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A Computational Framework for Investigating Novel Bacterial Conjugation Inhibitors
Get PDFAntimicrobial resistance (AMR) is a major global threat, contributing to an estimated 700,000 deaths annually. One of the main ways that AMR genes spread among bacteria is through conjugation. Therefore, it is crucial to develop conjugation inhibitors (COINs) to combat AMR. Shared characteristics between known COIN molecules are a hydrophobic tail, unsaturations, and a polar head. Considering these characteristics and accounting for the efficacy of 2-hexadecynoic acid and Tanzawaic Acids (TZAs) low toxicity, we designed a new set of TZA analogs. The predicted protein target of previously identified COINs is TrwD, an ATPase in the type IV secretion system (T4SS). This multi-protein complex plays a crucial role in bacterial conjugation. In this work, we set up a computational pipeline to screen our TZA analogs. This pipeline involves predicting the structure of the experimentally uncharacterized protein TrwD structure using homology-based protein structure prediction via Protein Homology/analogy Recognition Engine V 2.0 (Phyre2), and identifying binding pockets and potential binding poses are identified using a combined SwissDock and MELD (Modeling Employing Limited Data) accelerated molecular dynamics (MD) simulations (MELDxMD) approach. Preliminary results with ATP, the natural ligand for TrwD (the predicted target of COINs), demonstrate the effectiveness of our pipeline. SwissDock identified over 30 potential binding poses, which were grouped into five distinct clusters. The system was then optimized in AMBER under unbiased conditions to further refine the ligand binding predictions. These results validate the pipeline’s capacity to predict and refine binding poses. However, integrating the system into MELDxMD has proven challenging due to the use of a ligand and the GAFF force field. Despite efforts, difficulties arose in refining the binding poses and conducting detailed competitive simulations. Additional work is needed to fully integrate the system into MELDxMD, refine the binding poses, and evaluate the relative binding affinities of the novel COIN molecules. This study provides a robust framework for assessing COIN binding affinities and identifying promising candidates for synthesis and biological evaluation. Ultimately, this pipeline may aid in the development of novel therapeutics to combat AMR by inhibiting bacterial conjugation and curbing the spread of resistance genes
Transforming through Art: Trauma & Domestic Violence
Get PDFIn this thesis, I explored bodily transformation and resilience after trauma through the lens of personal experience with domestic violence. I created sculptural installations using my imagery of bruises, scars, and injuries to convey the ideas of reclamation, healing, and empowerment. The ephemeral quality of natural dyes reflects the impermanence of bruises mirroring the organic journey of recovery. I approach my work from a personal perspective. The sculptural forms serve as fragmented representations of traumatic memory. My artistic practice is deeply tied to materiality and process—choosing natural dyes, textiles referencing care and domestic spaces, sculptural forms derived from personal documentation, entomology pins, and suspended forms allowing for subtle movement. These choices create a space for reflection, inviting viewers to find personal resonance. My work offers an opportunity for my audience to reflect on one’s own ability to transform mentally and physically. Stemming from some of the darkest moments in life, the resultant pain and trauma can form into a renewed sense of beauty and strength. My artistic practice contributes to a larger dialogue about domestic violence, trauma-informed artmaking, and the role of materiality in the mending of one’s self. Ultimately, this work is an act of defiance, a refusal to be consumed by past wounds, and a declaration of the human spirit’s ability to transform
Fantasy Exchange
Get PDFFantasy Exchange is a visual and written examination of the perpetuation of violence against women and the influence it has on the performance of femininity within structural patriarchy. After briefly working with the Rochester Police Department in Rochester, New York, I found myself incredibly struck by the everyday violence that I was made to watch people endure. During my time there, I made note of everything I witnessed and noticed the way that women\u27s pain always seemed to have such a profound impact on me. Through image and text, this body of work explores visual metaphors of abuse found in everyday life using self-portraiture and performance. Through the process of building this body of work, I examine my own tendency to alter my performance of femininity in order to keep my own self-fantasy alive. Among these images are photographs of a woman discovering herself in a new landscape free from the hyper-sexualization of the feminine nude in which one can explore their body without the constraint of performance for the male gaze
Lovejoy: Imagination and Community
Get PDFLovejoy is a photographic portrait of memory, imagination and the future of a neighborhood in Buffalo, New York. For nearly a century, my great-grandparents, grandfather, uncles and cousins lived in the house on Goethe Street in Lovejoy. It was once a vibrant working-class community of immigrants from a few towns in Central and Southern Italy. In 2020, I moved back to Buffalo, regularly visiting my elderly relative who still lived there. She died later that same year. Photography, which has long been a form of self-expression for me, was the medium I had at hand when we started to clean out the house. Taking pictures in our family home before it sold was the start of a project that is both autobiographical and about the people in Lovejoy today. Even as the old stores were replaced with boarded up storefronts and the neighborhood gave way to post-industrial urban decay, a group of previous residents and their children stayed connected through a local social club and the church. Many travel to Lovejoy to play bocce and keep alive the community that in the past filled the streets. Taking pictures of these gatherings has made me realize that they are seeking to reconnect with their history, just as I am. I use the tools of documentary to create a subjective and personal project. My photographs are the result of my wandering through the neighborhood, arranging to meet people through my contacts in the community, and engaging in a form of participant observation. As I photograph the ne
