Digital Commons Network^™

Probing The Complexity Of Cellular Rna Folding: Ensembles, Intermediates, And Isoforms

Faculty, Staff and Students Publications

RNA molecules populate complex structural landscapes that are continuously reshaped throughout the RNA lifecycle by equilibrium and non-equilibrium processes. Resolving these structural landscapes represents a central challenge in RNA biochemistry. We review recent advances in RNA chemical probing, sequencing, and computational deconvolution technologies that are revolutionizing our ability to measure the complexities of RNA folding in cells and the deep involvement of these complexities in RNA functional mechanisms. We highlight new methods for deconvolving structural ensembles, distinguishing isoform-specific architectures using long-read sequencing, capturing co-transcriptional folding intermediates in vivo, and measuring higher-order RNA structures while also underscoring remaining challenges. We conclude …

Addendum: Raf/Mek/Extracellular Signal-Related Kinase Pathway Suppresses Dendritic Cell Migration And Traps Dendritic Cells In Langerhans Cell Histiocytosis Lesions, Jun Tang, Camille Bigenwald, Madhavika Serasinghe, Karen Phaik Har Lim, Howard Lin, Tsz-Kwong Man, Romain Remark, Samantha Baxter, Veronika Kana, Stefan Jordan, Zoi Karoulia, Wing-Hong Kwan, Marylene Leboeuf, Elisa Brandt, Helene Salmon, Kenneth Mcclain, Poulikos Poulikakos, Jerry Chipuk, Willem J M Mulder, Carl E Allen, Miriam Merad

Faculty, Staff and Students Publications

No abstract provided.

Vetiver Phytoremediation Of Nitrate-Rich Munition Wastewater: Biomass Valorization Within A Circular Economy Framework, Arash Aliasghar, Rupali Datta, Zhiming Zhang, Christos Christodoulatos, Dibyendu Sarkar

Michigan Tech Publications

Industrial munition facilities generate nitrate-rich wastewater that requires effective and sustainable treatment before discharge. While vetiver grass (Chrysopogon zizanioides)-based phytoremediation has shown promise in nitrogen removal, most studies have been limited to small-scale experiments under low nitrogen concentrations, providing limited guidance for system-level design under elevated loading. This study evaluates a greenhouse-scale phytoremediation system using vetiver grass to treat wastewater containing 1000 mg N/L nitrate and 50 mg/L COD. Plant coverage densities of 2%, 4%, and 6% (w/v) were assessed to quantify optimum density as a design parameter for optimizing nitrate removal. A 6% coverage achieved the highest efficiency, reducing …

Mir172-Ap2 Controls Age-Dependent Regeneration Competence In Populus, Kaiwen Lyu, Abdul Azeez, Victor Busov

Michigan Tech Publications

Plants maintain remarkable regenerative potential, yet this capacity declines with developmental age, limiting clonal propagation and biotechnological applications. Here, we show that the miR172-AP2 module serves as a central determinant of regeneration competence in Populus. Regenerative capacity declines progressively along the shoot developmental gradient, correlating with elevated miR172 and reduced AP2 transcript levels. Functional analyses demonstrate that AP2 promotes both shoot and root regeneration by directly activating downstream transcriptional programmes, including AINTEGUMENTA-LIKE1, BIG LEAF and LIKE APETALA1, which regulate organogenic growth and developmental competence. Elevated miR172 or cytokinin signalling represses AP2, reducing regenerative outcomes, indicating that hormonal and developmental signals …

Revised Draft Final Butte Mine Waste Repository Operation And Maintenance (O&M) Plan, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Reply To “Comment On Primary Care Providers' Perspectives On Telehealth Medicare Annual Wellness Visits For Older Adults In Midwestern Health System”, Vaibhavi Mone, Jungyoon Kim

Health Services and Informatics Research

No abstract provided.

