Life Sciences Commons^™

Building Patient-Facing Technology: A Redcap-Based Approach, Yun Jiang, Yang Gong

Faculty, Staff and Student Publications

This work describes the architecture design of a patient-facing technology (PFT) based on the Research Electronic Data Capture (REDCap) platform and other tools to support cancer patients in self-tracking and managing medication concerns and symptoms during transitions of care. The design is guided by the Chronic Care Model (CCM) and User-Centered Design (UCD) principles for a personalized application to inform, engage, and empower patients. We describe the evolutional details of four major versions, which represent milestones of our PFT, highlighting how specific objectives were achieved and the barriers encountered. Additionally, patient representatives were involved in the evaluation of prototypes, and …

Unraveling Complex Temporal Patterns In Ehrs Via Robust Irregular Tensor Factorization, Joyce C Ho, Xiaoqian Jiang, Sivasubramanium V Bhavani

Faculty, Staff and Student Publications

Electronic health records (EHRs) contain diverse patient data with varying visit frequencies. While irregular tensor factorization techniques such as PARAFAC2 have been used for extracting meaningful medical concepts from EHRs, existing methods fail to capture non-linear and complex temporal patterns and struggle with missing entries. In this paper, we propose REPAR, an RNN REgularized Robust PARAFAC2 method to model complex temporal dependencies and enhance robustness in the presence of missing data. Our approach employs Recurrent Neural Networks (RNNs) for temporal regularization and a low-rank constraint for robustness, enabling precise patient subgroup identification and improved clinical decision-making in noisy EHR data. …

Generalizable Self-Supervised Learning For Brain Cta In Acute Stroke, Sunil A Sheth, Luca Giancardo

Faculty, Staff and Student Publications

Acute stroke management involves rapid and accurate interpretation of CTA imaging data. However, generalizable models for multiple acute stroke tasks able to learn from unlabeled data do not exist. We propose a linear probed self-supervised contrastive learning utilizing 3D CTA images and the findings section of radiologists' reports for pretraining. Subsequently, the pretrained model was applied to four disparate tasks: large vessel occlusion (LVO) detection, acute ischemic stroke detection, acute ischemic stroke, intracerebral hemorrhage classification, and ischemic core volume prediction. The tasks chosen are particularly challenging as they cannot be directly extracted from the radiology reports findings with keywords. The …

Pain Phenotyping Indicators In Older Adults With Chronic Low Back Pain: A Secondary Analysis Of A Randomized Controlled Trial, Jennifer Kawi, Constance M Johnson, Paul J Christo, Claudia M Campbell

Faculty, Staff and Student Publications

Purpose: A multimodal approach to clinical care is often recommended for chronic low back pain (cLBP); however, treatment responses are highly variable. Phenotyping could help determine subgroups of patients, allowing for targeted and tailored interventional approaches.

Patients and methods: 263 (Mage=69.8 (7.2); 64.6% female) individuals with cLBP participated in the parent study, a 3-arm, randomized clinical trial examining auricular point acupressure treatment outcomes. Parent study participants were randomized (1:1:1) to APA ear points targeted to cLBP (T-APA, n=92), non-targeted to cLBP (NT-APA, n=91), or education control (n=89). The current study used latent class analysis to identify clustering for pain severity …

Explainable Diagnosis Prediction Through Neuro-Symbolic Integration, Jinlian Wang, Liwei Wang, Jungwei W Fan, Hongfang Liu

Faculty, Staff and Student Publications

Diagnosis prediction is a critical task in healthcare, where timely and accurate identification of medical conditions can significantly impact patient outcomes. Traditional machine learning and deep learning models have achieved notable success in this domain but often lack interpretability which is a crucial requirement in clinical settings. In this study, we explore the use of neuro-symbolic methods, specifically Logical Neural Networks (LNNs), to develop explainable models for diagnosis prediction. Essentially, we design and implement LNN-based models that integrate domain-specific knowledge through logical rules with learnable weights and thresholds. Our models, particularly Mmulti-pathway and Mcomprehensive, demonstrate superior performance over traditional models …

Reusable Generic Clinical Decision Support System Module For Immunization Recommendations In Resource-Constraint Settings, Hua Min, Yang Gong, Dean F Sittig, Paul Biondich, Adam Wright, Christian Nøhr, Timothy Law, David Robinson, Arild Faxvaag, Nina Hubig, Ronald Gimbel, Lior Rennert, Xia Jing

