Digital Commons Network^™

Blue Carbon Science, Management And Policy Across A Tropical Urban Landscape, Daniel A. Friess, Yasmine M. Gatt, Tze Kwan Fung, Jahson B. Alemu I, Natasha Bhatia, Rebecca Case, Siew Chin Chua, Danwei Huang, Valerie Kwan, Kiah Eng Lim, Yudhishthra Nathan, Yan Xiang Ow, Daniel Saavedra-Hortua, Taylor M. Sloey, Erik S. Yando, Hassan Ibrahim, Lian Pin Koh, Jun Yu Puah, Serena Lay-Ming Teo, Karenne Tun, Lynn Wei Wong, Siti Maryam Yaakub

Biological Sciences Faculty Publications

The ability of vegetated coastal ecosystems to sequester high rates of “blue” carbon over millennial time scales has attracted the interest of national and international policy makers as a tool for climate change mitigation. Whereas focus on blue carbon conservation has been mostly on threatened rural seascapes, there is scope to consider blue carbon dynamics along highly fragmented and developed urban coastlines. The tropical city state of Singapore is used as a case study of urban blue carbon knowledge generation, how blue carbon changes over time with urban development, and how such knowledge can be integrated into urban planning alongside …

Estimating The Distribution Of Oryzomys Palustris, A Potential Key Host In Expanding Rickettsial Tick-Borne Disease Risk, Catherine A. Lippi, Samuel Canfield, Christina Espada, Holly D. Gaff, Sadie J. Ryan

Biological Sciences Faculty Publications

Increasingly, geographic approaches to assessing the risk of tick-borne diseases are being used to inform public health decision-making and surveillance efforts. The distributions of key tick species of medical importance are often modeled as a function of environmental factors, using niche modeling approaches to capture habitat suitability. However, this is often disconnected from the potential distribution of key host species, which may play an important role in the actual transmission cycle and risk potential in expanding tick-borne disease risk. Using species distribution modeling, we explore the potential geographic range of Oryzomys palustris, the marsh rice rat, which has been …

The Coral Bleaching Automated Stress System (Cbass): A Low-Cost, Portable System For Standardized Empirical Assessments Of Coral Thermal Limits, Nicholas R. Evensen, Katherine E. Parker, Thomas A. Oliver, Stephen R. Palumbi, Cheryl A. Logan, James S. Ryan, Courtney N. Klepac, Gabriela Perna, Mark E. Warner, Christian R. Voolstra, Daniel J. Barshis

Biological Sciences Faculty Publications

Ocean warming is increasingly affecting marine ecosystems across the globe. Reef-building corals are particularly affected by warming, with mass bleaching events increasing in frequency and leading to widespread coral mortality. Yet, some corals can resist or recover from bleaching better than others. Such variability in thermal resilience could be critical to reef persistence; however, the scientific community lacks standardized diagnostic approaches to rapidly and comparatively assess coral thermal vulnerability prior to bleaching events. We present the Coral Bleaching Automated Stress System (CBASS) as a low-cost, open-source, field-portable experimental system for rapid empirical assessment of coral thermal thresholds using standardized temperature …

Variation In Establishment Success For American Mistletoe [Phoradendron Leucarpum (Raf.) Reveal & M.C. Johnst. (Viscaceae)] Appears Most Likely To Predict Its Distribution In Virginia And North Carolina, United States, Nicholas P. Flanders, Christopher P. Randle, Eric L. Walters, Lytton J. Musselman

Biological Sciences Faculty Publications

Dispersal limitation and variation in habitat suitability may determine an association of American mistletoe [Phoradendron leucarpum (Raf.) Reveal & M.C. Johnst. (Viscaceae)] with forested wetlands in Virginia and North Carolina, United States. Here, we first tested the alternative hypothesis that variation in host availability drives this habitat relationship. We used a generalized linear model to show a positive effect of forested wetland habitat on American mistletoe occurrence after accounting for both variation in host availability and differences among regions in host use. We then used seed sowing experiments to quantify how light availability and flood regime determine the viability …

Adjusting For Gene-Specific Covariates To Improve Rna-Seq Analysis, Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton

Mathematics & Statistics Faculty Publications

Summary

This paper suggests a novel positive false discovery rate (pFDR) controlling method for testing gene-specific hypotheses using a gene-specific covariate variable, such as gene length. We suppose the null probability depends on the covariate variable. In this context, we propose a rejection rule that accounts for heterogeneity among tests by employing two distinct types of null probabilities. We establish a pFDR estimator for a given rejection rule by following Storey's q-value framework. A condition on a type 1 error posterior probability is provided that equivalently characterizes our rejection rule. We also present a suitable procedure for selecting a tuning …

Preservice Secondary Science Teachers' Reflections In Using Modeling & Simulation Applications As Instructional Tools For Learning, Mary C. Enderson, Elizabeth Langran (Ed.), Paula Christensen (Ed.), Jarrod Sanson (Ed.)

