Digital Commons Network^™

Ambient Writing In A Terrain Of Threatened Subjectivity: Unfolding Codes, Tainted Models And Holey Spaces, Phil Smith

School of Art, Design and Architecture

No abstract provided.

Fluorescence Lifetime Sorting Reveals Tunable Enzyme Interactions Within Cytoplasmic Condensates, Leyla E Fahim, Joshua M Marcus, Noah D Powell, Zachary A Ralston, Katherine Walgamotte, Eleonora Perego, Giuseppe Vicidomini, Alessandro Rossetta, Jason E Lee

Faculty, Staff and Students Publications

Ribonucleoprotein (RNP) condensates partition RNA and protein into multiple liquid phases. The multiphasic feature of condensate-enriched components creates experimental challenges for distinguishing membraneless condensate functions from the surrounding dilute phase. We combined fluorescence lifetime imaging microscopy (FLIM) with phasor plot filtering and segmentation to resolve condensates from the dilute phase. Condensate-specific lifetimes were used to track protein-protein interactions by measuring FLIM-Förster resonance energy transfer (FRET). We used condensate FLIM-FRET to evaluate whether mRNA decapping complex subunits can form decapping-competent interactions within P-bodies. Condensate FLIM-FRET revealed the presence of core subunit interactions within P-bodies under basal conditions and the disruption of …

Plural Molecular And Cellular Mechanisms Of Pore Domain, Timothy J Abreo, Emma C Thompson, Anuraag Madabushi, Kristen L Park, Heun Soh, Nissi Varghese, Carlos G Vanoye, Kristen Springer, Jim Johnson, Scotty Sims, Zhigang Ji, Ana G Chavez, Miranda J Jankovic, Bereket Habte, Aamir R Zuberi, Cathleen M Lutz, Zhao Wang, Vaishnav Krishnan, Lisa Dudler, Stephanie Einsele-Scholz, Jeffrey L Noebels, Alfred L George, Atul Maheshwari, Anastasios Tzingounis, Edward C Cooper

Faculty, Staff and Students Publications

KCNQ2 variants in children with neurodevelopmental impairment are difficult to assess due to their heterogeneity and unclear pathogenic mechanisms. We describe a child with neonatal-onset epilepsy, developmental impairment of intermediate severity, and KCNQ2 G256W heterozygosity. Analyzing prior KCNQ2 channel cryoelectron microscopy models revealed G256 as a node of an arch-shaped non-covalent bond network linking S5, the pore turret, and the ion path. Co-expression with G256W dominantly suppressed conduction by wild-type subunits in heterologous cells. Ezogabine partly reversed this suppression. Kcnq2G256W/+ mice have epilepsy leading to premature deaths. Hippocampal CA1 pyramidal cells from G256W/+ brain slices showed hyperexcitability. G256W/+ pyramidal …

Dimensionality Reduction For Visualizing Spatially Resolved Profiling Data Using Spasne, Yuansheng Zhou, Chen Tang, Xue Xiao, Xiaowei Zhan, Tao Wang, Guanghua Xiao, Lin Xu

Faculty, Staff and Student Publications

Background: Spatially resolved profiling technologies to quantify transcriptomes, epigenomes, and proteomes have been emerging as groundbreaking methods for comprehensive molecular characterizations. Dimensionality reduction and visualization is an essential step to analyze and interpret spatially resolved profiling data. However, state-of-the-art dimensionality reduction methods for single-cell sequencing data, such as the t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP), were not tailored for spatially resolved profiling data.