The Purpose Of Integration Beyond Expression: Emerging Human Patterns And Possible Selves In A Computational Model Of Self-Reflection, Lore Olson

Electronic Theses and Dissertations 2020 - Present

Self-reflection encompasses the dual modes of Integration and Expression, the processes of actively attempting to know oneself and doing something with that knowledge. Each mode serves a distinct purpose; however, the long-standing idea that Integration is needed before Expression can occur has been challenged by the demonstrated ability to create and maintain a small, stable identity through constant Expression. Across three studies, a theory was tested of the Integration mode as a method of quickly and sustainably distributing clusters of organization across the self-structure, allowing for diversity in the selves one can coherently express. Study one replicated the previously observed …

Impact Of After-School Care On Maternal Income: Evidence From Canadian Administrative Data, Ailin He, Laetitia Renée, Nagham Sayour

All Works

This paper estimates the average causal effect of access to subsidized before- and after-school care on the labour market outcomes of mothers. Specifically, we analyze a major policy reform implemented in Quebec (Canada) in 1998, which required all public primary schools to provide before- and after-school care at a low fixed fee, thereby reducing costs and expanding availability for families. We identify the intent-to-treat effect of the reform on service use and maternal labour market outcomes using administrative tax return data and a triple difference design. We find that, 7 years after implementation, the policy led to a substantial increase …

Wendi Kraemer V. Township Of Rostraver

2026 Decisions

USDC for the Western District of Pennsylvania

Final Bpsou Unreclaimed Sites: Ur-46 Remedial Action Work Plan (Rawp), Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Coping With Adversity: Exploring The Role Of Protective Factors And Their Impact On School Enrollment And Satisfaction Among Adolescents Living With Hiv In Low-Resource Settings, Jennifer Nattabi

Brown School Graduate Student Theses and Dissertations

Globally, an estimated 2.38 million children and adolescents (0–19 years) are living with HIV, with 80% residing in sub-Saharan Africa. In Uganda, adolescents remain at high risk, with approximately 6,600 new infections among 10–19-year-olds in 2023. Despite expanded access to antiretroviral therapy (ART), adolescents Living with HIV (ALHIV) continue to experience poor outcomes, including low viral suppression and high mortality, largely driven by non-adherence. However, ART adherence represents only one dimension of their lived experience. ALHIV must also navigate intersecting adversities, including poverty, stigma, orphanhood, and exposure to sexual and gender-based violence, while meeting academic expectations, particularly in boarding school …

Trends And Disparities In Cardiometabolic Disease Prevalence By Physical Activity Among Us Adults: Nhanes 2007–2018, Zhijing Xu, Jinyu Hu Hu, Jackie Finik, Xiang Qi, Ruotong Liu, Yaguang Zheng, Bei Wu

Department of Family Science and Human Development Scholarship and Creative Works

Background: Cardiometabolic diseases (CMDs) significantly contribute to U.S. morbidity. Physical activity (PA) is associated with lower CMD prevalence, yet trends in CMD prevalence by PA level and associated disparities remain underexplored.

Methods: We analyzed 2007–2018 NHANES data from 26,380 adults aged ≥20 years. CMDs included diabetes, cardiovascular disease (CVD), and chronic kidney disease (CKD; eGFR < 60 mL/min/1.73 m² or ACR ≥30 mg/g). PA was categorized as no activity, some/irregular activity, or regular activity. Age-standardized prevalence and survey-weighted logistic regression estimated trends (reference: 2007–2008) and adjusted odds ratios (aORs).

Results: Diabetes prevalence increased, with higher odds in 2013–2014 (OR = 1.27; 95% CI: 1.01–1.60), 2015–2016 (OR = 1.41; 1.08–1.84), and 2017–2018 (OR = 1.45; 1.16–1.80) and an absolute increase of 2.49% (0.85 to 4.13). No significant trends were observed for CKD (absolute change: 0.11%; …

Evaluation Of Mechanical Properties And Seal Strength Of Medical Packaging Materials Before And After Supercritical Co₂ Sterilization, Camila Madriz Pizarro

Theses

The sterilization of medical devices is critical in the prevention of infections in healthcare settings. Ethylene oxide (EtO), gamma irradiation, and steam sterilization have been the standard sterilization processes in healthcare settings, where the packaging system remains the most important barrier between the sterilized instrument/device. Safety concerns and regulatory pushback on conventional sterilization methods have pushed for further research on new sterilization techniques. Among the emerging sterilization technologies, one candidate that has garnered considerable attention is Supercritical CO2 sterilization. However, there is a lack of literature to support the compatibility between scCO2 and common medical packaging materials. The present study …