Faculty, Staff and Student Publications

Clinical decision support systems (CDSS) are routinely employed in clinical settings to improve quality of care, ensure patient safety, and deliver consistent medical care. However, rule-based CDSS, currently available, do not feature reusable rules. In this study, we present CDSS with reusable rules. Our solution includes a common CDSS module, electronic medical record (EMR) specific adapters, CDSS rules written in the clinical quality language (CQL) (derived from CDC immunization recommendations), and patient records in fast healthcare interoperability resources (FHIR) format. The proposed CDSS is entirely browser-based and reachable within the user's EMR interface at the client-side. This helps to avoid …

Temporal Ensemble Logic For Integrative Representation Of The Entirety Of Clinical Trials, Hongyu Chen, Pengze Li, Xing He, Shiqiang Tao, Cui Tao, Jiang Bian, Licong Cui, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Clinical trials are typically specified with protocols that define eligibility criteria, treatment regimens, follow-up schedules, and outcome assessments. Temporality is a hallmark of all clinical trials, reflected within and across trial components, with complex dependencies unfolding across multiple time points. Despite their importance, clinical trial protocols are described in free-text format, limiting their semantic precision and the ability to support automated reasoning, leverage data across studies and sites, or simulate trial execution under varying assumptions using Real-World Data. This paper introduces a formalized representation of clinical trials using Temporal Ensemble Logic (TEL). TEL incorporates metricized modal operators, such as “always …

Rank Aggregation Methods And Tools In Genomic Data Analysis

Faculty, Staff and Student Publications

Rank aggregation (RA) is the process of consolidating disparate rankings into a single unified ranking. It holds immense potential in the field of genomics. RA has applications in diverse research areas, such as gene expression analysis, meta-analysis, gene prioritization, and biomarker discovery. However, there are many challenges in the application of the RA approach to biological data, such as dealing with heterogeneous data sources, rankings of mixed quality, and evaluating the consolidated rankings. In this review, we present an overview of the existing RA methods with an emphasis on those that have been tailored to the complexities of genomics research. …

Session Introduction: Translating Big Data Imaging Genomics Findings To The Individual: Prediction Of Risks And Outcomes In Neuropsychiatric Illnesses

Faculty, Staff and Student Publications

This PSB 2025 session is focused on opportunities, challenges and solutions for translating Big Data Imaging Genomic findings toward powering decision making in personalized medicine and guiding individual clinical decisions. It combines many of the scientific directions that are of interest to PSB members including Big Data analyses, pattern recognition, machine learning and AI, electronic health records and others.

Depletion Of Adipose Stroma-Like Cancer-Associated Fibroblasts Potentiates Pancreatic Cancer Immunotherapy, Zhongming Zhao, Mikhail G Kolonin

Faculty, Staff and Student Publications

This study shows that populations of CAFs have distinct effects on pancreatic cancer progression and shows that depletion of CAFs expressing adipose markers potentiates tumor/metastasis suppression effects of immune checkpoint blockade.

Gene Expression Changes In Human Cerebral Arteries Following Hemoglobin Exposure: Implications For Vascular Responses In Sah, Devin W Mcbride, Kumar T Peeyush, Spiros L Blackburn

Faculty, Staff and Student Publications

Subarachnoid hemorrhage (SAH), characterized by the presence of hemoglobin (Hb) in the subarachnoid space, significantly impacts cerebral vessels, leading to various pathological outcomes. The toxicity of cell-free Hb released from erythrocytes and its metabolites after SAH causes vasoconstriction and neuronal damage, and correlates with delayed ischemic neurological deficits (DIND). While animal models have provided substantial and invaluable data in the research of aneurysmal SAH, the specific effects of subarachnoid blood on cerebral arteries remain greatly understudied. Here, we describe the changes in the genetic profile of human cerebral arteries exposed to free Hb for 48 h. We performed an ex …

Lower Extremity Individual Muscle Forces In Females During Loaded Hex-Bar Squat Jumps, Jadon Konkel

Theses and Dissertations

The purpose of this study was to describe the individual muscle forces and contributions to extensor force occurring during the propulsive phase of unloaded jumps in females and explore how these are influenced by increasing loads using the hex bar modality. Ten, college-aged females (height: 1.66 ± 0.09 m; weight: 68.63 ± 9.66 kg) with weightlifting experience performed hexagonal bar squat jumps at bodyweight (BW), BW+20% and BW+40% of 1RM. Traditional motion capture techniques were employed to collect dominate lower limb kinematics and kinetics. Individual muscle forces were estimated utilizing Static Optimization in OpenSim using a Gait2392 musculoskeletal model. Muscle …