Results: Here we developed a spatially resolved t-SNE (SpaSNE) method to integrate both spatial and molecular information. We applied it to a variety of public spatially resolved profiling datasets that were …

Can Trichoderma Spp. Contribute To The Bioremediation And Biostimulation Of Plants In Soil Contaminated With Herbicides?, Elaine Damiani Conte, Elton José Da Rosa, Gabriel Rieth Silvestrini, Daiane Da Silva Motta, Christiane Fernandes De Oliveira, Carine Cocco, Gabriel Fernandes Pauletti, Taísa Dal Magro, Joséli Schwambach

School of Earth, Environmental, & Marine Sciences Faculty Publications

This work aimed to evaluate the potential of Trichoderma spp. in the bioremediation of herbicides and biostimulation of plants in herbicide-contaminated soils. In the first phase, the experiment followed a completely randomized design in a 4 × 3 × 4 factorial scheme with five replications, four strains of Trichoderma spp., three herbicides, and four herbicide doses. The mycelial growth speed index (MGSI) of Trichoderma spp. was obtained by growing it in a Petri dish with PDA associated with different doses of herbicides and evaluated every 24 h for 10 days. Results indicated the selection ofTrichoderma harzianumT1A to continue …

Intrinsic Adaptive Plasticity In Mouse And Human Sensory Neurons, Lisa A Mcilvried, John Smith Del Rosario, Melanie Y Pullen, Andi Wangzhou, Tayler D Sheahan, Andrew J Shepherd, Richard A Slivicki, John A Lemen, Theodore J Price, Bryan A Copits, Robert W Gereau

Faculty, Staff and Student Publications

In response to changes in activity induced by environmental cues, neurons in the central nervous system undergo homeostatic plasticity to sustain overall network function during abrupt changes in synaptic strengths. Homeostatic plasticity involves changes in synaptic scaling and regulation of intrinsic excitability. Increases in spontaneous firing and excitability of sensory neurons are evident in some forms of chronic pain in animal models and human patients. However, whether mechanisms of homeostatic plasticity are engaged in sensory neurons of the peripheral nervous system (PNS) is unknown. Here, we show that sustained depolarization (induced by 24-h incubation in 30 mM KCl) induces compensatory …

The Association Of The Chemotherapy Response Score And Homologous Recombination Deficiency In Patients Undergoing Interval Tumor Reductive Surgery Following Neoadjuvant Chemotherapy, Roni Nitecki Wilke, Jinsong Liu, Shannon Neville Westin, Bryan M Fellman, Travis T Sims, Melissa Pham, Kelly Rangel, Esther Sey, Jose Alejandro Rauh-Hain, Karen H Lu, Anil K Sood, Nicole D Fleming

Faculty, Staff and Student Publications

Objectives: In patients undergoing interval tumor reductive surgery, a good response to neoadjuvant chemotherapy may limit available tumor for homologous recombination deficiency testing. The objective of this study was to assess whether the chemotherapy response score predicts homologous recombination status.

Methods: We identified patients with advanced epithelial ovarian cancer (diagnosed January 2019 to 20 June 2023) who received neoadjuvant chemotherapy, underwent interval surgery, and for whom a chemotherapy response score was reported (1=no or minimal tumor response, 2=appreciable tumor response, 3=complete or near complete response with no residual tumor). Comparisons were made using ANOVAs or Kruskal-Wallis test for continuous variables …

Circakb: A Comprehensive Knowledgebase Of Circadian Genes Across Multiple Species, Xingchen Zhu, Xiao Han, Zhijin Li, Xiaobo Zhou, Seung-Hee Yoo, Zheng Chen, Zhiwei Ji

Faculty, Staff and Student Publications

Circadian rhythms, which are the natural cycles that dictate various physiological processes over a 24-h period, have been increasingly recognized as important in the management and treatment of various human diseases. However, the lack of sufficient data and reliable analysis methods have been a major obstacle to understanding the bidirectional interaction between circadian variation and human health. We have developed CircaKB, a comprehensive knowledgebase of circadian genes across multiple species. CircaKB is the first knowledgebase that provides systematic annotations of the oscillatory patterns of gene expression at a genome-wide level for 15 representative species. Currently, CircaKB contains 226 time-course transcriptome …

Land-Use Effects On Soil Organic Matter And Related Soil Properties In A Mixed Agricultural–Forest Landscape Of Central Wisconsin, Usa, Kathryn L. Hofmeister, Gwen Feitl, Kaylee Tackett, Leah Fleury, Lucas E. Nave