Teaching & Learning Faculty Publications

Preparing preservice teachers to construct learning environments integrating technological tools is a challenge that higher education continues to tackle. One way to address this challenge is to have preservice teachers integrate modeling & simulation (M&S) tools while teaching, reflect on the experience, and attempt to identify ways to make improvements in instructional practices. This case study of five preservice secondary science teachers, enrolled in a course along with student teaching, was designed to study M&S tools integrated into instruction and how preservice teachers thought about the experience. Participants taught at least one lesson integrating M&S tools where they were to …

Enhancing The Conformational Stability Of The Cl-Par-4 Tumor Suppressor Via Site-Directed Mutagenesis, Samjhana Pandey, Krishna K. Raut, Antoine Baudin, Lamya Djemri, David S. Libich, Komala Ponniah, Steven M. Pascal

Chemistry & Biochemistry Faculty Publications

Intrinsically disordered proteins play important roles in cell signaling, and dysregulation of these proteins is associated with several diseases. Prostate apoptosis response-4 (Par-4), an approximately 40 kilodalton proapoptotic tumor suppressor, is a predominantly intrinsically disordered protein whose downregulation has been observed in various cancers. The caspase-cleaved fragment of Par-4 (cl-Par-4) is active and plays a role in tumor suppression by inhibiting cell survival pathways. Here, we employed site-directed mutagenesis to create a cl-Par-4 point mutant (D313K). The expressed and purified D313K protein was characterized using biophysical techniques, and the results were compared to that of the wild-type (WT). We have …

Utilizing Markov Chains To Estimate Allele Progression Through Generations, Ronit Gandhi

Honors Program: Senior Projects (Public)

All populations display patterns in allele frequencies over time. Some alleles cease to exist, while some grow to become the norm. These frequencies can shift or stay constant based on the conditions the population lives in. If in Hardy-Weinberg equilibrium, the allele frequencies stay constant. Most populations, however, have bias from environmental factors, sexual preferences, other organisms, etc. We propose a stochastic Markov chain model to study allele progression across generations. In such a model, the allele frequencies in the next generation depend only on the frequencies in the current one.

We use this model to track a recessive allele …

Monoclonal Antibodies Against Methyl Glucuronoxylan Epitopes For Understanding Xylan Structure And Modification, Utku Avci

Turkish Journal of Botany

Lignocellulosic biomass is an abundant and renewable source that could be utilized for production of many bioproducts. It mainly consists of cellulose, hemicellulose, and lignin, all of which come together to form a recalcitrant wall that impedes production of bioproducts. In order to overcome the recalcitrant nature of the biomass, it is important to fully understand how cell wall components are synthesized and assembled. Xylan is one of the hemicellulosic components of the wall that contributes to recalcitrance. Xylan has substitutions on the backbone that are formed by the orchestration of many enzymes. For example, glucuronoxylan methyltransferases are responsible for …

Phytochemical Investigation Of Alkaloid Fractions Of Fumaria Vaillantii And F. Asepala And Their Antifungal Influence On Gene Expression Pattern In Aspergillus Species, Monir Mohseni, Azra Ataie Azimi, Babak Delnavaz Hashemloian, Mozhgan Farzamisepehr

Turkish Journal of Botany

The genus Fumaria is known for its strong medicinal effects. This research aimed to assess the phytochemical profile in various alkaloid fractions from Fumaria vaillantii Loisel and Fumaria asepala Boiss. grown in the Saveh region of the central province of Iran and their antifungal activity against Aspergillus flavus and Aspergillus niger was investigated in laboratory conditions. Also, the types and amount of alkaloid compounds and the effect of compounds on the expression of key genes of aflatoxin biosynthesis were conducted in order to investigate the ability of alkaloids of two Fumaria species to prepare environmentally friendly disinfectants. The total alkaloid …

Dr Mahesh Nagarajan

Honorary Graduates 榮譽博士

No abstract provided.