A Bayesian Deep Segmentation Framework For Glioblastoma Tumor Segmentation Using Follow-Up Mris, Juan C Rodriguez Quintero, Octavio Arevalo, Kangyi Zhao, Jay-Jiguang Zhu, Roy F Riascos, Mahboubeh Madadi, Xiaoqian Jiang, Shayan Shams

Faculty, Staff and Student Publications

Background: Glioblastoma (GBM) is the most common malignant brain tumor with an abysmal prognosis. Since complete tumor cell removal is impossible due to the infiltrative nature of GBM, accurate measurement is paramount for GBM assessment. Preoperative magnetic resonance images (MRIs) are crucial for initial diagnosis and surgical planning, while follow-up MRIs are vital for evaluating treatment response. The structural changes in the brain caused by surgical and therapeutic measures create significant differences between preoperative and follow-up MRIs. In clinical research, advanced deep learning models trained on preoperative MRIs are often applied to assess follow-up scans, but their effectiveness in this …

Nutrient Transport And Transformation In Anaerobic Co-Digestion Of Crop Residues And Swine Manure, Shelby Stoner

Theses and Dissertations

Cover crops may improve soil quality, water quality, soil health, reduce soil fertilizer use, and increase nutrient availability to cash crops. The benefits of cover crops are discussed due to the below ground presence of cover crops, but the aboveground biomass can serve as a source of sustainable energy through anerobic digestion. The nutrients in the above ground biomass can also be recycled and reused through land application of digestion effluent. We have tested anaerobic co-digestion of different biomass feedstocks: cover crops, soybean stalk, and corn stover with swine manure using both small and pilot scale digesters. Nutrients, specifically NPK, …

Larval Environments Affect The Implementation Of The Sterile Insect Technique On Aedes Mosquitoes, Katherine G. Evans

Theses and Dissertations

Sterile Insect Technique (SIT) is an effective method for controlling pests and has been increasing in popularity to control Aedes mosquitoes. SIT involves inundating an area with sterilized male mosquitoes to reduce egg hatch and ultimately the number of wild adults. Previous research indicates that enacting mortality early in the larval life of Aedes mosquitoes can result in counter-productive effects, due to reduced competition among developing larvae. I hypothesize that the effectiveness of SIT at reducing adult populations is modified by densitydependent mortality and density-dependent growth among larvae. I performed two field-to-lab studies and developed an individual-based model to test …

Scrolling For Two: An Exploration Of Pregnant Women's Social Support And Information Seeking Behaviors Using Technology During The Covid-19 Pandemic, Sarah Knowlton

Theses and Dissertations

Pregnant women faced additional challenges in accessing reliable support and pregnancy- related information, leading to increased distress during the COVID-19 pandemic. Quarantine measures limited doctor’s appointments and isolated pregnant women from their families, which meant that meaningful connections and convenient information was important.

The purpose of this study is to explore the implications of COVID-19 social distancing on pregnant women, with a focus on three questions: 1) what digital technologies did pregnant women use for support and information seeking purposes during the pandemic? 2) how did pregnant women use technology to seek social support during the pandemic? 3) how did …

Examining Educational And Career Transition Points Among A Diverse, Virtual Mentoring Network, Damaris Javier, Gabrielle Saleh, Jamboor K Vishwanatha

Faculty, Staff and Student Publications

Given the differences in trajectory for under-represented minorities in biomedical careers, we sought to explore how a virtual mentoring program, the National Research Mentoring Network (NRMN), and its platform (MyNRMN), may facilitate transitions in the science, technology, engineering, mathematics, and medicine (STEMM) pipeline. The purpose of this study was to describe how the size of an MyNRMN member’s mentoring network and level of engagement correlate with academic and career transitions. We examined MyNRMN platform user data from March 2020 to May 2021 (n = 2993). Logistic regression estimated the odds of a career or academic transition related to NRMN …

Intelligent Biology And Medicine: Accelerating Innovative Computational Approaches, Zhongming Zhao

Faculty, Staff and Student Publications

In this editorial, we summarize the 2023 International Conference on Intelligent Biology and Medicine (ICIBM 2023) conference which was held on July 16-19, 2023 in Tampa, Florida, USA. We then briefly describe the nine research articles included in this special issue. ICIBM 2023 scientific program included four tutorials and workshops, four keynote lectures, four eminent scholars' presentations, 11 concurrent scientific sessions, and a poster session. We had total of 88 scientific oral presentations, including 62 regular oral presentations and 26 flash talks, as well as 46 poster presentations. The topics of these presentations covered artificial intelligence (AI), data sciences, bioinformatics, …