Michigan Tech Publications

Soil organic matter (SOM) influences a wide range of ecosystem processes, including nutrient cycling, water movement, plant productivity, and biodiversity. In agricultural landscapes, adjacent land uses often differ in SOM contents and related soil properties, such as soil organic carbon (SOC) stocks, but the direction and magnitude of these effects are inconsistent across studies. We assessed how land uses differed in SOM and related properties in a representative US Midwest agricultural–forest landscape to support land-use and management decisions by local landowners and producers. We measured SOM, bulk density (Db), root biomass, and pH, and estimated SOC stocks, in a Typic …

The Latter-Day Saint Indian Placement Program: An Examination Through An Experiential Lens, Quinn Elise Christiansen

Theses and Dissertations

The Indian Placement Program, operated by the LDS Church from around 1947 to 2000, was influenced by the Church's belief in a connection between Native Americans to a Book of Mormon group known as the Lamanites. This group held a special status within the LDS Church because of their believed Israelite heritage as well as a prophecy promising their conversion in the last days. Spencer W. Kimball, motivated by both personal goals and his authority within the LDS Church, expanded on a successful experience of a young Native girl, Helen John, growing it into the broader Indian Placement Program. This …

Label Free, Capillary-Scale Blood Flow Mapping In Vivo Reveals That Low-Intensity Focused Ultrasound Evokes Persistent Dilation In Cortical Microvasculature, Yubing Y Shen, Jyoti V Jethe, Ashlan P Reid, Jacob Hehir, Marcello Magri Amaral, Chao Ren, Senyue Hao, Chao Zhou, Jonathan A N Fisher

2020-Current year OA Pubs

Non-invasive, low intensity focused ultrasound is an emerging neuromodulation technique that offers the potential for precision, personalized therapy. An increasing body of research has identified mechanosensitive ion channels that can be modulated by FUS and support acute electrical activity in neurons. However, neuromodulatory effects that persist from hours to days have also been reported. The brain's ability to provide blood flow to electrically active regions involves a multitude of non-neuronal cell types and signaling pathways in the cerebral vasculature; an open question is whether persistent effects can be attributed, at least partly, to vascular mechanisms. Using an in vivo optical …

Intrinsic Adaptive Plasticity In Mouse And Human Sensory Neurons, Lisa A Mcilvried, John Smith Del Rosario, Melanie Y Pullen, Andi Wangzhou, Tayler D Sheahan, Andrew J Shepherd, Richard A Slivicki, John A Lemen, Theodore J Price, Bryan A Copits, Robert W Gereau

2020-Current year OA Pubs

In response to changes in activity induced by environmental cues, neurons in the central nervous system undergo homeostatic plasticity to sustain overall network function during abrupt changes in synaptic strengths. Homeostatic plasticity involves changes in synaptic scaling and regulation of intrinsic excitability. Increases in spontaneous firing and excitability of sensory neurons are evident in some forms of chronic pain in animal models and human patients. However, whether mechanisms of homeostatic plasticity are engaged in sensory neurons of the peripheral nervous system (PNS) is unknown. Here, we show that sustained depolarization (induced by 24-h incubation in 30 mM KCl) induces compensatory …

Distinct Properties And Activation Of Hexameric And Heptameric Pannexin 1 Channel Concatemers, Smriti Gupta, Yu-Hsin Chiu, Mohan C Manjegowda, Bimal N Desai, Kodi S Ravichandran, Douglas A Bayliss

2020-Current year OA Pubs

Pannexin 1 (PANX1) is a member of a topologically related and stoichiometrically diverse family of large pore membrane ion channels that support the flux of signaling metabolites (e.g., ATP) and fluorescent dyes. High-resolution structural analyses have identified PANX1 as a heptamer despite early evidence suggesting that it might be a hexamer. To determine if PANX1 channel activity is supported in both hexameric and heptameric conformations, we examined properties of concatenated PANX1 constructs comprising either six or seven subunits with intact or truncated C-termini (the latter to mimic caspase-cleavage activation). In whole-cell recordings from PANX1-deleted cells, the C-tail-truncated hexameric and heptameric …