Multi-Omic Analysis Of Molecular Changes In Haloferax Volcanii Biofilm Development, Joshua Koller

Theses

Biofilms are the predominant lifestyle of microorganisms and offer protection against environmental stress. Archaeal biofilm development remains poorly understood relative to its bacterial counterpart, and the fundamental differences between these two domains prevent direct extrapolation from bacterial models. To address this gap, we used quantitative proteomics and transcriptomics to characterize the molecular changes accompanying biofilm formation and maturation in the model archaeon Haloferax volcanii. Protein and transcript abundance were measured across seven conditions spanning both lifestyles and multiple timepoints, with glycosylated proteoforms quantified as entities distinct from their unmodified counterparts, covering both established biofilm-associated structures and newly identified candidates. Known …

Changes In Water Quality And Microbiota Over Two Years In Florida Hard Clam (Mercenaria Mercenaria) Hatcheries, Bonnie Getter

Electronic Theses and Dissertations 2020 - Present

This thesis characterized the water quality and bacterial communities in nine hard clam hatcheries over two production years through weekly or biweekly water quality and chemistry monitoring, monthly bacterial plating in the second year of production, and select 16S microbiome sampling at select hatcheries to address production bottlenecks and support the reliable production of high-quality seed for Florida’s growing hard clam aquaculture industry. Logistic regression models showed that water source was distinguished by pH, salinity, alkalinity, and nitrite, whereas geographic location was distinguished by temperature, salinity, nitrate, and calcium; temperature, dissolved oxygen, salinity, and alkalinity distinguished seasons. Vibrio bacteria differed …

Cover And Contents

Turkish Journal of Physics

No abstract provided.

The Effect Of Spin Polarization On Ion-Acoustic Solitary Waves In Quantum Plasmas, Amirhosein Rezvani, Sedigheh Miraboutalebi, Leila Rajaei, Mahmoodreza Sharifian

Turkish Journal of Physics

The exchange interaction, a fundamentally quantum-mechanical phenomenon, can significantly modify the classical description of cold, overdense plasmas. These quantum effects can be systematically analyzed within the framework of quantum magnetohydrodynamic (QMHD) theory, which enables the use of separate momentum equations for spin-up and spin-down electron populations. In this study, we adopt this approach to incorporate exchange interactions for both spin species and investigate the excitation of ion-acoustic wave (IAW) solitons in the plasma system. Using a perturbative expansion method, the governing equations are reduced to a nonlinear Schrödinger equation (NLSE), which admits solitonic wave solutions. The stability of these solitons …

Radiation Pressure And Membrane Dynamics In Cavity Optomechanics: Interaction Hamiltonian And Quantization, Mahmut Can Özuygur

Turkish Journal of Physics

Cavity optomechanics explores the interaction between light confined in optical cavities and mechanical oscillators, primarily driven by radiation pressure forces. These interactions enable significant advances in precision measurements, quantum information processing, and tests of fundamental quantum mechanics. This paper presents a detailed analysis of membrane vibration and radiation pressure force within a cavity optomechanical system. The membrane's equation of motion is derived, the radiation pressure force is evaluated within the Lorentz force formalism, and the corresponding interaction Hamiltonian is formulated. Quantization of the resulting Hamiltonian enables the investigation of quantum phenomena, including entanglement generation and quantum state transfer, and provides …

Observational Constraints On The Structure-Induced Dark Energy Model, Ali̇ Kazim Çamlibel

Turkish Journal of Physics

A new phenomenological dark energy model, originally associated with large-scale structure formation and proposed as a solution to the fine-tuning and coincidence problems related to the cosmological constant, was analyzed within the framework of General Relativity in a Friedmann-Robertson-Walker spacetime and its model parameters were estimated using cosmic chronometers and recent DESI data. It turns out that the proposed model can serve as an alternative evolving dark energy model with a novel equation of state function. Given the form of this phenomenological energy density ansatz, which rises with the nonlinear structure growth in the universe and declines as cosmic voids …