Site-Specific Modification Of Antibodies Utilizing Microbial Transglutaminase For Improved Immunoassay Performance, Emily Beitello

Theses and Dissertations

Immobilization strategies used for fixing antibodies to solid phase surfaces significantly contribute to the antigen capture capacity and influences the performance and sensitivity of immunoassays. Traditional methodologies result in the random orientation and/or the weak attachment of immobilized antibodies. Different formats of immunoassays scope in applicability to many fields of research and everyday use. Improving the efficiency of immobilizing antibodies in immunoassays is a beneficial endeavor to increase assay sensitivity. Here, we investigated the use of enzyme-mediated conjugation of antibodies to facilitate a highly oriented immobilization. Microbial transglutaminase (mTG) catalyzes the covalent bond formation between a plethora of primary amine …

Converting Cover Crop Biomass To Biogas And Volatile Fatty Acids, Tuba Yasmin Lubna

Theses and Dissertations

Cover crops are commonly used for their environmental benefits, including improved soil health and reduced soil erosion. However, there is limited use for the aboveground biomass, except for oilseed crops. The objectives of this study were to (1) characterize the selected winter cover crop biomass at three growth stages, (2) evaluate the biogas and volatile fatty acids (VFAs) yield, and (3) examine the concurrent alkali pretreatment and ensiling effects on biogas yield. Wild pennycress, golden pennycress, CoverCress^TM, annual ryegrass, cereal rye, pea, and clover biomass were harvested at three growth stages. Results showed that biogas yield increased with …

Environmentally Friendly Chelation For Enhanced Algal Biomass Deashing, Agyare Asante, George Daramola, Ryan W. Davis, Sandeep Kumar

Civil & Environmental Engineering Faculty Publications

High ash content in algal biomass limits its suitability for biofuel production by reducing combustion efficiency and increasing fouling. This study presents a green deashing strategy using nitrilotriacetic acid (NTA) and deionized (DI) water to purify Scenedesmus algae, which was selected for its high ash removal potential. The optimized sequential treatment (DI, NTA chelation, and DI+NTA treatment at 90–130 °C) achieved up to 83.07% ash removal, reducing ash content from 15.2% to 3.8%. Elevated temperatures enhanced the removal of calcium, magnesium, and potassium, while heavy metals like lead and copper were reduced below detection limits. CHN analysis confirmed minimal …

Summer Research Fellowship Project Descriptions 2025, Clark Science Center's Summer Research Fellows Program

SURF Abstracts (Women in Science)

A summary of research done by Smith College’s 2025 Summer Research Fellowship (SURF) Program participants. Ever since its 1967 start, SURF has been a cornerstone of Smith’s science education. Supervised by faculty mentor-advisors drawn from the Clark Science Center and connected to its eighteen science, mathematics, and engineering departments and programs and associated centers and units. At summer’s end, SURF participants were asked to summarize their research experiences for this publication.

Husbandry Of Jellyfish And Ctenophores: Why Gelatinous Forms Thrive In Their Natural Habitat And Yet Often Struggle To Survive In Aquaria, Regina Garza Ramirez

Undergraduate Theses and Capstone Projects

Recent observations in the behaviors of several gelatinous forms in the wild have demonstrated that human impacts to their environment have likely accelerated growth of their populations tremendously. Interestingly enough, population growth of jellyfish and ctenophores in aquariums and artificial habitats is less often observed under controlled conditions, while they often bloom in rapidly changing environments of nature. Seeking the knowledge of aquarists and researchers that have worked directly with gelatinous animals through interviews, and documenting the experiences of each individual, allowed acquisition of data that can be used to compare the reproductive success of these animals in captivity and …

Consumption Of The Food Groups With The Revised Benefits In The New Wic Food Package: A Scoping Review, Qi Zhang, Priyanka T. Patel, Bidusha Neupane, Caitlin M. Lowery, Futun Alkhalifah, Faezeh Mahdavi, Esther May Sarino

Epidemiology, Biostatistics, & Environmental Health Faculty Publications

Background: On 18 April 2024, the United States Department of Agriculture (USDA) published the first food package changes to the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) in over a decade, which reduced some food benefits (juice, milk, canned fish, and infant fruits and vegetables) and offered substitutes (cash-value vouchers (CVVs) or cash-value benefits (CVBs) to redeem for fruits and vegetables, cheese, soymilk, or other dairy products). Methods: To assess the impact of the changes on the consumption and redemption of these food groups, a systematic search was conducted, identifying 23 peer-reviewed publications between 2010 and 2024. …

Diversifying Ecology Education For Everyone Through More Inclusive, Interdisciplinary, And Accessible Teaching, Loren B. Byrne, Emily S. J. Rauschert, Vikki L. Rodgers, Gillian Bowser, Et Al.