Opaque Ontology: Neuroimaging Classification Of Icd-10 Diagnostic Groups In The Uk Biobank, Ty Easley, Xiaoke Luo, Kayla Hannon, Petra Lenzini, Janine Bijsterbosch

2020-Current year OA Pubs

BACKGROUND: The use of machine learning to classify diagnostic cases versus controls defined based on diagnostic ontologies such as the International Classification of Diseases, Tenth Revision (ICD-10) from neuroimaging features is now commonplace across a wide range of diagnostic fields. However, transdiagnostic comparisons of such classifications are lacking. Such transdiagnostic comparisons are important to establish the specificity of classification models, set benchmarks, and assess the value of diagnostic ontologies.

RESULTS: We investigated case-control classification accuracy in 17 different ICD-10 diagnostic groups from Chapter V (mental and behavioral disorders) and Chapter VI (diseases of the nervous system) using data from the …

Geometric Morphological Analysis Of The Edfu Temple, Yara M. Soliman, Ashraf H. Ibrahim, Ahmed M. Awad

Journal of Art, Design and Music

The paper discusses the influence of nature on the design principles utilized by ancient Egyptian civilization, emphasizing how philosophers and artists learned from natural forms. It introduces the concept of Morphology, which examines the structures and forms of living and inanimate objects, categorized into eight types: Geometric, Chaotic, Plant, Animal, Human, Motor, Ecological, and Symbolic. The research focuses on applying the Geometric Morphological system to Edfu Temple, highlighting the need for contemporary designers to consider both form and content, rather than merely aesthetic shapes. The study aims to create an analytical framework using geometric determinants—unity, balance, scale, rhythm, proportion, abstraction, …

Vol. 13 Iss. 2

Discussions

No abstract provided.

Vol 18. Iss. 1

Discussions

No abstract provided.

Global Scientific Production On Stakeholder Engagement In Community Forestry: A Bibliometric Analysis, Whisnu Febry Afrianto

Jurnal Penelitian Kehutanan Wallacea

Community forestry is a concept that presents management and utilization rights to local communities through empowering communities in sustainably managing forest resources and engaging them in forest conservation movements. This study aims to investigate the scope of stakeholder engagement in community forestry using a bibliometric review. Understanding stakeholders' participation in community forest management through a 30-year bibliometric analysis is essential for achieving historical insights, deciding conflicts, and discussing global forest landscape topics. The data was obtained from the Scopus database. Analysis of references with 808 publications and an annual publication growth rate of 6.49% (1981 – 2023) was used to …

Potential Of Native Tree Species For Post-Nickel Mining Land Restoration, Fadly Suhati, Putu Oka Ngakan, Risma Illa Maulany, Nasri Nasri, Andi Siady Hamzah, Putu Supadma Putra

Jurnal Penelitian Kehutanan Wallacea

Due to the absence of topsoil, low pH, and contamination by various heavy metals, revegetation of post-nickel mining land, which is generally carried out by planting economically valuable species, is usually unsuccessful. This study aims to identify tree species suitable for revegetation on post-nickel mining land in Kolaka Regency, Indonesia. Nine plots measuring 20 m x 20 m were distributed in the revegetated post-nickel mining land at three different age categories (1, 5, and 10 years) to observe the growth of revegetation trees, which are introduced species and native tree species that naturally invade the revegetation area. In total, there …

Episode 9: Update From The Sidelines, Sara Gras

Season 01

This episode provides an update on developments related to the inclusion of trans athletes in interscholastic sports, including the Second Circuit’s en banc decision in the Soule v. Connecticut case, the general Title IX Final Rule litigation, transvestigation during the Summer Olympics, and a recent Senate hearing on an entirely different subject that foreshadows what the next four years holds for trans athletes. My guest for this episode is one my research assistants, Emily Raedisch, a 2nd year law student at Seton Hall Law. She researched and wrote this episode. Court opinions and documents: Soule v. Connecticut Ass’n of Sch., …

