. Faircloth, Travis C. Glenn, Shahid Karim

Faculty Publications

The Gulf Coast tick, Amblyomma maculatum, inhabits the Southeastern states of the USA bordering the Gulf of Mexico, Mexico, and other Central and South American countries. More recently, its U.S. range has extended West to Arizona and Northeast to New York state and Connecticut. It is a vector of Rickettsia parkeri and Hepatozoon americanum. This tick species has become a model to study tick/Rickettsia interactions. To increase our knowledge of the basic biology of A. maculatum we report here a draft genome of this tick and an extensive functional classification of its proteome. The DNA from a single …

Factors Associated With Fathers’ Attendance In A Latino Family Obesity Prevention Program, Sayaka Nagao-Sato, Silvia Alvarez De Davila, Aysegul Baltaci, Roxana Linares, Alejandro Omar Peralta Reyes, Youjie Zhang, Ghaffar Hurtado Choque, Marla Reicks

Journal of Human Sciences and Extension

Community-based programs may contribute to Latino pediatric obesity prevention; however, attendance remains low. This study aimed to identify factors associated with Latino father/male caregiver attendance in family-based adolescent obesity prevention programs conducted as part of a randomized controlled trial. The study used cross-sectional data from 137 fathers in the program, involving eight weekly sessions to improve their children’s energy balance-related behaviors. Evaluation data were collected at baseline and post-intervention. Fathers in a waitlisted control group attended sessions after post-intervention data collection. Attendance patterns were identified using cluster analysis: consistently high attendance (50% of fathers), declining attendance (19%), and non-attendance (31%) …

An Analytic Needs Assessment For Extension Education: Views From Extension Professionals And Faculty, Joseph L. Donaldson, Donna Graham, Shannon Arnold, Lisa K. Taylor, K. S. U. Jayaratne

Journal of Human Sciences and Extension

This study describes professional development for Extension educators and curricula expectations for those preparing for Extension careers – as perceived by members of the American Association for Agricultural Education (AAAE) and Joint Council of Extension Professionals (JCEP). We relate and differentiate findings from two surveys with open-ended questions. Regarding professional development, JCEP respondents identified program planning and evaluation, but AAAE respondents prioritized research methods. JCEP respondents prioritized practical experiences in Extension Education college courses, and AAAE members reported some practical Extension experiences in the college curriculum. College faculty may apply the results for impactful academic, professional development, and research programs.

Rewarding Relationships: A Quasi-Experimental Design Evaluating The Impact Of An Extension Public Relations Seminar, Ashley Mcleod-Morin, Lauri M. Baker, Cheryl Boyer, Anissa M. Zagonel, Angela B. Lindsey

Journal of Human Sciences and Extension

While Extension communication units have seen success in implementing brand strategies to raise awareness of Extension, the public value and need for Extension programming continue to be misunderstood. College students have the potential to ensure the future of Extension is viable. To expose undergraduate students to the brand and value of Extension, a public relations seminar was developed and delivered by a state Extension specialist to 95 students enrolled in an agricultural technical writing course at a land-grant university. The seminar served as a treatment in the quasi-experimental design, which included information about the land-grant mission, Extension resources, and potential …