Arts & Sciences Faculty Publications

Educating more students about ecology and its beneficial applications to societal issues is urgent yet challenging. To address this challenge, diversifying ecology education is a key way to make ecology more inclusive, accessible, and interdisciplinary for more people than ever. Advancing this goal requires ecology educators to develop a more expansive view of (1) how to engage more diverse undergraduate students in ecology courses, especially those from historically underrepresented groups and non-majors, (2) the interdisciplinarity of content in those courses, and (3) the learner-centered pedagogies used to engage students. We suggest ways that ecologists can advance “ecology education for everyone” …

Assessment Of Bifidobacterium Longum Itt 13 As A Probiotic Candidate, Eleana Keatley

Masters

Probiotics are live microorganisms that when administered in adequate amounts confer a health benefit on the host. Beneficial microbes are found in several sites throughout the body such as the oral cavity, skin, respiratory tract, vagina, urinary tract, breast tissue and the gut. In this research, the culture Bifidobacterium longum ITT 13, which was previously isolated from a neonatal faecal sample, was examined for its potential as a probiotic candidate. Probiotics can have numerous desirable characteristics. The pertinent ones to this research are being of human or animal origin, not prone to antibiotic resistance, demonstration of antagonistic activity towards pathogens, …

Synthesis And Assessment Of Biobased Acrylated Epoxidized Soybean Oil Resins For Stereolithography 3d Printing Of Microfluidic Devices, Natalie S. Romero Figueroa

College of Graduate Studies: Theses & Dissertations

This research focuses on the development and characterization of a biobased photocurable resin synthesized from soybean oil for use in stereolithography (SLA) 3D printing of microfluidic devices. The study explores a sustainable alternative to petroleum-based resins by performing an acrylation reaction on epoxidized soybean oil (ESO) to produce acrylated epoxidized soybean oil (AESO), which was then formulated into a photocurable resin with the addition of a photo initiator. The fabrication process involved designing microfluidic molds in SolidWorks and printing them using an Elegoo Mars 4 SLA printer under various exposure and layer thickness parameters. The printed samples consisted of microchannels …

Enhancing The Mechanical Properties Of Sla 3d-Printed Bio-Resin From Linseed Oil Using Cellulose And Lignin Biopolymers, Chukwunonso A. Ikedionu

College of Graduate Studies: Theses & Dissertations

Abstract

This research explores the development of bio resin from linseed oil by the process of epoxidation and acrylation to produce acrylated epoxidized linseed oil (AELO). Lignin and cellulose biopolymers were added as reinforcement at varying weight fractions of 1 wt.%, 2.5 wt.%, and 5 wt.%, and their mechanical performance was compared against pure AELO. The formulations were printed using an Elegoo SLA 3D printer to create standardized test specimens like tensile bars, compression cylinders, and hardness blocks, which were all prepared according to the ASTM testing standard.

The results indicate that reinforcement effects depend on both filler type and …

Research Report: Cold-Hardy Hydrangeas For Landscape And Cut Flowers, Rebecca G. Sideman, Kaitlyn Orde, Ella Lukacz, Cathy Neal

Faculty Publications

This research report describes the performance of several cold-hard “panicle” (H. paniculata), “smooth” (H. arborescens), and “oakleaf” (H. quercifolia) hydrangea as landscape plants and for cut flower production in Durham, NH. We established a replicated planting of sixteen newer hydrangea cultivars at Woodman Farm in summer 2020. Preliminary data from these young shrubs indicates that there are wide differences in flower production, stem quality, flowering time and duration, and postharvest floral quality – among other traits.

Epithelial Responses And Remodeling In The Submandibular Gland Post-Irradiation, Victoria Gellatly

Electronic Theses & Dissertations (2024 - present)

Radiation therapy for head and neck cancer often causes irreversible salivary gland dysfunction, resulting in chronic xerostomia. Understanding the cellular and molecular mechanisms underlying this dysfunction is essential for developing regenerative therapies. Given the cellular complexity of the salivary gland single-cell RNA sequencing (scRNA-seq) provides a powerful approach to investigate cell-type-specific injury responses to ionizing radiation (IR) and uncover transcriptional changes that may be masked in bulk analyses. This study investigates the cellular and molecular responses of the murine submandibular gland (SMG) to irradiation, with a focus on epithelial loss and remodeling, and regenerative failure. In order to effectively use …