On Cosmological Equation Of State From The First Law Of Thermodynamics, Ch'ng Han Siong

Turkish Journal of Physics

We derive several equations of state for different types of energy from the first law of thermodynamics. We derive the equation of state of a Machian universe from the well-known energy formulaE=mc2. This equation of state is consistent with previously reported results. We then propose hypothetical forms of energy that lead to the equations of state of the Chaplygin gas, generalized Chaplygin gas, and modified Chaplygin gas. We also obtain the energy density of the Chaplygin gas by dividing the hypothetical energy by the volume of the universe, and find that it is consistent with previously reported results. Finally, we …

Design And Fabrication Of Petri Dish Optimized For High-Frequency Acoustic Microscopy Using 3d Printing, Tuna Pesen, Beyza Ceren Eren, Arda İnanç, Bora Akgün

Turkish Journal of Physics

High-frequency imaging in acoustic microscopy requires the use of Petri dishes with thin and acoustically transparent bottoms to minimize signal attenuation and distortion. Commercially available options suitable for this purpose are often expensive or limited in compatibility with custom setups. Here, we present a cost-effective and easily customizable alternative developed in our laboratory, consisting of a 3D-printed frame combined with commercially available stretch film. The stretch film serves as an ultrathin (8 µm thickness) base that supports efficient high-frequency acoustic transmission, enabling clear and reliable imaging. Beyond acoustic microscopy, the adaptable design is also compatible with other modalities such as …

Arthroscopic Saucerization Of A Medial Discoid Meniscus In A Young Female Athlete: A Case Report, Travis Hodge, Brett Norris, Ryan Sorenson, Peter Schultz, Michael Dempewolf

Student Publications

A discoid meniscus is a congenital abnormality of the meniscus characterized by a disk-shaped configuration. Although medial involvement is uncommon, symptomatic cases may present in young, active individuals with mechanical knee symptoms that limit sports participation. A 15-year-old female athlete presented with chronic medial knee pain, mechanical symptoms, and an inability to fully extend the knee despite failed conservative management. MRI demonstrated a complete discoid medial meniscus with a central tear. Arthroscopy confirmed a discoid medial meniscus without significant peripheral instability. Arthroscopic saucerization was performed while preserving a stable peripheral rim. By the conclusion of the three-month follow-up, the patient …

Plans Being Laid For Fsc Homecoming, Florence Times

Documents

Plans for Homecoming 1958

Sex-Aware Causal Inference Assessment Of The Immune System In Complex Neurodegenerative Diseases, Frida Lona-Durazo, Ross P Byrne, Marc-Olivier Pilon, Michael D Greicius, Marie-Pierre Dubé, Michael E Belloy, Russell L Mclaughlin, Sarah A Gagliano Taliun

2020-Current year OA Pubs

Sex differences, in terms of prevalence, symptoms and disease progression, are established in the aetiology of complex neurodegenerative diseases, including amyotrophic lateral sclerosis, Parkinson's disease and Alzheimer's disease, but the underlying biology driving these differences remains poorly understood. There is emerging evidence from genetic and functional analyses affirming the role of the immune system in such diseases, but a thorough assessment of sex differences in the link between the immune system and neurodegenerative diseases remains lacking. Here, we applied a robust causal inference approach, two-sample Mendelian randomization, to evaluate the causal effect of immune-related protein levels on three neurodegenerative diseases …

Contributions Of Arginine And Nitrosative Stress To Huntington’S Disease Progression, Ian D. Gaudet

Electronic Theses and Dissertations 2020 - Present

Neuroinflammation is a well-established component of Huntington's disease (HD) pathogenesis, yet the intricate molecular mechanisms that govern this process remain a topic of ongoing research and debate. This dissertation elucidates a novel pathway linking arginine metabolism and nitrosative stress to core HD pathology. We found that the arginine transporter SLC7A2 is selectively upregulated in various HD cellular models and patient samples. Our findings reveal that this upregulation drives an overactive inflammatory response, leading to abnormally high inducible nitric oxide synthase (iNOS) induction and subsequent nitric oxide (NO) production, which causes excessive protein nitrosylation and an increase in mitochondrial fragmentation.

