Digital Commons Network^™

Perspectives On The Future Of The Profession Of Microbiology, Todd L Kelson, Heidi B Kaplan, Michelle Dziejman, Shilpa Gadwal, Irene Hulede, Jennifer Bennett, Roger Greenwell, Shelley Payne, Kyle Maclea, Eric Miller, Diana L Vullo, Rebecca Sparks-Thissen, Astral Bertolio, Jorge Cervantes

Faculty, Staff and Student Publications

The Profession of Microbiology (POM) embodies the bulk of the American Society for Microbiology (ASM) members and represents the career preparation arm of the ASM for academia, industry, and clinical lab professions. The ASM Council on Microbial Sciences hosted a virtual retreat in 2025 to identify the future of the POM. The retreat presentations centered on workforce development, professional development, innovations in technology, and interdisciplinary collaborations. Various aspects were identified, such as the need to prepare for careers in industry, as an important goal of future training. It was also clear that scientists, in all walks of life, need professional …

Enhanced Oviposition Preferences And Larval Performance Of Hermetia Illucens L. In Fruit Wastes Fermented By Effective Microorganisms, Resti Rahayu, Robby Jannatan, Muhamad Ronaldo, Risa Ukhti Muslima

Makara Journal of Science

Organic waste comprises a considerable portion of global waste, requiring effective management. The ability of the black soldier fly (Hermetia illucens, BSF) to convert organic waste into biomass has been well reported. However, bioconversion can be hindered by fiber-rich substrates, a challenge that can be addressed through substrate pretreatment. This study examined the oviposition preferences and larval performance of BSFs in several fruit wastes fermented by effective microorganisms (EMs), which were compared to non-fermented substrates. The oviposition attractants utilized pineapple peel and overripe soursop, with larval performance evaluated among different treatments, i.e., non-fermented pineapple peel (NFP), fermented pineapple …

Computational Screening Of Anticancer Peptides From Cordyceps Militaris Targeting Apoptosis, Angiogenesis, And Metastasis, Joanne Lim, Adeline Yoke Yin Chia, Sunita Chamyuang, Tang Yin Quan

Makara Journal of Science

Cancer remains a major global health issue, and current therapies often lack efficacy and have severe adverse effects. Anticancer peptides (ACPs) have emerged as promising therapeutic agents due to their specific targeting mechanisms and minimal toxicity. This study aimed to identify novel ACPs from Cordyceps militaris through computational screening, evaluate their anticancer potential, predict their mechanisms of action through molecular docking, and analyze their pharmacokinetic profiles. Initially, 15 protein sequences from Cordyceps militaris were retrieved from the National Center for Biotechnology Information database and subjected to in silico gastrointestinal digestion using BIOPEP-UWM. The resulting peptides were subjected to predictive analysis …

Quantitative Structure-Activity Relationship, Pharmacokinetics, Drug-Likeness, Toxicity, And Molecular Docking Studies Of 4-N-(Methyl)-4-Aminoquinoline Derivatives As Antimalarial Compounds, Muhamad Jalil Baari, Devi Hardiyanti

Makara Journal of Science

Antimalarial drug resistance has encouraged various innovations to develop novel drug compounds that are effective, feasible, and safe, adhering to health standards. One way to do that is by observing and predicting the biological activity of drug compounds using quantitative structure–activity relationship (QSAR) analysis. In this study, QSAR analysis was conducted on the 4-N-(methyl)-4-aminoquinoline derivatives, which effectively inhibit the growth of Plasmodium falciparum as a source of malaria. The research stages involved molecular structure modeling, molecular geometry optimization using the AM1 semi-empirical method, and QSAR descriptor calculations, including electronic (atomic charges (q), HOMO and LUMO energies, polarizability (α), …

Enzyme-Free Colorimetric Sensing Of Glucose Using Silver Nanoparticles With A Green Stabilizing Agent From Capsicum Chinense Jacq Extract, Boyfannie Ivan Putra, Hermin Sulistyarti, Muhammad Mashuri Utama, Aura Ananda Haryanto, Rurini Retnowati, Mohamad Rafi, Akhmad Sabarudin