Developing Mesoporous Silica Nanoparticle-Based Stimuli-Responsive Nanocarriers For Delivery Of Small Molecule Therapeutics Against Colon Cancer Cells, Nisitha Lakmal Wellala Wijewantha

Dissertations and Theses

This dissertation delves into the innovative application of mesoporous silica nanoparticles (MSNs) for targeted drug delivery in colorectal cancer (CRC), one of the most prevalent and deadly forms of cancer worldwide. The initial focus of the research is on developing enzyme-responsive MSNs loaded with veratridine (VTD), an alkaloid derived from natural sources that demonstrates potent anticancer activity. The nanoparticles have been engineered to deliver VTD selectively to CRC cells, releasing the payload upon being exposed to specific enzymes primarily secreted by these cells. This strategy has dual advantages of amplifying the anticancer effects while minimizing potential side effects on healthy …

Of Transcription Factor And Transformation: Elucidating Gene Function In The Common Ice Plant, Mesembryanthemum Crystallinum, Chinenye Lilian Izuegbunam

Dissertations and Theses

Abiotic stresses negatively affect plant growth and development across the globe, which also affect the production of food, feed, biofuel, and fiber to meet the demands of a growing population. Thus, developing novel strategies to increase abiotic stress tolerance in crops is necessary. One of these strategies is exploring transcription factors (TFs) in Crassulacean Acid Metabolism (CAM) plants to improve plant abiotic stress tolerances. Therefore, the first objective of this dissertation determine the abiotic stress tolerance function of a CAM TF, McHB7opt in Arabidopsis. This study found that McHB7opt increased stress-responsive pathways related to seed germination and early seedling development. …

Analyzing Pulmonary Abnormality With Superpixel Based Graph Neural Networks In Chest X-Ray, Ronaj Pradhan

Dissertations and Theses

In recent years, the utilization of graph-based deep learning has gained prominence, yet its potential in the realm of medical diagnosis remains relatively unexplored. Convolutional Neural Network (CNN) has achieved state-of-the-art performance in areas such as computer vision, particularly for grid-like data such as images. However, they require a huge dataset to achieve top level of performance and challenge arises when learning from the inherent irregular/unordered nature of physiological data. In this thesis, the research primarily focuses on abnormality screening: classification of Chest X-Ray (CXR) as Tuberculosis positive or negative, using Graph Neural Networks (GNN) that uses Region Adjacency Graphs …

Designing Metal-Organic Supercontainers For Functional Applications: From Selective Anion Binding To Surface Enhanced Raman Scattering, Kriti Chitrakar

Dissertations and Theses

Synthetic container molecules that emulate biological structures and feature well-defined nanocavities have attracted tremendous interest among supramolecular chemists due to their promising potentials in ion recognition, catalysis, and chemical sensing. Our laboratory has developed a new class of container molecules, namely, metal-organic supercontainers (MOSCs), which feature both endo and exo cavities suitable for binding guest molecules. The overarching theme of this thesis was to use synthetic manipulations to modify the chemical structure and enhance the functional application of MOSCs in two specific areas, anion binding and chemical sensing. For the application of anion binding, we have designed and synthesized a …

Non-Pharmaceutical Symptom Management In Patients With Pcos, Allison Stern

Capstone Showcase

Polycystic Ovarian Syndrome (PCOS) is a relatively common diagnosis among biological females. There are many variations of presentations among patients with PCOS that require an individualized and tailored treatment plan for symptom management. Although there are pharmaceutical medications that can be used for PCOS symptoms, some patients’ symptoms might not be fully managed, or they might prefer to focus on non-pharmaceutical options for their symptoms instead. Therefore, it is important for clinicians to be familiar with alternatives to the mainstay of pharmaceutical treatment.

Inpatient Management Of An Intravenous Drug User With Tetanus, Nina Paris

Capstone Showcase

Tetanus is rare in the United States now due to the tetanus vaccine but there is still the potential too see patients with tetanus. IV drug users, neonates, and geriatric populations are at an increased risk of developing tetanus. Tetanus is caused by Clostridium tetani, a spore forming and exotoxin releasing anaerobic bacteria. The symptoms of tetanus are caused by the exotoxin tetanospasmin which inhibits the release of inhibitory neurotransmitters, leading to sustained neuronal stimulation. The classic symptoms of tetanus are lockjaw (trismus), neck stiffness, back arching, and fever. Patients can be febrile, tachycardic, tachypneic, and hypertensive on exam. …