Recurrent And Metastatic Head And Neck Cancer: Mechanisms Of Treatment Failure, Treatment Paradigms, And New Horizons, William T. Barham, Marshall Patrick Stagg, Rula Mualla, Michael Dileo, Sagar Kansara

School of Medicine Faculty Publications

Background: Head and neck cancer is a deadly disease with over 500,000 cases annually worldwide. Metastatic head and neck cancer accounts for a large proportion of the mortality associated with this disease. Many advances have been made in our understanding of the mechanisms of metastasis. The application of immunotherapy to locally recurrent or metastatic head and neck cancer has not only improved oncologic outcomes but has also provided valuable insights into the mechanisms of immune evasion and ultimately treatment failure. Objectives: This review paper will review our current understanding of biological mechanisms of treatment failure and metastasis. Published and ongoing …

Elastomeric Nanocomposite With Solvent-Free, One Step, In Situ Shear Exfoliation Of Graphite To Graphene, Ashiqur Rahman, Md Abdur Rahman Bin Abdus Salam, Matthew G. Boebinger, Ahmed Touhami, Jennifer Lynch, Ali Ashraf

Physics & Astronomy Faculty Publications

A graphene nanoflake (GNF)-enhanced elastomeric nanocomposite (G-EMC) is fabricated following an innovative, cost-effective, single-step, in situ shear exfoliation (ISE) method from low-cost bulk material, graphite, where uniform mixing happens simultaneously within the elastomer matrix. Electron microscopy, atomic force microscopy, and photo-induced force microscopy results show good dispersion of GNFs with exfoliation to a few layers and uniform distribution in the elastomer matrix. X-ray photoelectron spectroscopy analysis shows less than 1% oxygen-containing functional groups/impurity, enhanced bonding through the formation of edge sites as fracture occurs across the GNF basal plane, and pi-pi interactions with newly exfoliated planar basal plane surfaces of …

Evaluating Forest And Land Rehabilitation Using Remote Sensing: A Case Study In Maros Regency, Syamsu Rijal, Munajat Nursaputra, Chairil A

Jurnal Penelitian Kehutanan Wallacea

Remote sensing technology has become crucial in vegetation monitoring, particularly for assessing vegetation density. Despite its broad application, its use in evaluating land rehabilitation efforts remains limited. The increasing extent of degraded lands has underscored the importance of effective forest and land rehabilitation activities. Traditionally, evaluating these efforts involves direct site visits to monitor plant growth annually for three years post-planting, which is time-consuming, labor-intensive, and costly. According to rehabilitation standards, a program is successful if 75% of the planted vegetation survives until the end of the third year. This study presents an efficient alternative by evaluating a rehabilitation site …

Promoting Private Conservation In Patra Seroja Ecopark, Dumai Municipality, Riau Province, Indonesia, Mokhamad Asyief Khasan Budiman, Yoppie Christian, Andy Afandy, Budi Prabowo, Desmiwati Desmiwati

Jurnal Penelitian Kehutanan Wallacea

This paper documents the voluntary conservation practices in Patra Seroja Ecopark Forest by Indonesia’s state-owned oil and gas company, Pertamina Ltd. - Refinery Unit II Dumai, Province of Riau, west coast of Sumatera Island. The company voluntarily allocated, financed, and managed 102 hectares of land in their private area to conserve and protect its in-situ biodiversity and preserve environmental service as a secondary objective. The results of studies and assessments carried out, the management application has fulfilled the Privately Protected Area (PPA) management criteria by IUCN regarding the orientation, biodiversity, management model, and utilization. However, PPA is not recognized legally …

Pfas In Landfill Leachate: Practical Considerations For Treatment And Characterization, Fabrizio Sabba, Christian Kassar, Teng Zeng, Synthia P. Mallick, Leon Downing, Patrick J. Mcnamara