Makara Journal of Science

Diabetes mellitus (DM) is a significant global health issue characterized by abnormal glucose levels in the human body. DM diagnostics are often based on invasive sampling from blood, which poses a potential risk of infection and tissue damage. Therefore, a non-enzymatic and non-invasive method for glucose monitoring is demanded as a simple alternative to glucose detection in urine samples. In this work, enzyme-free glucose determination is based on the formation of silver nanoparticles stabilized by Capsicum chinense Jacq extract (CCJ-AgNPs). Under alkaline conditions, glucose functions as a reducing agent for silver ions, and the extract acts as a stabilizer to …

Microplastic Degradation Using Laccase Enzyme From Trametes Hirsuta: In The Silico Study, Hanzhola Gusman Riyanto, Diana Sylvia

Makara Journal of Science

Microplastics are a serious global problem that arises worldwide because of their widespread use. Exposure to microplastics can negatively affect human and environmental health. In this study, we used molecular docking methods with MOE software (version 2014.0901) to investigate the interaction between the laccase enzyme and several microplastic compounds as a preliminary study of microplastic degradation using enzymes. The Quantitative Structure Analysis Relationship (QSAR) analysis revealed that all microplastic ligands had higher Pa values than Pi, indicating that the laccase enzyme may be biologically active. The findings of the present study show that polyamide (PA) has the lowest binding energy …

The Relationship Between Reef Fish And Coverage Of Coral And Turf Algae In Coral Reef Ecosystems Of Biak Island, Papua, Ludi Parwadani Aji, Risandi Dwirama Putra, Muhammad Abrar, Rikoh Manogar Siringoringo, Giyanto Giyanto

Makara Journal of Science

In this study, we examine the influence of benthic coverage on fish diversity in coral reef ecosystems. Benthic and reef fish community surveys were conducted at 14 sites using underwater photographic transect and underwater visual census methods, respectively. Coral cover (26.1%) was found to be lower than turf algae cover (42.1%). A total of 56 fish species, comprised of 14 carnivores, 21 corallivores, and 21 herbivores, were recorded. The most widely distributed carnivore and herbivore species were Lethrinus harak and Ctenochaetus striatus, respectively. Two species of butterflyfish, Chaetodon citrinellus and Chaetodon trifasciatus, were the most widely distributed species …

A Tissue Renewal-Based Mechanism Drives Colon Tumorigenesis, Ryan M. Boman, Gilberto Schleiniger, Christopher Raymond, Juan P. Palazzo, Anne Shehab, Bruce M. Boman

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Our Goal is to identify how colorectal cancer (CRC) arises in the single-layered cell epithelium (simple columnar epithelium) that lines the luminal surface of the large intestine. Background: We recently reported that the dynamic organization of cells in colonic epithelium is encoded by five biological rules and conjectured that colon tumorigenesis involves an autocatalytic tissue renewal reaction. Introduction Our objective was to define how altered crypt turnover explains tissue disorganization that leads to adenoma morphogenesis and CRC. Hypothesis: Changes in rate of tissue renewal-based cell polymerization leads to epithelial expansion and tissue disorganization during adenoma histogenesis. Methods: Accordingly, we created …

Pepquerymhc: Rapid And Comprehensive Tumor Antigen Prioritization From Immunopeptidomics Data, Seunghyuk Choi, Bing Zhang

Faculty, Staff and Students Publications

Determining tumor-specificity of MHC-bound peptides is crucial for cancer immunotherapy development, yet current methods struggle with class II peptides and non-reference sequences. We introduce PepQueryMHC, an ultra-fast tool that integrates MHC-bound peptide sequences with translated RNA-seq reads for efficient tumor antigen prioritization. We demonstrate its versatility in prioritizing class I and II tumor antigens, mapping the cellular origins of presented peptides, and resolving uncertainties surrounding the prevalence of proteasome-spliced peptides.

