Digital Commons Network^™

Stratomod: Predicting Sequencing And Variant Calling Errors With Interpretable Machine Learning, Nathan Dwarshuis, Peter Tonner, Nathan D Olson, Fritz J Sedlazeck, Justin Wagner, Justin M Zook

Faculty, Staff and Students Publications

Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for their application. Currently, assessing such tradeoffs relies on intuition about how a certain pipeline will perform in a given genomic context. We present StratoMod, which addresses this problem using an interpretable machine-learning classifier to predict germline variant calling errors in a data-driven manner. We show StratoMod can precisely predict recall using Hifi or Illumina and leverage StratoMod's interpretability to measure contributions from difficult-to-map and homopolymer regions for …

Implementation Of Inquiry-Based Science Practices, Christian Larson

Graduate Teacher Education

This paper was a synthesis of current research on the implementation of inquiry-based learning (IBL) in high school science classrooms. The research was a combination of quantitative, qualitative, and mixed-method studies done to investigate the barriers to implementation, the importance of proper training and resources, and the effectiveness of IBL practices on student success and interest in science. The research showed several different barriers noted in historical implementation of IBL practices an educational leader should note and prepare for when attempting to implement these strategies. It also showed the positive effect of relevant and meaningful professional development opportunities at many …

What Is Truly Best For Students For Them To Succeed In High School Classrooms Today, Matthew Ortt

Graduate Teacher Education

This paper examined research studies that explored what is truly best for student success in the field of education. This topic aimed to determine the best way to teach students or ensure they reach their full potential through research findings from various qualitative, quantitative, and mixed-method studies. These studies examined the areas of school start times and student’s daily schedules, academic structure and how classes are being offered, student mental health, and the use of technology in the classroom. The research showed a plethora of ways that could help students succeed and gave great insights into data that may already …

Long-Term Human Immune Reconstitution, T-Cell Development, And Immune Reactivity In Mice Lacking The Murine Major Histocompatibility Complex: Validation With Cellular And Gene Expression Profiles., Milita Darguzyte, Philipp Antczak, Daniel Bachurski, Patrick Hoelker, Nima Abedpour, Rahil Gholamipoorfard, Hans A Schlößer, Kerstin Wennhold, Martin Thelen, Maria A Garcia-Marquez, Johannes Koenig, Andreas Schneider, Tobias Braun, Frank Klawonn, Michael Damrat, Masudur Rahman, Jan-Malte Kleid, Sebastian J Theobald, Eugen Bauer, Constantin Von Kaisenberg, Steven R Talbot, Leonard D. Shultz, Brian Soper, Renata Stripecke

Faculty Research 2024

Background: Humanized mice transplanted with CD34+ hematopoietic cells (HPCs) are broadly used to study human immune responses and infections in vivo and for testing therapies pre-clinically. However, until now, it was not clear whether interactions between the mouse major histocompatibility complexes (MHCs) and/or the human leukocyte antigens (HLAs) were necessary for human T-cell development and immune reactivity. Methods: We evaluated the long-term (20- week) human hematopoiesis and human T-cell development in NOD Scid Gamma (NSG) mice lacking the expression of MHC class I and II (NSG-DKO). Triplicate experiments were performed with HPCs obtained from three donors, and humanization was confirmed …

Scaling Individual Tree Transpiration With Thermal Cameras Reveals Interspecies Differences To Drought Vulnerability, Mostafa Javadian, Donald M. Aubrecht, Joshua B. Fisher, Russell L. Scott, Sean P. Burns, Jen L. Diehl, J. William Munger, Andrew D. Richardson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Understanding tree transpiration variability is vital for assessing ecosystem water-use efficiency and forest health amid climate change, yet most landscape-level measurements do not differentiate individual trees. Using canopy temperature data from thermal cameras, we estimated the transpiration rates of individual trees at Harvard Forest and Niwot Ridge. PT-JPL model was used to derive latent heat flux from thermal images at the canopy-level, showing strong agreement with tower measurements (R2 = 0.70–0.96 at Niwot, 0.59–0.78 at Harvard at half-hourly to monthly scales) and daily RMSE of 33.5 W/m2 (Niwot) and 52.8 W/m2 (Harvard). Tree-level analysis revealed species-specific responses to …

