Digital Commons Network^™

Evaluation Of Qpcr To Detect Shifts In Population Composition Of The Rhizobial Symbiont Mesorhizobium Japonicum During Serial In Planta Transfers, Kenjiro W. Quides, Yoobeen Lee, Teresa Hur, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Microbial symbionts range from mutualistic to commensal to antagonistic. While these roles are distinct in their outcome, they are also fluid in a changing environment. Here, we used the Lotus japonicus–Mesorhizobium japonicum symbiosis to investigate short-term and long-term shifts in population abundance using an effective, fast, and low-cost tracking methodology for M. japonicum. We use quantitative polymerase chain reaction (qPCR) to track previously generated signature-tagged M. japonicum mutants targeting the Tn5 transposon insertion and the flanking gene. We used a highly beneficial wild type and moderately beneficial and non-beneficial mutants of M. japonicum sp. nov. to demonstrate the specificity …

Contributors

Marvels & Tales

No abstract provided.

Protocol: New York State Race, Ethnicity, And Insurance Disparities In Follow-Up Prostate Cancer Screening, Seth Greenspan, Mansi Chandra, Hyun Woo Joo, Netanel Sapir, Jonathan Gorman, Jie Yang, Xiaoning Li, Barghav Cavale, Allegra Fierro, Annie Laurie Laurie Shroyer, John P. Fitzgerald

Department of Urology Faculty Publications

Using de-identified reports from the Statewide Planning and Research Cooperative System (SPARCS) data, this descriptive study will identify the impact of socioeconomic status (SES) metrics on the follow-up prostate cancer screening care within 3 years of index prostate cancer screening test in NYS. The socioeconomic status metrics will be subclassified into race, insurance, and ethnicity and each of these sub-components will be evaluated for its impact on the follow-up cancer screening care. The exclusion criteria for this study includes patients records with unknown age, age <55 or >75, previous history of prostate cancer or radical prostatectomy, previous prostate biopsy, female sex, lives …

Policies Regulating Gender In Schools: Companion To Identity By Committee (2022), Scott Skinner-Thompson

Research Data

This document, Policies Regulating Gender in Schools: Companion to Identity by Committee (2022), https://docs.google.com/spreadsheets/d/1K6iUkLnmDfaSVykyRaZ3Yqt7XNM9leGO-MQA6p2VbV4/edit?usp=Sharing, was published as an electronic supplement to the article, Scott Skinner-Thompson, Identity by Committee, 57 Harv. C.R.-C.L. L. Rev. 657 (2022), available at https://scholar.law.colorado.edu/faculty-articles/1586.

Deutj: An Imagej Plugin For Improved Automatic Masking And Segmentation Of Images From Confocal Microscopy, Sunny Cui

Independent Student Projects and Publications

Due to advances in microscopic imaging, there are a plethora of biological molecules that can now be tagged and subsequentially imaged from almost any cell, organism, or tissue. However, the ability of software to analyze these images remains to be a challenge. ImageJ is open source software that allows for the processing of these images, but faces challenges when dealing with images that show weak contrast between objects of interest and background. DeutJ is an ImageJ plugin that color corrects and brightness corrects gradients that inhibit segmentation in confocal microscopy images. It can analyze hundreds of images from a given …

An Updated Classification Of Meditation Methods Using Principles Of Taxonomy And Systematics, Jonathan D. Nash, Andrew B. Newberg

Marcus Institute of Integrative Health Faculty Papers

This paper revisits the proposal for the classification of meditation methods which we introduced in our initial 2013 publication, “Toward a Universal Taxonomy and Definition of Meditation”. At that time, we advanced the thesis that meditation methods could be effectively segregated into three orthogonal categories by integrating the taxonomic principle of functional essentialism and the paradigm of Affect and Cognition; and we presented relevant research findings which supported that assertion. This iteration expands upon those theoretical and methodological elements by articulating a more comprehensive Three Tier Classification System which accounts for the full range of meditation methods; and demonstrates how …

Suffolk Journal, Vol.86, No. 10, 2/08/2023, Suffolk Journal

Suffolk Journal

No abstract provided.