Eif3d And Eif3e Mediate Selective Translational Control Of Hypoxia That Can Be Inhibited By Small Molecules, Stephen C Purdy, Kate Matlin, Christopher Alderman, Amber Baldwin, Natasha Shrivastava, Goksu Sarioglu, Somnath Dutta, Kristofor J Webb, Arthur Wolin, Dillon P Boulton, Annika Gustafson, Jyoti Kapali, John D Landua, Michael T Lewis, M Cecilia Caino, James C Costello, William Old, Xiang Wang, Rui Zhao, Heide L Ford, Neelanjan Mukherjee

Faculty, Staff and Students Publications

Exposure to hypoxia is linked to increased cellular plasticity and enhanced metastasis, effects that are primarily attributed to the transcriptional activation of large gene programs downstream of hypoxia-inducible factors (HIFs). However, translational effects in hypoxia, which likely precede transcriptional effects, have remained largely unexplored. Using ribosome profiling, we uncovered a selective translational response in acute hypoxia that is eukaryotic initiation factor (eIF)3d/eIF3e dependent and controls downstream hypoxic responses, including HIF1α accumulation and cellular invasion. We further demonstrated that eIF3e copy number and eIF3e and eIF3d expression signatures are associated with worsened outcomes for patients with breast cancer. Finally, we identified …

Liberal Or Restrictive Postoperative Transfusion In Patients At High Cardiac Risk: The Top Randomized Clinical Trial, Panos Kougias, Sherene E Sharath, Min Zhan, Jeffrey L Carson, L Erin Norman, Zhibao Mi, Rupsi Pal, Hasan Dosluoglu, J Gregory Modrall, George A Sarosi, Peter Nelson, Shipra Arya, Alexandra Scrymgeour, Jade Ollison, Lawrence A Calais, Vijay Nambi, L Parker Gregg, Shuaib M Abdullah, Shirling Tsai, Natasha Becker, Justin C Choi, Louisa Chiu, Salvatore Scali, Neal R Barshes, Samir Awad, Mohammed Moursi, Matthew C Koopmann, Mitchell Sally, Daniel Ihnat, Archana Ramaswamy, Warren Gasper, Edith Tzeng, Mark A Wilson, Gale Tang, Grant Huang, Kousick Biswas

Faculty, Staff and Students Publications

Importance: Postoperative red blood cell transfusion guidelines recommend transfusion for hemoglobin levels less than 7 g/dL. However, the safety of this strategy in patients at high risk of cardiac events undergoing major operations remains unclear.

Objective: To evaluate the risk of death or major ischemic events within 90 days after a liberal transfusion strategy compared with a restrictive transfusion strategy in patients at high risk of cardiac events who had undergone major vascular or general surgery operations and developed postoperative anemia.

Design, setting, and participants: This parallel, single-blind, randomized clinical superiority trial included 1428 veterans (≥18 y) at high cardiac …

Esat-6 And Cfp-10 Reactive Igg In Patients With Tuberculosis Inhibits Intracellular Bacteria, Joshua R. Miles, Pei Lu, Shuangyi Bai, Genesis P. Aguillón-Durán, Javier E. Rodríguez-Herrera, Bronwyn M. Gunn, Blanca I. Restrepo, Lenette L. Lu

School of Medicine Publications

Perspectives beyond the CD4 T cell interferon (IFN)-γ paradigm are needed to understand immunity in tuberculosis (TB). Growing data in patients across a spectrum of TB highlight that changes in antibody Fc domain glycosylation and Fc effector functions correlate with disease and impact Mycobacterium tuberculosis (Mtb) infection. How antigen-specific antibodies within polyclonal responses affect bacteria is less clear. This study examines antibodies targeting ESAT-6 and CFP-10, Mtb virulence proteins essential for pathogenesis. Data from patients with TB show that polyclonal immunoglobulin (Ig)G reactive to ESAT-6 and CFP-10 diverges from other Mtb and non-Mtb antigens with enhanced sialylation, …