Regular Nonsteroidal Anti-Inflammatory Drug Use Increases Stress Fracture Risk In The General Population: A Retrospective Case-Control Study, Alexandra Ciuciu, Chris Mulholland, Michael A. Bozzi, Chris C. Frymoyer, Leonardo Cavinatto, David Yaron, Marc I. Harwood, Jeremy D. Close, Christopher J. Mehallo, Ryan E. Tomlinson

Department of Orthopaedic Surgery Faculty Papers

Previous studies have shown that the use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with increased stress fracture risk. This phenomenon has been studied predominantly in high-activity individuals, so data regarding the general population are limited despite the substantial economic and resource burden of stress fracture injuries within the general US population. Furthermore, our preclinical studies demonstrate that regular use of NSAIDs also diminishes the intrinsic ability of bone to resist fracture. To determine the association of regular NSAID use with stress fractures in the general population, we surveyed subjects presenting with either stress fracture or uncomplicated ankle sprain to …

A Proteomics Approach To Study Mouse Long Bones: Examining Baseline Differences And Mechanical Loading-Induced Bone Formation In Young-Adult And Old Mice, Christopher J Chermside-Scabbo, John T Shuster, Petra Erdmann-Gilmore, Eric Tycksen, Qiang Zhang, R Reid Townsend, Matthew J Silva

2020-Current year OA Pubs

With aging, bone mass declines and the anabolic effects of skeletal loading diminish. While much research has focused on gene transcription, how bone ages and loses its mechanoresponsiveness at the protein level remains unclear. We developed a novel proteomics approach and performed a paired mass spectrometry and RNA-seq analysis on tibias from young-adult (5-month) and old (22-month) mice. We report the first correlation estimate between the bone proteome and transcriptome (Spearman

Interleukin-1 Receptor-Associated Kinase 1 In Cancer Metastasis And Therapeutic Resistance: Mechanistic Insights And Translational Advances., Mariana K Najjar, Munazza S Khan, Chuling Zhuang, Ankush Chandra, Hui-Wen Lo

Faculty, Staff and Student Publications

Interleukin-1 Receptor Associated Kinase 1 (IRAK1) is a serine/threonine kinase that plays a critical role as a signaling transducer of the activated Toll-like receptor (TLR)/Interleukin-1 receptor (IL-1R) signaling pathway in both immune cells and cancer cells. Upon hyperphosphorylation by IRAK4, IRAK1 forms a complex with TRAF6, which results in the eventual activation of the NF-κB and MAPK pathways. IRAK1 can translocate to the nucleus where it phosphorylates STAT3 transcription factor, leading to enhanced IL-10 gene expression. In immune cells, activated IRAK1 coordinates innate immunity against pathogens and mediates inflammatory responses. In cancer cells, IRAK1 is frequently activated, and the activation …

Thrombotic, Cardiovascular, And Microvascular Complications Of Myeloproliferative Neoplasms And Clonal Hematopoiesis (Chip): A Narrative Review, Andrew I Schafer, Douglas L Mann

2020-Current year OA Pubs

The most common causes of morbidity and mortality in the myeloproliferative neoplasms (MPNs), with the exception of myelofibrosis, are venous and arterial thrombosis, as well as more recently discovered cardiovascular disease (CVD). Clonal hematopoiesis of indeterminate potential (CHIP) is the subclinical finding in an individual of somatic mutations that are also found in clinically overt MPNs and other myeloid malignancies. The prevalence of "silent" CHIP increases with age. CHIP can transform into a clinically overt MPN at an estimated rate of 0.5 to 1% per year. It is likely, therefore, but not proven, that many, if not all, MPN patients …