Standing Genetic Variation As A Potential Mechanism Of Novel Cave Phenotype Evolution In The Freshwater Isopod, Asellus Aquaticus, Lizet R. Rodas, Serban M. Sarbu, Raluca Bancila, Devon Price, Žiga Fišer, Meredith E. Protas

Natural Sciences and Mathematics | Faculty Scholarship

Novel phenotypes can come about through a variety of mechanisms including standing genetic variation from a founding population. Cave animals are an excellent system in which to study the evolution of novel phenotypes such as loss of pigmentation and eyes. Asellus aquaticus is a freshwater isopod crustacean found in Europe and has both a surface and a cave ecomorph which vary in multiple phenotypic traits. An orange eye phenotype was previously revealed by F2 crosses and backcrosses to the cave parent within two examined Slovenian cave populations. Complete loss of pigmentation, both in eye and body, is epistatic to the …

Leaf-Counting In Monocot Plants Using Deep Regression Models, Xinyan Xie, Yufeng Ge, Harkamal Walia, Jinliang Yang, Hongfeng Yu

School of Computing: Faculty Publications

Leaf numbers are vital in estimating the yield of crops. Traditional manual leaf-counting is tedious, costly, and an enormous job. Recent convolutional neural network-based approaches achieve promising results for rosette plants. However, there is a lack of effective solutions to tackle leaf counting for monocot plants, such as sorghum and maize. The existing approaches often require substantial training datasets and annotations, thus incurring significant overheads for labeling. Moreover, these approaches can easily fail when leaf structures are occluded in images. To address these issues, we present a new deep neural network-based method that does not require any effort to label …

Economics Of Deficit Irrigation Utilizing Soil Moisture Probes In The Western Corn Belt, Emily O’Donnell, Lia Nogueira, Cory Walters, E Wesley F. Peterson, Suat Irmak

Department of Agricultural Economics: Faculty Publications

Effective irrigation management is critical for future food supplies and the prosperity of producers engaged in irrigation production. Through a deficit irrigation field experiment, we determine the financial impact on producers caused by changing irrigation costs, corn prices, extreme weather events, and restricting irrigation levels. Results suggest that the optimal economic strategy within our constrained optimization model is to fully irrigate, with the economic impact highly dependent on commodity prices, restriction level, and irrigation costs. The greatest economic losses caused by irrigation restrictions come from decreases in yield. Some simulations resulted in negative profits, indicating that a switch to alternative …

An Expedition To Public Lands, Matthew B. Olsen

CAFE Symposium 2023

A look into common ideas appearing in the US public land system. These ideas include "nature as commodity," "nature as unpeopled," and "nature as pristine." The specific areas looked into are Havasu National Wildlife Refuge, Prescott National Forest, Grand Canyon National Park, Gold Butte National Monument, and Death Valley National Park.

Analysis Of “A Forest Under The Sea”- Studying Giant Kelp’S Benefits To Ecosystems, And Evaluating Kelp Restoration, Natalie V. Boyd

CAFE Symposium 2023

I wrote a research paper on how Giant Kelp needs to be restored due to the rising ocean temperatures. There are two methods that I specifically focused on and learned about which are "Super Kelp" and "Green Gravel." Giant Kelp is critical to our ecosystem and marine life specifically due to all the benefits that it supplies. For example, kelp forests can sequester up to 20 times more carbon than a land forest. Unfortunately, the kelp is dying off rapidly now because of climate change; specifically the rising temperatures and increased ocean acidification. In order to save the kelp, action …

Escalating Costs Of Self-Injury Mortality In The 21st Century United States: An Interstate Observational Study., Ian Rh Rockett, Bina Ali, Eric D. Caine, Donald S. Shepard, Aniruddha Banerjee, Kurt B. Nolte, Hilary S. Connery, G Luke Larkin, Steven Stack, Franklin M M White, Haomiao Jia, Jeralynn S. Cossman, Judith Feinberg, Amanda N. Stover, Ted R. Miller