A Decision Support Model For Building Material And Component Reuse In The Context Of Circular Buildings, Havva Aksel

Journal of Sustainable Construction Materials and Technologies

Construction activities cause significant environmental impacts such as waste generation, pollution, resource consumption, and land use, which are expected to increase with global construction demands. To mitigate these environmental problems, the circular building occurs as an emerging concept depending on in the circular economy, which aims to minimize waste and redefine the “end-of-life” concept by reducing, reusing, recycling, and recovering materials. The reuse of building materials and components (BMCs) from existing structures represents a crucial strategy for achieving circularity in the built environment. Within this framework, design plays a key role. However, designing with reclaimed BMCs remains complex due to …

Neuroprotective Effects Of Aqueous Extract Of Bryophyllum Pinnatum Against Lead Acetate Induced Damage In The Cerebellum Of Rats, O. A. Bamgbose, O. D. Akanji, E. O. Olayemi, D. O. Taiwo-Ola, K. O. Odubela, B. A. Akanbi, P. B. Fakunle

AUIQ Complementary Biological System

Lead is a persistent environmental toxin with pronounced neurotoxic effects, particularly on the central nervous system. This study evaluated the impact of lead acetate on the cerebellar cortex of adult Wistar rats and assessed the neuroprotective effects of aqueous Bryophyllum pinnatum extract. Twenty adult Wistar rats (180–220 g) were randomly assigned to four groups (n = 5): Control (distilled water), T1 (0.075 mg/kg lead acetate), T2 (100 mg/kg B. pinnatum), and T3 (lead + B. pinnatum). Treatments were administered orally for 21 days. Cerebellar tissues were processed for biochemical and histological analysis, and data were analyzed using GraphPad Prism v10.1.Lead …

Cytological Changes In Buccal Mucosa Among Yemeni Qat Chewers In Hadhramout Governorate: A Comparative Cross-Sectional Study, Saleh H. Ben Sumaidea, Hassan Pyar, Abdullah O. Bin Nashwan, Abdullah M. Bin Fadhl, Abeer A. Marabi, Ahmed A. Al-Shetri, Gumaan S. Rassam, Halima K. Joher, Mashhoor A. Bin Shehab, Mohammed S. Bin Mosalem

AUIQ Complementary Biological System

Qat (Catha edulis) chewing is a common practice in Yemen, associated with oral mucosal irritation. The objective of the current study is to compare cytological findings of buccal mucosa between Qat chewers and non-chewers. A comparative cross-sectional study was designed. Buccal smears were collected from chewers (n = 100) and non-chewers (n = 100), fixed, and stained with Harris hematoxylin staining. Smears were assessed for inflammatory changes and cytological atypia by two blinded examiners; disagreements were resolved by consensus. The inflammatory cells were observed in 21% of chewers compared to 8% of controls (P = 0.009), while …

Despair Amongst Brazil’S Youth: Does The Hague Convention On International Child Abduction Need More Bite?, Ishani Sanyal

Pace International Law Review

For decades, international child abduction by one parent from the legal custody of the other has been a persistent issue which continues to be overlooked by international organizations and countries from around the world. While the Hague Convention on the Civil Aspects of International Child Abduction has helped to initiate certain progress in addressing acts of international child abduction by parents, signatory states including Brazil have failed to enforce rulings and provisions of the convention. This article addresses how the convention does not account for structural inadequacies of Brazilian court systems which prevent thorough enforcement of international custody and visitation …

Conserving Conservation Servitudes: The Role Of The Prior Public Use Doctrine In Protecting Privately Conserved Land In The United States And Australia, Olivia Clausen

Pace International Law Review

Both the United States and Australia would benefit from more conservation of private land, and conservation servitudes can help both countries achieve this. However, in the United States and Australia, the power of eminent domain is a threat to the perpetuity of conservation servitudes. The prior public use doctrine, a common law doctrine in the United States arising out of the public trust doctrine, could limit eminent domain in these cases and provide protection to conservation servitudes. This doctrine states that land devoted to one public use (such as conservation) may not be condemned for another inconsistent public use unless …

Memories Of Dr. Eric Bergsten From The 2004 International Program, Christopher Boies

Pace International Law Review

No abstract provided.