Vol. 33, No. 12 / Vol. 34, No. 1 - Whole No. 178, Bernadette Bosky

Mythprint

Mythprint is the monthly bulletin of the Mythopoeic Society, a nonprofit educational organization devoted to the study, discussion, and enjoyment of myth and fantasy literature, especially the works of J.R.R. Tolkien, C.S. Lewis, and Charles Williams. To promote these interests, the Society publishes three magazines, maintains a World Wide Web site, and sponsors the annual Mythopoeic Conference and awards for fiction and scholarship, as well as local and written discussion groups.

Why We Need A Constitutional Right To Healthy Environment In Canada

Fordham Environmental Law Review

The increasing demand for constitutional recognition of the right to a healthy environment (‘RTHE’) has been a matter of public concern and debate in many countries, including Canada.2 This paper asks, will a constitutional RTHE within the Canadian Constitution add any value when statutes already exist to protect the environment (and thereby health)? The present environmental statutes work towards protecting the environment, and by protecting the environment, public health can be protected.3 Together, both of them form a ‘healthy environment’, ie., an environment that fosters a healthy life.4 This paper will argue that there is additional value in recognizing a …

The Cost Of Training A Machine: Lighting The Way For A Climate-Aware Policy Framework That Addresses Artificial Intelligence's Carbon Footprint Problem

Fordham Environmental Law Review

While artificial intelligence (AI) has been a subject of great debate in spaces such as due process, discrimination, and privacy, an area that is lacking in legal scholarship is the technology’s environmental impact. AI promises to be a silver bullet in the increasingly urgent fight against climate change, yet it comes with a considerable cost to our planet. Current industry trends involve AI models being trained on increasingly larger datasets and training methodologies that prioritize brute-force over efficiency. Thus, as AI models increase in complexity and size, so too does the computing power—and energy—required to train and deploy them. Every …

“Forget The Rest ...”: Notes On Magnetic Tape And Other Antiquated Media As Archives Of Afro-Atlantic Liturgy, David Font-Navarrete

Yale Journal of Music & Religion

The virtuosic complexity of Afro-Cuban orisha music has led scholars and artists to enshrine it as a “classical” tradition, and it has become one of most iconic and closely-studied sacred music traditions of the historical Afro-Atlantic. This essay traces the legacies of several analog-era multimedia technologies in orisha music traditions: reel-to-reel and cassette tapes; limited edition and out-of-print books and phonograph discs; ephemeral texts such as album liner notes; and photographic negatives, prints, and slides. The tapes and photos — along with a vast body of informal, unpublished, and out-of-print documents of Afro-Cuban orisha liturgy — are seldom archived by …

Kk 44 Full Issue, Kritika Kultura

Kritika Kultura

No abstract provided.

The Beacon, October 11, 2024, Beacon Staff

The Beacon, 2024-2025

The joys that come with the fall season; Celebrating Hispanic Heritage Month; Talent Showcased at music concert; NW students' favorite fall classics; Coldplay signs off with new album; It's more than just a meeting space; Former NW student athlete comes back to coach; Students are able to embrace fall fun; Students recall amazing SSP experiences; Hispanic Heritage Month; Things to consider as a first-time voter; Chopsticks: 1, Forks: 0; Gennis invented by Mark DeYounge; Raider volleyball gains career highs; Quarterback switch at Doane football game; Preparing students for success; A Homecoming full of running events;

Towards An Iot-Enabled Digital Earth For Sdgs: The Data Quality Challenge, Msb Syed, Paula Kelly, Paul Stacey, Damon Berry

Articles

Digital Earth (DE), a technology offering real-time visualisation of Earth's processes, has shown promising results in aiding decision-making for a sustainable world, raising awareness about individual impacts on our planet, and supporting the United Nations Sustainable Development Goals (UN SDGs) agenda. However, both DE and SDGs face a common obstacle: Data Quality (DQ). This review investigates the challenge of DQ in the context of DE for SDGs and explores how IoT can address this challenge and extend the reach of DE to support SDGs. Furthermore, the study discusses three core aspects; first, the potential of IoT as a data source …

2024 October 11 - State Of The University Address, Office Of The President, East Tennessee State University

Office of the President Speeches

No abstract provided.