Pathology Research and Scholarship

BACKGROUND: Estimating the economic costs of self-injury mortality (SIM) can inform health planning and clinical and public health interventions, serve as a basis for their evaluation, and provide the foundation for broadly disseminating evidence-based policies and practices. SIM is operationalized as a composite of all registered suicides at any age, and 80% of drug overdose (intoxication) deaths medicolegally classified as 'accidents,' and 90% of corresponding undetermined (intent) deaths in the age group 15 years and older. It is the long-term practice of the United States (US) Centers for Disease Control and Prevention (CDC) to subsume poisoning (drug and nondrug) deaths …

Black Vulture Skull, Briana K. Zaffiro, David W. Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Skull from 8 cm total length [Coragyps atarus (Black Vulture)]

Cannabis Drug Development And The Controlled Substances Act, Gabrielle Feliciani

Duke Journal of Constitutional Law & Public Policy Sidebar

Cannabis is a federally illegal drug in the United States, yet thirty-seven states and four territories have now enacted laws allowing the production, distribution, and consumption of cannabis for medical use. An estimated 5.5 million individuals in medical-use states are qualified to purchase cannabis to treat and mitigate symptoms for conditions ranging from cancer to post-traumatic stress disorder to chronic pain. But, only three cannabis drugs have been approved by the Food and Drug Administration (FDA).

The current state of federal illegality creates a problem of supply and demand—consumer demand for cannabis is high, but the number of approved drug …

Coral Gardens Reef, Belize: An Acropora Spp. Refugium Under Threat In A Warming World, Lisa Greer, H. Allen Curran, Karl Wirth, Robert Humston, Ginny Johnson, Lauren Mcmanus, Candice Stefanic, Tara Clark, Halard Lescinsky, Kirah Forman-Castillo

Geosciences: Faculty Publications

Live coral cover has declined precipitously on Caribbean reefs in recent decades. Acropora cervicornis coral has been particularly decimated, and few Western Atlantic Acropora spp. refugia remain. Coral Gardens, Belize, was identified in 2020 as a long-term refugium for this species. This study assesses changes in live A. cervicornis coral abundance over time at Coral Gardens to monitor the stability of A. cervicornis corals, and to explore potential threats to this important refugium. Live coral cover was documented annually from 2012– 2019 along five permanent transects. In situ sea-surface temperature data were collected at Coral Gardens throughout the study period …

2023 February 8 - Undergraduate Curriculum Council Minutes, Undergraduate Curriculum Council, East Tennessee State University

Undergraduate Curriculum Council Minutes

No abstract provided.

Efficacy And Clinicogenomic Correlates Of Response To Immune Checkpoint Inhibitors Alone Or With Chemotherapy In Non-Small Cell Lung Cancer, Lingzhi Hong, Muhammad Aminu, Shenduo Li, Xuetao Lu, Milena Petranovic, Maliazurina B Saad, Pingjun Chen, Kang Qin, Susan Varghese, Waree Rinsurongkawong, Vadeerat Rinsurongkawong, Amy Spelman, Yasir Y Elamin, Marcelo V Negrao, Ferdinandos Skoulidis, Carl M Gay, Tina Cascone, Saumil J Gandhi, Steven H Lin, Percy P Lee, Brett W Carter, Carol C Wu, Mara B Antonoff, Boris Sepesi, Jeff Lewis, Don L Gibbons, Ara A Vaporciyan, Xiuning Le, J Jack Lee, Sinchita Roy-Chowdhuri, Mark J Routbort, Justin F Gainor, John V Heymach, Yanyan Lou, Jia Wu, Jianjun Zhang, Natalie I Vokes

Faculty, Staff and Student Publications

The role of combination chemotherapy with immune checkpoint inhibitors (ICI) (ICI-chemo) over ICI monotherapy (ICI-mono) in non-small cell lung cancer (NSCLC) remains underexplored. In this retrospective study of 1133 NSCLC patients, treatment with ICI-mono vs ICI-chemo associate with higher rates of early progression, but similar long-term progression-free and overall survival. Sequential vs concurrent ICI and chemotherapy have similar long-term survival, suggesting no synergism from combination therapy. Integrative modeling identified PD-L1, disease burden (Stage IVb; liver metastases), and STK11 and JAK2 alterations as features associate with a higher likelihood of early progression on ICI-mono. CDKN2A alterations associate with worse long-term outcomes …