A Crappy Job: Understanding Septic System Engagement In Rural Great Lakes Communities, Amanda Buday

Journal of Contemporary Water Research and Education

This study analyzes survey data from three eastern Lake Michigan watersheds to understand how rural homeowners engage in onsite wastewater treatment system (OWTS) maintenance. Responses about awareness and use of best management practices (BMPs), knowledge of system age, and barriers to recommended maintenance were used to develop a behavioral typology of homeowner engagement, with profiles ranging from proactive maintenance to passive noncompliance. This typology was then used to examine how management styles vary across geographic context, sociodemographic factors, and support for policy tools to promote proactive system care. While many homeowners report following recommended OWTS practices – even when facing …

Formulation And Characterisation Of Isoniazid By Spray Drying For Use By Dry Powder Inhalers To Treat Tuberculosis, Damiana Gabrielli, Seán Roche

SURE Journal: Science Undergraduate Research Experience Journal

The targeted delivery of antibiotics by dry powder inhalers (DPIs) is an increasingly important area of research, driven by the growing global burden of respiratory infections and the advantages of localized drug delivery to the lungs. Over the past five years, respiratory infections have risen significantly, with recent epidemiological data indicating a global increase in incidence by over 30%, largely due to factors such as air pollution, antimicrobial resistance, and emerging respiratory pathogens. One major challenge in developing DPI formulations for antibiotics is the need to optimize the particle physicochemical properties for deep lung deposition while accommodating the high doses …

Suitability Of Mobile Phase Recycling For Methylxanthine Quantification In Coffee Samples Using Hplc, Kaitlin O’Keeffe, Marcos Mariano, Brian Murphy

SURE Journal: Science Undergraduate Research Experience Journal

Caffeine, theobromine and theophylline fall under a drug class known as methylxanthines. These three compounds are of major interest in the food industry due to their presence in popular foods and beverages such as tea, coffee, and chocolate. As these compounds can cause physical and mental stress at high dosages, their quantification is essential to ensure product safety and quality. Here, we describe an eco-friendly HPLC method developed to quantify the amount of these analytes in coffee samples sourced across the SETU Waterford, Cork Road campus. Using an isocratic mixture of water and methanol, a mobile phase recycling approach was …

An Analysis Of Fodmap Intake And Common Dietary Sources In The Irish Population, Sophie Ree, Farzana H. Ieha, Breige Mcnulty, Janette Walton, Suzanne L. Doyle

SURE Journal: Science Undergraduate Research Experience Journal

Background/Objectives: Fermentable Oligosaccharides Disaccharides Monosaccharides and Polyols (FODMAPs) are a group of short chain carbohydrates that are poorly absorbed in the small intestine and can lead to gastrointestinal discomfort in sensitive individuals, particularly in those with irritable bowel syndrome (IBS). First-line treatment of IBS is a low FODMAP diet. However, little is known regarding FODMAP intake and the commonly consumed high FODMAP foods in the Irish population. This study aimed to investigate the FODMAP content of foods commonly consumed in the Irish diet.

Subjects/Methods: This study conducted a retrospective analysis of the 2011 National Adult Nutrition Survey (n=1500 adults, 4-day …

Concentration-Dependent Effects Of Green Tea Extract On The Growth And Metabolism Of Lacticaseibacillus Rhamnosus: An In Vitro Analysis, Jingxian Zeng, Francesco Noci, Kishor Keekan, Ulrich Hoeche