Reducing Restraint Use And Workplace Violence With The Broset Violence Checklist, Alexandria Anderson

Dissertations

Problem: Psychiatric mental health nurses have an increased rate of workplace violence due to the acuity of patients they care for. When aggressive behavior cannot be resolved verbally, physical methods such as restraints may be utilized. Restraint use can result in unwanted consequences for both the patient and the nurse. Predicting risk of violence can be useful at reducing violence and restraint use through early risk identification.

Methods: The Broset Violence Checklist (BVC) was implemented as a way to predict aggression risk in an in-patient psychiatric unit within a mid-western hospital. This study utilized a pre- and post-intervention approach to …

The Carbon Crater: Comparing Anthropogenic Greenhouse Gas Emissions To Historical Planetary Events, Hal T. Nelson, Paul Reynolds, Brian W. Jewett

Public Administration Faculty Publications and Presentations

Equilibrium climate sensitivity modeling relies heavily on paleoclimate records that were affected by meteorite impacts and volcanic explosions. This paper conducts a thought experiment by re-assembling known data and theories to shed new light on anthropogenic carbon waste. Anthropogenic activity, meteorite impacts and volcanic explosions all extract material from the Earth’s crust and deposit it in the atmosphere. This thought experiment tests if the mass of anthropogenic greenhouse gas emissions from 1851 to 2021 is comparable to the mass of atmospheric emissions from historical planetary events. Approximately 3.60 trillion tons of anthropogenic carbon dioxide equivalents are converted into volume and …

Ex Vivo And In Vitro Methods As A Platform For Studying Anthropogenic Effects On Marine Mammals: Four Challenges And How To Meet Them, Juan M. Vazquez, Jane I. Khudyakov, Carla B. Madelaire, Céline A. Godard-Codding, Heli Routti, Emily K. Lam, Elizabeth R. Piotrowski, Greg B. Merrill, Jillian H. Wisse, Kaitlin N. Allen, Justin Conner, Pierre Blévin, Demetri D. Spyropoulos, Anders Goksøyr, José P. Vázquez-Medina

Pacific Faculty Work

Marine mammals are integral to global biodiversity and marine health through their roles in coastal, benthic, and pelagic ecosystems. Marine mammals face escalating threats from climate change, pollution, and human activities, which perturb their oceanic environment. The diverse biology and extreme adaptations evolved by marine mammals make them important study subjects for understanding anthropogenic pressures on marine ecosystems. However, ethical and logistical constraints restrict the tractability of experimental research with live marine mammals. Additionally, studies on the effects of changing ocean environments are further complicated by intricate gene-environment interactions across populations and species. These obstacles can be overcome with a …

Genetic Knock-In Of Eif2ak3 Variants Reveals Differences In Perk Activity In Mouse Liver And Pancreas Under Endoplasmic Reticulum Stress, Shivesh Ghura, Noah R. Beratan, Xinglong Shi, Elena Alvarez-Periel, Sarah E. Bond Newton, Cagla Akay-Espinoza, Kelly L. Jordan-Sciutto

Farber Institute for Neuroscience Staff Papers and Presentations

Common single-nucleotide variants (SNVs) of eukaryotic translation initiation factor 2 alpha kinase 3 (EIF2AK3) slightly increase the risk of disorders in the periphery and the central nervous system. EIF2AK3 encodes protein kinase RNA-like endoplasmic reticulum kinase (PERK), a key regulator of ER stress. Three exonic EIF2AK3 SNVs form the PERK-B haplotype, which is present in 28% of the global population. Importantly, the precise impact of these SNVs on PERK activity remains elusive. In this study, we demonstrate that PERK-B SNVs do not alter PERK expression or basal activity in vitro and in the novel triple knock-in mice expressing the exonic …