An Ultra-Low-Power, Area-Efficient All-Analog Trojan with Temporal Power Supply Triggering
No full textWith the rapid expansion of the Internet of Things and rising concerns over intellectual property protection, hardware security has become increasingly vital—particularly in defending against hardware trojans. While much of the existing research targets digital trojans, analog hardware trojans remain largely unexplored, presenting unique opportunities for developing innovative attack vectors and mitigation strategies. This thesis introduces a novel all-analog temporal trojan that functions entirely within the analog domain. The design incorporates power supply noise detection and charge-accumulator techniques to enable precise control over attack execution and payload delivery. It also leverages novel circuit techniques to reduce power and area overhead, enhance concealment, and increase resilience to process variations and accidental triggering. The system is implemented in a 55 nm CMOS process and validated through simulation, physical layout, and silicon fabrication, with post-silicon testing and mitigation studies planned. The functionality of the Trojan is demonstrated within an analog front-end for ECG-based biometric authentication, showcasing its potential to corrupt analog data streams while evading standard detection methods. The goal of the trojan is two-fold: to demonstrate the wide-reaching and disruptive potential of analog trojans, and to motivate the development of robust defenses against such stealthy and persistent threats
Personalized Nutrition Recommendations for Arab Communities: Transforming Diet and Health through Machine Learning
Get PDFA lack of cultural understanding in traditional nutrition approaches prevents proper adherence to healthy dietary patterns among individuals. The Arab population faces unique challenges due to cultural dietary customs and lifestyle changes that have made obesity and diet illnesses major global public health challenges. The rapid shift to high-calorie but undernourished foods and less physical activity has resulted in alarming rate increases of obesity, cardiovascular diseases, and type 2 diabetes. The lack of cultural understanding in traditional nutrition approaches prevents proper adherence to healthy dietary patterns among individuals. This study focuses to fills the existing gap by applying Artificial Intelligence (AI) and Machine Learning (ML) methods to establish personal dietary recommendations for Arab populations. This research uses advanced AI methodologies to evaluate dietary behaviors while combining cultural food tastes and health status information into personalized dietary recommendations. The dietary recommendation process utilizes four machine learning models comprising SVM and Logistic Regression together with Random Forest and Gradient Boosting. The system creates customized dietary plans by evaluating several aspects including BMI values and health issues and dietary limitations together with caloric consumption information and cultural food choices. Furthermore, the research shows that Artificial Intelligence (AI) implements dietary interventions better than traditional approaches because it produces targeted recommendations which reflect individual culture. The evaluation of the model’s performance measured its accuracy together with precision and recall which yielded encouraging outcomes towards promoting healthier eating habits. To provide fair and ethical recommendations, the implementation requires solutions for data biases, solutions for restricted access to regional dietary data, and transparent algorithms. The study advances AI-driven personalized nutrition research through its framework that integrates AI techniques into culturally appropriate dietary interventions. Future research needs to work on extending data sources while integrating immediate feedback from users alongside advanced AI model development to improve forecasting precision. The implementation of AI-driven dietary systems has the potential to transform public health policies and improve nutritional outcomes for diverse populations
The Role of Digitalization Technologies in Enhancing Supply Chain Performance in the Service Industry: A Framework for Decision-Makers
No full textDigitalization technologies are proving to be effective in many different situations across the service industry. Technologies such as AI, blockchain, big data, IoT, IoE, 6G, digital twin, and cobots are showing positive effects when implemented in different types of companies. This research highlights the important role of digitalization technologies in enhancing supply chain performance within the service industry. Despite their adoption across sectors, limited research examines their specific impact on service supply chains. A comprehensive search of 3 academic databases identified 429 peer-reviewed studies published since 2019. PRISMA was implemented, resulting in a final dataset of 66 studies. A survey consulting 34 experts in the field on the effects of digitalization on supply chain performance within the service industry was conducted, as well as a case study on an online retail company. The findings reveal a positive correlation between digital technologies and supply chain performance. Despite significant progress in digital technologies, a unified and accessible framework to systematically integrate all eight technologies with the service supply chains remains absent. To address this gap, the author developed a generic framework applicable to both Product Service Supply Chains (PSSCs) and Service Only Supply Chains (SOSCs). This provides actionable guidance to decision-makers, helping them identify strategic implementation points for digitalization technologies to enhance supply chain performance. Key performance metrics including order entry method, lead time, total cost, and customer relationship are explicitly mapped to technology applications, enabling organizations to prioritize investments based on measurable outcomes. The framework’s validity and practicality were rigorously tested through a multi-stage Delphi method involving industry experts, ensuring alignment with real-world operational challenges and technological capabilities. Additionally, a case study in the e-commerce sector demonstrated its applicability, revealing significant improvements in operational efficiency and customer satisfaction metrics following technology implementation. Both validation methods confirmed a strong positive relationship between digitalization and enhanced supply chain performance in service-driven environments. These findings underscore the framework’s potential to service as a strategic tool for organizations pursuing digital transformation in complex service environments
Improving the Accessibility of Speech for Deaf and Hard-of-Hearing Individuals Through Affective Captions
No full textCaptions have traditionally served as a bridge between the spoken word and its written representation, helping make speech accessible to Deaf and Hard-of-Hearing (DHH) individuals. It is worth considering, however, how much from speech is left out by this ’bridging’ between sound and visuals. This dissertation describes a research project that has, over six studies, looked at this very issue. We first examined whether there is an issue here at all. What does the experience of DHH individuals with captioning systems tell us about these systems’ shortcomings? For one, we found, captions are felt as monotonous and ambiguous. While communication is multimodal, and DHH individuals also use non-speech cues such as facial expressions or body language to disambiguate a speaker’s intended meanings, these channels are imperfect. Relying on conventional captioning systems is, at their worst, an alienating experience – a lot is lost in these audiovisual translations of speech, and what is lost matters. Study 2 looked into interventions to captioning systems that could close the gap between spoken words and text. Through various prototypes, it aimed at understanding what dimensions from speech would make captions most helpful: prosody, emotions, or a combination of both. Emotions, we found, were the best compromise between utility and legibility. Study 3 explored the design space of these ’affective’ captions. What typographic parameters can best be modulated to depict an emotion’s valence and arousal levels? The investigation looked both at subjective preferences and objective measures. We found that valence should be depicted through color. For arousal, either font-size or font-weight should be used, with the former preferred for videos with looser legibility requirements. Studies 4–6 constitute the final phase of this work, looking over how haptics can be shaped to convey a speaker’s arousal, and what are the consequences of doing so. Study 4 experimentally selected a wrist-worn vibrotactile mapping for arousal, identifying a single short pulse at 75 Hz (amplitude scaled to arousal) as the best compromise between comfort and discriminability. Study 5 then compared five captioning conditions on longer clips and found that a combined approach – valence via color plus arousal via both font-weight and haptics – significantly increased Narrative Engagement for DHH viewers over both a neutral baseline and a visuals-only affective style. Finally, Study 6 measured arousal-decoding accuracy on short clips and showed that adding haptic cues reliably reduced absolute error in perceived arousal, whereas visual weight did not yield a main effect. Together, these studies indicate that multimodal affective captions can be both more engaging and more informative than conventional captions. Taken as a whole, this dissertation demonstrates an approach for taking captions beyond verbatim transcription, incorporating affective dimensions of speech. Across six studies, we showed that affective captions are not only technically feasible but also valued by DHH viewers: they can increase engagement, clarify emotional nuance, and support decoding of subtle aspects of speech. By combining visual typography with haptic signals, we offer both conceptual and methodological advances toward more expressive and inclusive captioning systems. Beyond the specific designs and findings, the broader contribution is to reframe captioning as a fertile, multimodal design space capable of accommodating diverse communication needs
Assessing, selling and onboarding Transformative Agreements at an R2 Institution
No full textTransformative agreements can help libraries expand content offerings and subsidize publishing costs. RIT Libraries, new to these agreements, has joined 4 over the past year in a process driven by Electronic Resources and Acquisitions/Serials. We will walk the audience through the assessment criteria for the two of the agreements we joined (Cambridge and Springer), along with lessons learned. The assessment criteria include: cost, impact on access to content, a scan of publishing activities on campus, as well as turnaway data obtained from vendors and a new implementation of Celus 5 for Counter 5 data.
We will share the language used to obtain buy-in from campus stakeholders, as well as steps we took to advertise our new agreements with the RIT community. We will also share the cross-departmental lessons learned. We discovered that Transformative Agreements overall were new to many RIT Libraries staff. We offer recommendations on how to educate other departments about the nature of these agreements and how to work with reference librarians, liaisons to departments, and bibliographers who will be impacted. Though Transformative Agreements offer opportunities there are also many challenges to bringing them on-board for the first time