SURE Journal: Science Undergraduate Research Experience Journal

Green tea extract (GTE) is widely recognised for its bioactive compounds, which exhibit potential health benefits, including modulation of gut microbiota. However, the concentration-dependent effects of GTE on specific probiotic strains remain underexplored. The aim of this study was to systematically evaluate the concentration-dependent effects of green tea extract (GTE) on Lacticaseibacillus rhamnosus (L. rhamnosus). The promoting and inhibiting effects of GTE in the range of 0–50 mg/mL were analysed in vitro by OD₆₀₀ growth curve, pH change and colony forming unit (CFU) count. The experimental results showed that the concentration range of 0.05–2.05 mg/mL in the low concentration group …

The Influence Of Perceived Social Support On Mental Health During Injury In Female Gaa Athletes., Clodagh M. O’Connor, Samantha Glynn Kelly

SURE Journal: Science Undergraduate Research Experience Journal

Injury recovery in sport involves not only physical rehabilitation but also significant psychological challenges, particularly for female athletes in amateur and elite environments. This study aimed to explore the perceived social support received by injured female Gaelic Athletic Association (GAA) athletes and the effect it had on their mental health during injury. A qualitative research design was employed to gain an in-depth understanding of the experiences of injured female athletes. Data were collected through semi-structured, one-on-one interviews, allowing for open-ended responses and the exploration of individual perspectives. The sample consisted of 10 female athletes aged between 18 and 32 years, …

Advancing Skin Cancer Diagnostics: A Comparative Analysis Of Convolutional Neural Network Models For Skin Lesion Classification, Jesse Osuji, Tania Malik

SURE Journal: Science Undergraduate Research Experience Journal

For many years, skin cancer diagnosis and cancer research have been major focal points in the healthcare sector. Accurate classification of different types of skin lesions, including cancerous ones, is essential for proper diagnostics. Many machine learning (ML) techniques and models are used to solve various problems across various domains. One of such techniques is called neural networks. Convolutional Neural Networks (CNNs) are primarily used in computer vision-based problems, allowing computer systems to process and understand images. CNNs offer a potential tool for diagnosing skin lesions from images, occasionally demonstrating superior accuracy compared to trained dermatologists. This project explores various …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Innocent Until Proven Guilty, Disenfranchised All The Same: Hidden Voter Suppression Within American Jails, Kennedy Hill

Arkansas Law Review

Jails throughout the United States hold thousands of legally eligible voters who have not been convicted of a crime While those convicted of felonies are often statutorily disenfranchised, pretrial detainees retain their civil rights—including the right to vote. In theory, this should guarantee them a voice. In practice, pretrial detention operates like a legal disqualification. Without meaningful enforcement mechanisms, the right to vote becomes hollow.

This Comment argues that implementing a national standard based on the proactive policies of Massachusetts and Nevada will ensure accessible voting for pretrial detainees. To build that argument, this Comment first explores the low level …

Workplace Retaliation And The Intersection Of Protected Conduct And Job Performance, Chris M. Schmidt

Arkansas Law Review

A host of statutory schemes seek to ensure equal employment opportunities in the United States by eradicating workplace discrimination (“EEO laws”). Consider two foundational pillars necessary for these EEO laws to strike the desired balance between individual rights and workplace efficiency. First, employees require robust protection from retaliation if they engage in protected conduct—for example, by reporting perceived discrimination. Second, employers can—and ideally, should—make employment decisions based on how an employee performs the job.

The interests in robust protection and performance-based decision-making serve the purposes of our EEO laws and are well-established. Rarely do they conflict (to the contrary, they …

Conservatorship: An Enabler Of Involuntary Servitude, Jesse Long

Arkansas Law Review

What happens when the conflict of interest relates to the conservatee’s substantial talents and their potential earnings? In this circumstance, a conservator has a perverse incentive to profit off of and coerce their conservatee into labor which serves to benefit the conservator—a kind of involuntary servitude that would seem to implicate the plain text of the Thirteenth Amendment of the United States Constitution.

This Note proceeds in three parts. Part I describes the history of conservatorships, why they were created, and the problematic issues that have arisen from the conservatorship system. Part II analyzes how the lack of meaningful judicial …