To …

Bdelloid Rotifers Harbor A Voltage-Gated Proton Channel With Distinct Mechanistic Features, Liang Yan, Chiara Boschetti, Liang Hong

School of Biological and Marine Sciences

Bdelloid rotifers are renowned for their extraordinary resilience. They can survive desiccation and long-term freezing and revive once favorable conditions return. Such remarkable survival abilities suggest that the evolution of specialized molecular adaptations sustain pH homeostasis under extreme environmental stress. In the present study, we identify and functionally characterize an isoform of the voltage-gated proton channel (Hv) from the bdelloid rotifer Adineta ricciae, which we name ArHv2. Unlike its paralog ArHv1 and human Hv1 that activate only at positive membrane potentials and contribute modestly to proton extrusion under normal conditions, the ArHv2 activates even at negative potentials, enabling rapid and …

From Homogeneous To Heterogeneous Adaptive Bounded-Confidence Opinion Dynamics On Networks, Sally Hafez, Fatma R. Farag, Amira S. N. Tawadros

Northeast Journal of Complex Systems (NEJCS)

Adaptive bounded-confidence models (ABCMs) elucidate the coevolution of agent states and network structure via local interactions and rewiring mechanisms. Traditional formulations assume uniform interaction parameters, leading to distinct regime shifts encompassing fragmentation, polarization, and consensus. A symmetric heterogeneous extension of the adaptive bounded-confidence model is introduced, in which interaction parameters vary according to whether agents belong to the same or different groups. The model retains the original update and rewiring protocols but integrates within-group and between-group confidence bounds alongside tolerance thresholds. Initially, the classic homogeneous model is replicated to establish a reference point. Subsequently, the heterogeneous extension is assessed under …

Integrating Oncology Into Entry-Level Physical Therapist Curricula, Shana Harrington, Christopher M. Wilson, Morgan Zaranec, Lori Boright

Oncology Rehabilitation in Practice

Print issue available for $25.

Background: Cancer and its treatments commonly result in adverse effects that impair function, well-being, and quality of life, necessitating access to skilled physical therapists (PTs). Although oncology is an essential component of physical therapist practice, entry-level education in cancer rehabilitation has historically been limited. In 2025, the Essential Competencies for Physical Therapy Entry-Level Education in Oncology were developed through a mixed-methods, modified Delphi process, establishing 19 competencies across six domains and defining minimum expectations for new graduates. To support translation of these competencies into academic curricula, a practical implementation resource was needed.

Purpose: To …

Wavelet-Based Multiscale Analysis Of Cave Co₂ Concentration In Response To Short-Term High-Intensity Tourism Activities: Spatiotemporal Heterogeneity And Lag Characteristics, Mingda Cao, Wenwen Song, Yan Zhang, Jie Zhang, Zhiqiang Yao

International Journal of Speleology

High-intensity tourism activities can cause a significant increase in cave air CO₂ concentration, thereby affecting the cave micro-environment and secondary carbonate deposition. During the 2023 National Day Golden Week, high-frequency continuous monitoring of cave air CO₂ partial pressure (PCO_2(A)) and visitor numbers was conducted in Dawang Cave, Anhui Province. Wavelet transform and cross-correlation analyses were used to reveal the multi-scale response characteristics of CO₂ concentration to tourism activities. The results show that: (1) PCO_2(A) exhibited clear diurnal variations (higher during the day, lower at night) and decreased spatially with enhanced ventilation, controlled jointly by …

Decentring Philosophical Education In African Tertiary Education: Integrating Global Perspectives In The Classroom, Isaac Mutelo

Comparative Philosophy

The philosophical discourse has been dominated by Western perspectives, an approach that continues to influence curriculum design and delivery in higher education. The historical dominance of the Western philosophical canon in university curricula has contributed to the marginalisation of other equally significant philosophical traditions from Africa, Latin America, Asia, and Indigenous cultures. This approach has contributed significantly to the narrow and limited scope and relevance of philosophy as an academic field globally. Rather than advocating for the dominance and superiority of the Western-centred curriculum, this paper acknowledges the centrality of integrating global philosophical perspectives in the philosophy curriculum and discourse …