"If Someone Had Stopped The First World Racist, There Would Be No Racism Today": Empowering African American Muslim Elementary Students Through A Critical Literacy(Critlit) Project, Faten Baroudi

Theses and Dissertations

The Critical Literacy (CritLit) project promotes using critical texts to engage readers in examining their lived experiences and understanding of social justice issues. This study used a qualitative participatory approach with a narrative design to research the students’ engagement in a book club using critical texts. Participants were fourth- and fifth-grade African American students who participated in a 4-week project at a weekend Islamic school in Philadelphia. I organized my study into four sessions. Three book club sessions were audio-recorded and observed. Field notes were taken; pre and post-interviews were conducted; student/teacher reflections were collected with students’ notes and handouts; …

Medical School Watercooler Newsletter - October 11, 2024, Lindsay Hughes

Watercooler Newsletter

This is the Friday, October 11, 2024 edition of the Frederick P. Whiddon College of Medicine's newsletter -- Watercooler.

Contents include:

• Furr elected board chair of the American Academy of Family Physicians
• Students and alumni invited to Dean's Tailgate Oct. 26
• Biomedical Library to host Creative Arts and Storytelling in Health and Wellness Summit
• Pediatrics residents share important health messages at area schools
• Medical student presents prostate cancer research at urology meeting
• J-1 training session scheduled for Oct. 18

Feasibility Studies On Plant Architecture Traits Influence On Seed Cotton Yield Of Gossypium Hirsutum Zeromonopodial Genotypes And Assessment Of Ecological Suitability To Machine Harvesting, Subbarayan Sivakumar, Sadasivam Manickam, Banoth Madhu, Krishnan Bharathi Kumar, Krishnamoorthy Iyanar, Pokkaru Anantharaju, Patil Santosh Ganapati

Turkish Journal of Agriculture and Forestry

Mechanical harvesting has become crucial for cotton production in India due to increasing labor costs. This study aimed to identify suitable genotypes with moderate plant height and compact plant architecture for mechanization. Eight multi-location yield trials were conducted across central and southern India between 2019 and 2021. The combined ANOVA, LSD test, genotype plus genotype by environment interaction (GEE biplots) and correlation analysis was carried out using data from five genotypes for different plant architecture and yield traits. Results revealed significant variability (p ≤ 0.01) in plant height (PH) and seed cotton yield (SCY) among promising genotypes. Environmental factors had …

Assessing The Impact Of Land Use Change On Carbon And Soil Quality In Kashmir Himalayas, Yasir Hanif Mir, Mumtaz A. Ganie, Zahoor A. Baba, Shakeel Mir, M. Auyoub Bhat, Javid Ahmad Bhat, Aabid H. Lone, Fehim Jeelani Wani, Shuraik Kader, Lizny Jaufer, Artan Hysa, Alban Kuriqi

Turkish Journal of Agriculture and Forestry

The Kashmir Himalayas, a region of immense ecological importance, have experienced profound degradation by land-use changes, raising concerns about sustainability. This degradation carries significant global implications, including carbon loss, soil quality deterioration, habitat destruction, and loss of biodiversity. This study investigates various key land uses, including economically vital cash crops such as apples and saffron, the socially significant staple food crop rice, forest, and pasture systems. Findings reveals that forest and pasture maintain significantly better physical, chemical, microbial, and enzymes activities, and exhibit greater soil nutrient reserves and soil organic carbon (SOC) pools. Specifically, forest soils contain 20.21%, 28.22%, and …