Civil and Environmental Engineering Faculty Research and Publications

Per- and polyfluoroalkyl substances (PFAS) are widely used in consumer products and are particularly high in landfill leachate. The practice of sending leachate to wastewater treatment plants (WWTPs) is an issue for utilities that have biosolids land application limits based on PFAS concentrations. Moreover, landfills may face their own effluent limit guidelines for PFAS. The purpose of this review is to understand the most appropriate treatment technology combinations for mitigating PFAS in landfill leachate. The first objective is to understand the unique chemical characteristics of landfill leachate. The second objective is to establish the role and importance of known and …

Poor Outcome Of Rare Lactobacillus Bacteremia And Endocarditis In A Patient With Frequent Consumption Of Live Culture Yogurts, Paul Wasuwanich, Logan B. Brickner, Mark S. Rasnake, Rebecca J. Witherell

Journal of Community Hospital Internal Medicine Perspectives

Lactobacillus rhamnosus is a gram-positive bacterium commonly found in dairy products and used as a probiotic due to its resistance to acid and bile. While generally considered safe, rare cases of L. rhamnosus bacteremia and endocarditis have been reported, primarily in individuals with significant risk factors. This case discusses an elderly male with a history of cardiovascular diseases, diabetes, and asthma, who developed L. rhamnosus bacteremia and endocarditis after consuming large quantities of Greek yogurt. The patient initially presented with fatigue, myalgias, and fever, and was treated empirically with cefepime and vancomycin. On that occasion, blood cultures recovered L. rhamnosus …

Marginal Zone Lymphoma In A Case Of Hidradenitis Suppurativa Treated With Adalimumab Therapy., Anish K Shrestha, Rojina Pokherel, Greeshma N Gaddipati, Pankti S Desai

Journal of Community Hospital Internal Medicine Perspectives

Marginal zone lymphoma has seldom been described in relation to adalimumab used for treatment of hidradenitis suppurativa. Although studies have shown an increased risk of lymphoma with adalimumab, most of these studies were done in patients with underlying inflammatory bowel disease or rheumatoid arthritis where the disease itself presents as a confounder for lymphoma. Our case described adds to the role of chronic anti-TNF alpha therapy as a possible etiology of lymphoma.

Spontaneous Splenic Rupture Leading To The Diagnosis Of Cml, Nikita Dahake, Rachel Thomas, Brittany Corso

Journal of Community Hospital Internal Medicine Perspectives

Background: Spontaneous splenic rupture (SSR) is a known complication of hematologic malignancy. Rare cases have been reported in which patients presented with SSR prior to diagnosis of chronic myeloid leukemia (CML). We present a case of atraumatic SSR due to CML presenting as persistent abdominal pain.

Case Presentation: A 42-year-old man presented with persistent left upper quadrant pain radiating to the lower quadrants ongoing for many months. He additionally had many other systemic symptoms including weight loss, night sweats, dark tarry stools, and progressive fatigue. Initial laboratory tests showed an anemia and a leukocytosis of 170 K/mm3 which uptrended to …

Mafld: Exploring The Systemic Effects Beyond Liver., Utkarsh Dayal, Ujjwal Soni, Sourav Bansal, Kanishk Aggarwal, Chaitanya Chennupati, Sai Gautham Kanagala, Vasu Gupta, Ripudaman Singh Munjal, Rohit Jain

Journal of Community Hospital Internal Medicine Perspectives

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a growing global health concern which is driven by the increasing prevalence of diabetes and obesity. MAFLD is characterized by excessive fat accumulation in the liver, which encompasses a range of conditions, from simple hepatic steatosis to more severe forms. This condition is associated with various complications, including chronic kidney disease (CKD), Cardiovascular Disease (CVD), liver cirrhosis, and even malignancy. Recent research has highlighted a potential connection between gut dysbiosis and MAFLD, particularly in relation to CKD. This has underscored the significance of the gut-liver-kidney axis in understanding MAFLD's pathogenesis. Inflammation triggered by …

Gene Editing: Developments, Ethical Considerations, And Future Directions, Manav Parikh

Journal of Community Hospital Internal Medicine Perspectives

An examination of recent developments related to CRISPR technology, ethical considerations of the application of such technologies, and future directions for germline editing.