Evolution Of Chemical-Cue-Mediated Antipredator Behavior In Threespine Stickleback Populations Experiencing Northern Pike Predation, Dale R. Stevens, Melissa A. Graham, Christina I. Bardjis, Susan A. Foster, John A. Baker, Kaitlyn A. Mathis

Biology

Human-mediated environmental challenges are severely impacting local and global levels of biodiversity. Phenotypic plasticity can play a major role in aiding population persistence because plasticity can buffer populations from novel challenges. Given this role, it is possible for the degree of plasticity to evolve rapidly as it may place phenotypes near, but not exactly on, an adaptive peak for the new environment. Here, we asked if behavioral plasticity evolves following the introduction of a novel predator. We measured behavioral responses of threespine stickleback (Gasterosteus aculeatus) populations, with and without the introduced apex predator northern pike (Esox lucius), to three different …

Combination Sodium Nitrite And Hydralazine Therapy Attenuates Heart Failure With Preserved Ejection Fraction Severity In A “2-Hit” Murine Model, Kyle B. Lapenna, Zhen Li, Jake E. Doiron, Thomas E. Sharp, Huijing Xia, Karl Moles, Kashyap Koul, John S. Wang, David J. Polhemus, Traci T. Goodchild, Ravi B. Patel, Sanjiv J. Shah, David J. Lefer

School of Medicine Faculty Publications

BACKGROUND: Recent studies have suggested that cardiac nitrosative stress mediated by pathological overproduction of nitric oxide (NO) via inducible NO synthase (iNOS) contributes to the pathogenesis of heart failure with preserved ejection fraction (HFpEF). Other studies have suggested that endothelial NO synthase (eNOS) dysfunction and attenuated NO bioavailability contribute to HFpEF morbidity and mortality. We sought to further investigate dysregulated NO signaling and to examine the effects of a NO-based dual therapy (sodium nitrite+hydralazine) following the onset of HFpEF using a “2-hit” murine model. METHODS AND RESULTS: Nine-week-old male C57BL/6 N mice (n=15 per group) were treated concurrently with high-fat …

Endogenous Mirna-Based Innate-Immunity Against Sars-Cov-2 Invasion Of The Brain, Walter J. Lukiw, Aileen I. Pogue

School of Medicine Faculty Publications

The severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, possesses an unusually large positive-sense, single-stranded viral RNA (ssvRNA) genome of about ~29,903 nucleotides (nt). In many respects, this ssvRNA resembles a very large, polycistronic messenger RNA (mRNA) possessing a 5′-methyl cap (m7GpppN), a 3′- and 5′-untranslated region (3′-UTR, 5′-UTR), and a poly-adenylated (poly-A+) tail. As such, the SARS-CoV-2 ssvRNA is susceptible to targeting by small non-coding RNA (sncRNA) and/or microRNA (miRNA), as well as neutralization and/or inhibition of its infectivity via the human body’s natural complement of about ~2650 miRNA species. Depending on host cell and tissue …

What A Waste! An Evaluation Of Federal And State Medical And Biohazard Waste Regulations During The Covid-19 Pandemic And Their Impact On Environmental Justice, Samantha Newman

Villanova Environmental Law Journal (1991 - )

No abstract provided.

Severe Acute Respiratory Syndrome Coronavirus 2 (Sars-Cov-2) Testing And Detection During Peripartum Hospitalizations Among A Multicenter Cohort Of Pregnant Persons: March 2020-February 2021, Miranda J Delahoy, Flor Munoz, De-Kun Li, Carmen Sofia Arriola, Nanette Lee Bond, Michael Daugherty, Jeannette Ferber, Nickolas Ferguson, Louise Hadden, Jillian T Henderson, Stephanie A Irving, Mary Juergens, Venkatesh Kancharla, Mara Greenberg, Roxana Odouli, Gabriella Newes-Adeyi, Erin G Nicholson, Lawrence Reichle, Momodou Sanyang, Margaret Snead, Fatimah S Dawood, Allison L Naleway

Faculty, Staff and Students Publications

BACKGROUND: Identifying severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during peripartum hospitalizations is important to guide care, implement prevention measures, and understand infection burden.