Plastome Analysis Of Cultivated Apricots: Genome Structure, Nucleotide Diversity, And Phylogeny, Lungelo Khanyile, Kahraman Gürcan

Turkish Journal of Agriculture and Forestry

The genetic diversity and evolution of plastomes in P. armeniaca L. (common/cultivated apricot) have been poorly studied.Complete plastomes of 20 accessions and 10 F1 hybrids, identified as P. armeniaca L., were de novo assembled filtering from total DNAnt reads. These plastomes were subsequently analyzed with the Prunus genus accessions retrieved from the GenBank. The plastomesexhibited conservation of genomic structure, gene organization and order, with lengths ranging from 158,057 nt to 158,089 nt,displaying a narrow size variation. Except for “Zard” and its hybrids, the plastomes of apricot genotypes from different regions showedonly three haplotypes, indicating narrow genetic diversity in cultivated P. …

Quality Characteristics Of The Cv. Albion Strawberry (Fragaria X Ananassa Duch.)In Different Locations, Burhanetti̇n İmrak, Ayşegül Esra Gölcü, Songül Çömlekçi̇oglu, Mehmet Ramazan Bozhüyük, Jiri Mlcek, Gürsel Özkan, Sona Skrovankova

Turkish Journal of Agriculture and Forestry

Strawberries are one of the most popular berries in the world due to their distinctive aroma, flavor, and known healthproperties. A top day-neutral strawberry variety, the Albion, with its potential for high yields of large fruit, was grown in two differentlocations (Dağdibi and Hamidiye) at different altitudes (1410 and 1293 m) in Pozantı, a district of the Adana province in Türkiye, for lateseason production. Ripe fruits were harvested during the commercial harvest period, and several important physical and biochemicalparameters were examined. In addition, the fruit’s (berry’s) external and flesh color, fruit length and width, soluble solid content (SSC),antioxidant capacity, total …

Global Metabolome Profiles Of Lonicera Caerulea L. And Lonicera Caerulea Ssp.Kamtschatica (Sevast.) Gladkova, Muhammad Amjad Nawaz, Mayya P. Razgonova, Elena A. Rusakova, Elena N. Petrusha, Andrey S. Sabitov, Olga A. Chunikhina, Sezai̇ Erci̇şli̇, Nadezhda G. Tikhonova, Kirill S. Golokhvast

Turkish Journal of Agriculture and Forestry

Lonicera caerulea, commonly known as honeysuckle, is widespread in the Eurasian continent. Its berries are rich in bioactive compounds. However, limited studies have explored the metabolome composition of the berries of varieties and wild accessions in different subspecies of L. caerulea. Here we studied the metabolomic compositions of four varieties of L. caerulea ssp. caerulea and one variety and five wild accessions of L. caerulea ssp. kamtschatica (Sevast.) Gladkova, by using HPLC-ESI-MS and ESI-MS/MS analyses. We report the identification of 151 compounds in the two L. caerulea subspecies. In total, 88 and 84 compounds were detected in L. caerulea and …

Change In Plant Growth And Some Bioactive Components Of The Tomato Under Water Deficit With Exogenous Chrysin Treatment, Melek Eki̇nci̇, Ertan Yildirim, Selda Örs, Meti̇n Turan, Duran Şi̇mşek, Yüsra İnci̇

Turkish Journal of Agriculture and Forestry

Drought is one of the important factors that cause a decrease in productivity and quality in plant cultivation. Stress tolerance in plants can be increased or damage can be reduced by various exogenous applications. One of them is flavonoids, which have an important role in the response to stress through changes that occur at the endogenous level in the plant due to drought stress. The effects of exogenous treatment of chrysin, a member of the flavonoid group, on tomato seedlings grown under water deficit were examined. Different doses (C0: Control with no treatment, C1: 0.1 mM, C2: 0.5 mM and …

Cover And Contents

Turkish Journal of Agriculture and Forestry

No abstract provided.