Phasic And Repetitive Self-Touch Differ In Hemodynamic Response In The Prefrontal Cortex–An Fnirs Study, Sabrina Von Au, Ingo Helmich, Simon Kieffer, Hedda Lausberg

Exercise and Sport Studies: Faculty Publications

Introduction: Each individual touches the own body several 100 times a day. While some researchers propose a self-regulatory function of self-touch, others report that self-touching increases nervousness. This controversy appears to be caused by the fact that researchers did not define the kind of self-touch they examined and actually, referred to different types of self-touch. Thus, kinematically defining different types of self-touch, such as phasic (discrete), repetitive, and irregular, and exploring the neural correlates of the different types will provide insight into the neuropsychological function of self-touching behavior. Methods: To this aim, we assessed hemodynamic responses in prefrontal brain areas …

Managing Neonatal Pain: A Guideline For Non-Neonatal Providers, Kelly Stanton

Capstone Showcase

Neonatal pain, especially in settings outside of the NICU or newborn nursery, is often under-recognized or even unnoticed altogether. Many providers and parents do not know how to recognize when a neonate is in pain and many do not know how to minimize or alleviate this pain effectively. Even when providers know how to assess pain in neonates, they typically assess for acute pain in the presence of chronic pain, or vice-versa. Untreated pain in neonates harms brain development and can lead to behavior defects later in life for these babies. Due to these outcomes, the recognition and effective treatment …

Hopeful Oscillation: Metamodernism, Barbenheimer, And Our New Cultural Undercurrent, Jewel T. Miller

Capstone Showcase

Recent societal changes have pushed artwork and media away from postmodernism as a dominant cultural philosophy. In its place has risen a new theoretical approach, titled Metamodernism, which attempts to discover the meaning behind present day art and media’s strengthening affective qualities, and provide a possible label for this new post-postmodernist state. This is not only an important attempt at understanding the society we live in today but also its broader impact on how we communicate through media. This paper explores the rise of Metamodernism as a theoretical approach within media studies and philosophy, including the term’s inception and growing …

Comparison Of Various Intermittent Fasting Dietary Interventions To The Ketogenic Dietary Interventions And Its Effects In Mitigating Hunger In Obese Adults, Aston Earl Francis Jr

Theses and Dissertations

There have been many dietary strategies that can be used for fat loss and the most recent popular dietary interventions have been intermittent fasting and the ketogenic diet. Intermittent fasting (IF) dietary interventions and the ketogenic diet (KD) are popular diets that claim to promote weight loss which has also been speculated to have enhanced benefits than caloric restriction. Although these dietary strategies are growing in popularity, it is unclear if the intervention can manage hunger, which may increase adherence. The purpose of this paper is to systematically review the literature on the impact of IF protocols compared to KD …

Csi Botany: Dna Barcode “Fingerprints” Identify Cryptic Urban Flora, Luis R. Vega

Theses and Dissertations

As short genomic markers, DNA barcodes can play a role in conservation by identifying cryptic species and hybrids when morphological approaches fall short. Here we present our application of barcodes to the identities of two wetland taxa as part of an ongoing floristic inventory of Van Cortlandt Park (VCP), Bronx, NY. Previous barcode data by Marriott et al. (2018) identified the VCP lake water lily as the exotic Nymphaea alba, rather than the native N. odorata as historically described. In addition, cattails in the park were historically identified as the native Typha latifolia and the exotic T. angustifolia …

Effects Of Duckweed On Mosquito Oviposition And Larval Survivorship, Alyssa Gushka

Capstone Showcase

Invasive species are those non-natives to habitat and that negatively impact the environment or human health problems. Invasive mosquitoes threaten the environment and humans, as they transmit 17% of infectious diseases including malaria, West Nile virus and yellow fever. Aedes japonicas and Aedes albopictus are invasive mosquitoes that often deposit eggs in artificial containers. Chemical pesticides, such as Bacillus thuringiensis israelensis (BTI), utilizes endospores to release toxins into the larvae. However, BTI creates negative consequences for the environment and other species. Many plants are being examined to see if they can act as natural pesticides. Duckweeds are native to North …

The Positive Effects Of Medical Cannabinoids On The Dysregulated Endocannabinoid System In Autism Spectrum Disorder Patients, Caroline J. Reichelderfer