METHODS: This cross-sectional analysis used electronic health record data from hospitalizations during which pregnancies ended (peripartum hospitalizations) among a cohort of pregnant persons at 3 US integrated healthcare networks (sites 1-3). Maternal demographic, medical encounter, SARS-CoV-2 testing, and pregnancy and neonatal outcome information was extracted for persons with estimated delivery and pregnancy end dates during March 2020-February 2021 and ≥1 antenatal care record. Site-stratified multivariable logistic regression was used to identify factors associated with testing …

Acute High-Fat Diet Impairs Macrophage-Supported Intestinal Damage Resolution, Andrea A Hill, Myunghoo Kim, Daniel F Zegarra-Ruiz, Lin-Chun Chang, Kendra Norwood, Adrien Assié, Wan-Jung H Wu, Michael C Renfroe, Hyo Wong Song, Angela M Major, Buck S Samuel, Joseph M Hyser, Randy S Longman, Gretchen E Diehl

Faculty, Staff and Students Publications

Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term HFD feeding in a model of intestinal injury and found sustained damage with increased cecal dead neutrophil accumulation, along with dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD-treated mice showed reduced capacity to engulf dead neutrophils. Macrophage clearance of dead neutrophils activates critical barrier repair and antiinflammatory pathways, including IL-10, which was lost after acute HFD feeding and intestinal injury. IL-10 overexpression restored intestinal repair after HFD feeding and intestinal injury. Macrophage exposure …

Effects Of Adjuvants In A Rabies-Vectored Ebola Virus Vaccine On Protection From Surrogate Challenge, Catherine Yankowski, Drishya Kurup, Christoph Wirblich, Matthias J. Schnell

Department of Microbiology and Immunology Faculty Papers

Ebola virus is the primary contributor to the global threat of filovirus severe hemorrhagic fever, and Ebola virus disease has a case fatality rate of 50-90%. An inactivated, bivalent filovirus/rabies virus vaccine, FILORAB1, consists of recombinant rabies virus virions expressing the Ebola virus glycoprotein. FILORAB1 is immunogenic and protective from Ebola virus challenge in mice and non-human primates, and protection is enhanced when formulated with toll-like receptor 4 agonist Glucopyranosyl lipid adjuvant (GLA) in a squalene oil-in-water emulsion (SE). Through an adjuvant comparison in mice, we demonstrate that GLA-SE improves FILORAB1 efficacy by activating the innate immune system and shaping …

Covid Vaccines And Intellectual Property Rights: Evaluating The Potential For National Legislation Implementing Global Patent Waivers, Ashley Dabiere

Duke Law & Technology Review

Debates over the proper scope of intellectual property protections during the COVID-19 pandemic have occupied newspaper headlines since the first vaccines were developed nearly three years ago. Scholars and key politicians from several nations considered the implementation of a global patent waiver in an effort to make the vaccines more widely available in developing parts of the world. Although the question of whether such a waiver would fulfill this goal remains empirically unanswered and up for debate, the legal structure of United States patent law would make its implementation by Congress difficult given the value placed on intellectual property protections …

Association Of Circulating Mtdna With Cvd In Hemodialysis Patients And In Vitro Effect Of Exogenous Mtdna On Cardiac Microvascular Inflammation, Zhen Fan, Ya Feng, Li Zang, Yi Guo, Xiao-Yi Zhong

Faculty, Staff and Student Publications

BACKGROUND: Chronic kidney disease (CKD) patients sustain a fairly high prevalence of cardiovascular disease (CVD). Microvascular inflammation is an early manifestation of CVD, and the released mitochondrial DNA (MtDNA) has been proposed to be a crucial integrator of inflammatory signals. Herein, the aim of this study was to determine the relationship between CVD, microvessel, and circulating MtDNA in the settings of uremia.

METHODS: Forty-two maintenance hemodialysis (MHD) patients and 36 health controls were enrolled in this study. Plasma cell-free MtDNA was detected by TaqMan-based qPCR assay. CVD risk markers including high-sensitive C-reactive protein (Hs-CRP), monocyte chemoattractant protein-1 (MCP-1), fibrinogen, and …

Incidence And Clearance Of Anal Human Papillomavirus Infection In 16 164 Individuals, According To Human Immunodeficiency Virus Status, Sex, And Male Sexuality: An International Pooled Analysis Of 34 Longitudinal Studies, Feixue Wei, Marc T Goodman, Ningshao Xia, Jun Zhang, Anna R Giuliano, Gypsyamber D'Souza, Nancy A Hessol, Maarten F Schim Van Der Loeff, Jianghong Dai, Karin Neukam, Alexandra De Pokomandy, I Mary Poynten, Ronald B Geskus, Joaquin Burgos, Isabelle Etienney, Anna-Barbara Moscicki, Maria Gabriella Donà, Maura L Gillison, Alan G Nyitray, Rebecca G Nowak, Evy Yunihastuti, Huachun Zou, Carmen Hidalgo-Tenorio, Nittaya Phanuphak, Jean-Michel Molina, Alice M Schofield, Stephen Kerr, Song Fan, Yong Lu, Jason J Ong, Admire T Chikandiwa, Sirinya Teeraananchai, Nicola Squillace, Dorothy J Wiley, Joel M Palefsky, Damien Georges, Catharina J Alberts, Gary M Clifford

Faculty, Staff and Student Publications

Background: Understanding the natural history of anal high-risk human papillomavirus (hrHPV) infection is key for designing anal cancer prevention programs but has not been systematically characterized.

Methods: We reanalyzed data from 34 studies including 16 164 individuals in 6 risk groups defined by human immunodeficiency virus (HIV) status, sex, and male sexuality: men who have sex with men (MSM) and people with HIV (MSMWH), HIV-negative MSM, women with HIV (WWH), HIV-negative women, men who have sex with women (MSW) with HIV (MSWWH), and HIV-negative MSW. We used Markov models to estimate incidence and clearance of 13 hrHPV types and their …

The Bg News February 8, 2023, Bowling Green State University

BG News (Student Newspaper)

The BGSU campus student newspaper. February 08, 2023. Volume 102-Issue 17.

Risk Factors For Ebola Virus Persistence In Semen Of Survivors In Liberia, Jonathan Dyal, Aaron Kofman, Jomah Z Kollie, John Fankhauser, Romeo Orone, Moses J Soka, Uriah Glaybo, Armah Kiawu, Edna Freeman, Giovanni Giah, Henry D Tony, Mylene Faikai, Mary Jawara, Kuku Kamara, Samuel Kamara, Benjamin Flowers, Mohammed L Kromah, Rodel Desamu-Thorpe, James Graziano, Shelley Brown, Maria E Morales-Betoulle, Deborah L Cannon, Kaihong Su, Susanne L Linderman, Mateusz Plucinski, Eric Rogier, Richard S Bradbury, W Evan Secor, Katherine E Bowden, Christi Phillips, Mary N Carrington, Yeon-Hwa Park, Maureen P Martin, Maria Del Pilar Aguinaga, Robert Mushi, Dana L Haberling, Elizabeth D Ervin, John D Klena, Moses Massaquoi, Tolbert Nyenswah, Stuart T Nichol, David E Chiriboga, Desmond E Williams, Steven H Hinrichs, Rafi Ahmed, Benjamin T Vonhm, Pierre E Rollin, Lawrence J Purpura, Mary J Choi

Faculty, Staff and Student Publications

BACKGROUND: Long-term persistence of Ebola virus (EBOV) in immunologically privileged sites has been implicated in recent outbreaks of Ebola virus disease (EVD) in Guinea and the Democratic Republic of Congo. This study was designed to understand how the acute course of EVD, convalescence, and host immune and genetic factors may play a role in prolonged viral persistence in semen.

METHODS: A cohort of 131 male EVD survivors in Liberia were enrolled in a case-case study. "Early clearers" were defined as those with 2 consecutive negative EBOV semen test results by real-time reverse-transcription polymerase chain reaction (rRT-PCR) ≥2 weeks apart within …