Capstone Showcase

Autism Spectrum Disorder (ASD) is a developmental disability. The symptoms include a lack of social skills, a need for repetitive patterns of life, difficulty in communication, speaking deficits and numerous other symptoms. While the specific cause is unknown, there is much research being done on mechanisms including dysregulations of the immune system, endocannabinoid system, and overall brain (Nez Govorova 2021, Pol 2021). The Endocannabinoid system is a recently discovered branch of the nervous system composed of endocannabinoids which are produced naturally in the body; lipid-based neurotransmitters that bind to cannabinoid receptors (CBRs) and cannabinoid receptor proteins that are expressed throughout …

Vitamin D Enhanced Vitamin D Receptor (Vdr) Inhibition Of Nlrp3 Inflammasome Activation Can Attenuate The Development Of Autoimmune Thyroiditis, Alexzon Mandac

Capstone Showcase

Autoimmune Thyroiditis (AIT) is a prevalent autoimmune disease affecting approximately 2% of the population. Characterized by the gradual loss of thyroid function through an autoimmune attack on the thyroid gland, the disease manifests symptoms that negatively affect one’s quality of life. The mechanisms behind the disease’s pathophysiology are not fully understood; however, researchers are examining the involvement of the NLRP3 inflammasome in the disease. This thesis will address the question of whether Vitamin D can act as an inhibitor of the NLRP3 inflammasome and attenuate the progression of AIT in mouse model. Current investigations explore the effects of NLRP3 inhibition …

High Energy Blue Light Induces Oxidative Stress And Retinal Cell Apoptosis, Jessica Malinsky

Capstone Showcase

Blue light (BL) is a high energy, short wavelength spanning 400 to 500 nm. Found in technological and environmental forms, BL has been shown to induce photochemical damage of the retina by reactive oxygen species (ROS) production. Excess ROS leads to oxidative stress, which disrupts retinal mitochondrial structure and function. As mitochondria amply occupy photoreceptors, they also contribute to oxidative stress due to their selectively significant absorption of BL at 400 to 500 nm. ROS generation that induces oxidative stress subsequently promotes retinal mitochondrial apoptosis. BL filtering and preventative mechanisms have been suggested to improve or repair BL-induced retinal damage, …

What Is Active Learning? Perspectives From Five Stem Professors' Teaching Practices In Their Classrooms, Iliana Correa

Capstone Showcase

This senior thesis investigated what ways, if any, STEM professors incorporated active learning pedagogy in their undergraduate classroom in a small private university in the northeast USA. STEM pedagogy was investigated because of the increasing prominence of active learning methods in the classroom compared to the didactic type of teaching that was prominent in the past (Eichler, 2020). A qualitative case study of five STEM professors was conducted and involved collecting data from biographical questions, a one-hour interview, and the analysis of a document provided by the professor that could have been a lesson plan, an assignment, or an activity …

Elite Women In The Mediterranean 31 Bc – 1380 Ad: An Investigation Into Female Agency, Identity, And Patriarchy Across Classical And Christian Paradigms, Julia Maurer

Capstone Showcase

This paper explores the responses of elite women to patriarchal regimes across the Classical Pagan and Medieval Christian paradigms in the Mediterranean from 31 BC to 1380 AD. While the current historiography acknowledges the radical differences between the two worldviews fundamental to the core values of Western Civilization, an investigation of three women that can be taken to be emblematic examples of the periods in which they lived reveals a striking continuity in the nuanced social roles available to women. This continuity contradicts expectations of significant changes reflective of this revolutionary paradigm shift.

I utilize Julia Augusti, Vibia Perpetua, and …

Women Play Football Too: Feminist Theory And Uk Football, Mikayla Kummer

Capstone Showcase

Women's Football in the UK has constantly overshadowed by Men's Football and with the popularity of social media it may have complicated the issue. The way women have been treated in the media has always been different to how men were treated. Gender can be considered a performance and how women are treated by the press demands a performance from them. Through Offside, a play by Hollie Poetry and Sabrina Mahfouz, this essay explores the relationship between feminist theory, women's football and social media. Women athletes have consistently been asked about their personal lives, bodies, relationships and anything besides the …

A Chromosome-Scale Genome Sequence Of Sudangrass (Sorghum Sudanense) Highlights The Genome Evolution And Regulation Of Dhurrin Biosynthesis, Paul W. Bible, Jieqin Li, Wenmiao Tu, Jian Zheng, Peng Jin, Yanlong Liu, Junli Du, Jiacheng Zheng, Yi-Hong Wang, Qiuwen Zhan

Computer Science Faculty publications

Sudangrass [ Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower …