Digital Commons Network^™

Robust Relevance Feedback For Interactive Known-Item Video Search, Zhixin Ma, Chong-Wah Ngo

Research Collection School Of Computing and Information Systems

Known-item search (KIS) involves only a single search target, making relevance feedback-typically a powerful technique for efficiently identifying multiple positive examples to infer user intent-inapplicable. PicHunter addresses this issue by asking users to select the top-k most similar examples to the unique search target from a displayed set. Under ideal conditions, when the user's perception aligns closely with the machine's perception of similarity, consistent and precise judgments can elevate the target to the top position within a few iterations. However, in practical scenarios, expecting users to provide consistent judgments is often unrealistic, especially when the underlying embedding features used for …

Fashiondpo: Fine‑Tune Fashion Outfit Generation Model Using Direct Preference Optimization, Mingzhe Yu, Yunshan Ma, Lei Wu, Changshuo Wang, Xue Li, Lei Meng

Research Collection School Of Computing and Information Systems

Personalized outfit generation aims to construct a set of compatible and personalized fashion items as an outfit. Recently, generative AI models have received widespread attention, as they can generate fashion items for users to complete an incomplete outfit or create a complete outfit. However, they have limitations in terms of lacking diversity and relying on the supervised learning paradigm. Recognizing this gap, we propose a novel framework FashionDPO, which fine-tunes the fashion outfit generation model using direct preference optimization. This framework aims to provide a general fine-tuning approach to fashion generative models, refining a pre-trained fashion outfit generation model using …

Explaining Explanations: An Empirical Study Of Explanations In Code Reviews, Ratnadira Widyasari, Ting Zhang, Abir Bouraffa, Walid Maalej, David Lo

Research Collection School Of Computing and Information Systems

Code reviews are central for software quality assurance. Ideally, reviewers should explain their feedback to enable authors of code changes to understand the feedback and act accordingly. Different developers might need different explanations in different contexts. Therefore, assisting this process first requires understanding the types of explanations reviewers usually provide. The goal of this article is to study the types of explanations used in code reviews and explore the potential of Large Language Models (LLMs), specifically ChatGPT, in generating these specific types. We extracted 793 code review comments from Gerrit and manually labeled them based on whether they contained a …

How Are We Detecting Inconsistent Method Names? An Empirical Study From Code Review Perspective, Kisub Kim, Xin Zhou, Dongsun Kim, Julia Lawall, Kui Liu, Tegawendé F. Bissyandé, Jacques Klein, Jaekwon Lee, David Lo

Research Collection School Of Computing and Information Systems

Proper naming of methods can make program code easier to understand, and thus enhance software maintainability. Yet, developers may use inconsistent names due to poor communication or a lack of familiarity with conventions within the software development lifecycle. To address this issue, much research effort has been invested into building automatic tools that can check for method name inconsistency and recommend consistent names. However, existing datasets generally do not provide precise details about why a method name was deemed improper and required to be changed. Such information can give useful hints on how to improve the recommendation of adequate method …

Double Trouble: A Rare Cause Of Bilateral Upper Extremity Swelling, Lauren Abbas, Sheena Mckenzie

Advocate GME

No abstract provided.

Blue In The Face: Unraveling A Hypoxic Mystery, Lauren Abbas, Sheena Mckenzie

Advocate GME

No abstract provided.

Chapter 3. Moroccan Arabic-Spanish Bilinguals’ Linguistic Profile And Their Perspectives And Experiences On Learning Standard Arabic, Ramsés Ortín, Pilar Garrido

Writing and Language Studies Faculty Publications

We surveyed a group of Moroccan Arabic-Spanish speakers in the Region of Murcia, Spain, to examine their linguistic profiles, their attitudes towards their native Arabic dialect, their motivations to learn Standard Arabic and their learning experience with Standard Arabic. We found varying degrees of dominance in this group along with fluctuating patterns of dominance, proficiency and language use according to age and onset of acquisition of Spanish. This group displayed generally positive attitudes towards their own dialect and their motivation to learn Arabic was related to their religious and cultural connections. Most of them indicated that they had engaged in …

Where Should The Cancer Control Interventions Target: A Geospatial Hotspot Analysis For Major Cancer Mortality 2018 To 2022 In The United States, Chongliang Luo, Saira Khan, Liyan Jin, Aimee S James, Graham A Colditz, Bettina F Drake

2020-Current year OA Pubs

BACKGROUND: Identifying changes in geographic disparities of cancer mortality reveals locations where cancer prevention and control efforts should be focused/targeted. We use recent cancer surveillance data to demonstrate the geographic disparity of major cancer mortality rates in the United States and its shift compared with previous data.

METHODS: This cross-sectional study used the 2018 to 2022 county-level mortality rates of colorectal, lung, breast, and prostate cancers from the Centers for Disease Control mortality data. Counties with suppressed death counts were imputed by spatial regression models. Getis-Ord Gi* statistics were used to evaluate the spatial clustering of county mortality. Identified hotspot …

Dna Methylation Epitypes Of Burkitt Lymphoma With Distinct Molecular And Clinical Features, Nicole Thomas, Nancy L Bartlett, Et Al.

2020-Current year OA Pubs

UNLABELLED: The genetic subtypes of Burkitt lymphoma have been defined, but the role of epigenetics remains to be comprehensively characterized. We searched genomic DNA from 218 patients across four continents for recurrent DNA methylation patterns and their associations with clinical and molecular features. We identified DNA methylation patterns that were not fully explained by the Epstein-Barr virus status or mutation status, leading to two epitypes described here as HypoBL and HyperBL. Each is characterized by distinct genomic and clinical features including global methylation, mutation burden, aberrant somatic hypermutation, and survival outcomes. Methylation, gene expression, and mutational differences between the epitypes …

Integrating Nonindividual Patient Features In Machine Learning Models Of Hospital-Onset Bacteremia, M Cristina Vazquez-Guillamet, Jingwen Zhang, Alice Bewley, Andrew Atkinson, Heidi Holtz, Ziqian Wang, Nicole Brougham, Chenyang Lu, Marin H Kollef, Philip Payne, David Warren, Victoria J Fraser

2020-Current year OA Pubs

IMPORTANCE: Hospital-onset bacteremia and fungemia (HOB) are common and potentially preventable complications of hospital care.

OBJECTIVE: To assess whether nonindividual patient features, which summarize interactions with other patients and health care workers (HCWs), can contribute to predictive and causal machine learning models for HOB.

DESIGN, SETTING, AND PARTICIPANTS: This prognostic study included adult patients admitted to Barnes-Jewish Hospital, an academic hospital in St Louis, Missouri, in 2021. Analyses were developed between October 2023 and August 2024 and in April 2025.

EXPOSURE: Individual patient features were extracted from electronic health records and used to engineer nonpatient features, including interactions with HCWs …

Postoperative Delirium In Older Adults Undergoing Noncardiac Surgery, Heather L Lander, Andrew W Dick, Karen E Joynt Maddox, Mark A Oldham, Lee A Fleisher, Michael Mazzeffi, Stewart J Lustik, Jingjing Shang, Patricia W Stone, Marjorie S Gloff, Jacob Nadler, Isaac Wu, Raymond Zollo, Laurent G Glance

2020-Current year OA Pubs

IMPORTANCE: Understanding the association of postoperative delirium with adverse outcomes and the hospital-level variation of postoperative delirium is important for efforts to improve perioperative brain health.

OBJECTIVE: To examine (1) the association of postoperative delirium with 30-day mortality and complications and (2) hospital-level variation in postoperative delirium.

DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study examined hospitalizations among patients aged 65 years and older who underwent noncardiac surgery in US hospitals between January 1, 2017, and December 31, 2020. Data were analyzed between August 28, 2024, and April 10, 2025.

EXPOSURE: Postoperative delirium.

MAIN OUTCOMES AND MEASURES: The association of …

History Of Hypoxia Exposure Aids Future Cell Invasion According To Cell Type And Collagen Density, José A Almeida, Diego B Avila, Gregory D Longmore, Amit Pathak

2020-Current year OA Pubs

In cancer progression, tumor microenvironments (TME) progressively become denser and hypoxic, and cell migrate toward higher oxygen levels as they invade across the tumor-stromal boundary. Although cell invasion dependence on optimal collagen density is well appreciated, it remains unclear whether past oxygen conditions alter future invasion phenotype of cells. Here, we show that normal human mammary epithelial cells (MCF10A) and leader-like human breast tumor cells (BT549) undergo higher rates of invasion and collagen deformation after past exposure to hypoxia, compared with normoxia controls. Upon increasing collagen density by ∼50%, cell invasion under normoxia reduced, as expected due to the increased …

Distinct Patterns Of Weight Gain, Age, And Subcortical Microstructure In Early Adolescence, Shana Adise, Zhaolong Adrian Li, Jonatan Ottino-González, Filip Morys, Peter A Chiarelli, Tamara Hershey

2020-Current year OA Pubs

IMPORTANCE: Associations between childhood obesity and brain microstructural differences have been observed. It remains unknown whether these associations are driven by sex-specific excessive weight gain. Restriction spectrum imaging characterizes brain tissue microstructural health via water diffusion, where the restricted normalized isotropic (RNI) compartment assesses neuronal and glial cellularity, which may reflect neuroinflammation, synaptic pruning, or both.

OBJECTIVE: To identify associations among RNI scaling factor values, normal neurodevelopment, and weight gain during early adolescence.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study used data from the Adolescent Brain Cognitive Development (ABCD) Study, a 10-year, ongoing, multisite longitudinal cohort study conducted among youths …

Utility Of The Us Preventive Services Task Force For Preeclampsia Risk Assessment And Aspirin Prophylaxis, Thomas F Mcelrath, Antonina I Frolova, Et Al.

2020-Current year OA Pubs

IMPORTANCE: The US Preventive Services Task Force (USPSTF) guidelines on preeclampsia risk assessment and aspirin prophylaxis (AP) have not been evaluated for clinical utility.

OBJECTIVE: To evaluate which characteristics in the USPSTF guidelines identify risk status and the association of preeclampsia risk with AP recommendations.

DESIGN, SETTING, AND PARTICIPANTS: This observational cohort study enrolled from July 2020 to March 2023 with data analysis performed from October to December 2024. Enrollment occurred at 11 centers throughout the US or via direct-to-participant recruitment. Pregnant participants aged 18 years or older with a singleton pregnancy less than 22 weeks' gestation were selected via …

Using Meta-Analysis: What Exercise Helps Kids With Excess Weight The Most?, Marilyn Frenn

College of Nursing Faculty Research and Publications

No abstract provided.

Childhood Obesity Body Mass Index And Gut Microbiome: A Cluster Randomized Controlled Pilot Feasibility Study, Marilyn Frenn, Nita Salzman, Vy Lam, Mary Holtz, Andrea Moosreiner, Mauricio Garnier-Villarreal, Maharaj Singh

College of Nursing Faculty Research and Publications

Background:

Prebiotic fiber has been examined as a way to foster gut bacteria less associated with obesity. Tests of prebiotic fiber in reducing obesity have occurred mainly in animals, adults, and Caucasians when the highest obesity rates are in African American and Latinx youth. Response to prebiotic fiber is determined by the pre-existing intestinal microbiota. The type of microbiota varies based on diet and physical activity (PA), so it is important to examine acceptability and response to prebiotic fiber in those most at risk for obesity.

Methods:

This cluster randomized controlled feasibility trial included an online program designed to improve …

Identification Of Authentic Gnss Signals In Time-Differenced Carrier-Phase Measurements With A Software-Defined Radio Receiver, Zhen Zhu, Sanjeev Gunawardena, Eric Vinande, Jason Pontious

Faculty Publications

The time-differenced carrier phase can be computed from measurements recorded by a multi-global navigation satellite system software-defined radio receiver such as PyChips, from which the user displacement and receiver clock drift can be solved. PyChips is able to simultaneously track authentic and inauthentic signals in separate channels, which makes it possible to observe both types of measurements with corresponding navigation data. A random sample consensus algorithm has been introduced to assess the consistency between the measurements and data. This algorithm successfully separated authentic channels from inauthentic channels when they are broadcast simultaneously.

The State Of The Science Of Natural Family Planning: A Report From Nfp Scientists’ Meeting Held In Orlando, Fl, September 4, 2024, Michael D. Manhart, Richard J. Fehring

College of Nursing Faculty Research and Publications

A one-day meeting was held as a pre-conference to the Catholic Medical Association Annual Educational event in 2024. A panel of eighteen physicians, scientists, and researchers involved in NFP work was convened to review the available evidence in four topical areas: (i) evidence for effectiveness of NFP methods to postpone and achieve pregnancy, (ii) evidence for effectiveness in the postpartum and perimenopause transition periods, (iii) evaluate the current state of technology in NFP (specifically app and quantitative hormone monitoring), and (iv) evidence examining the impact of NFP on marital relations. In each topical area, the panel worked to reach a …

Conservation Management Effects On Soil And Agronomic Properties In A Furrow-Irrigated Corn System In East-Central Arkansas, Jeferson P. Pimentel, Christopher G. Henry, Kris R. Brye, Benjamin R. Runkle, Amanda J. Ashworth, Edgar Mersiovsky, Kevin C. Thompson

Biological and Agricultural Engineering Faculty Publications and Presentations

Cover crops can improve soil physical properties and help to sustain agricultural crop yields. A 6-year study conducted from 2017 to 2022 examined the effects of conservation soil management practices in a furrow-irrigated continuous corn (Zea mays L.) system on a silt-loam soil (Typic Albaqualf) in the Lower Mississippi River Delta region of eastern Arkansas. This study compared the effects of conventional tillage (CT), no-tillage (NT), and no-tillage with cover crops (CC) in selected soil physical and chemical properties (i.e., soil bulk density (D b), porosity (& fnof;t), field capacity (Theta FC), Permanent wilting point (Theta PWP), Plant available water …

Two Spectroscopy Devices Can Approximate Fruit And Vegetable Intake In A Racially And Ethnically Diverse Sample, Stephanie B Jilcott Pitts, Qiang Wu, Melissa N Laska, Nancy E Moran

Children’s Nutrition Research Center Staff Publications

Background: Assessing fruit and vegetable intake is important to determine the effectiveness of nutrition intervention studies. Few objective measures of fruit and vegetable intake have been directly compared within the same study participants.

Objectives: This study aims to compare the relative validity of 2 different skin spectrophotometry devices to serve as biomarkers of plasma carotenoid concentrations, self-reported fruit and vegetable intake (FVI), and carotenoid intake, to examine if both devices can be used to approximate FVI.

Methods: Human skin carotenoid scores (SCS, Veggie Meter-assessed) and color space measurement data from 2 prior studies were used. Participants' skin color space parameters …

Cell-Free Protein Synthesis Reactor Formats: A Brief History And Analysis, Dallin M. Chipman, Anna C. Woolley, Davu N. Chau, William A. Lance, Joseph P. Talley, Tyler P. Green, Benjamin C. Robbins, Bradley Charles Bundy

Faculty Publications

Cell-free protein synthesis (CFPS) has transformed protein production capabilities by eliminating cellular constraints, enabling the rapid expression of difficult-to-produce proteins in an open, customizable environment. As CFPS applications expand from fundamental research to industrial production, therapeutic manufacturing, and point-of-care diagnostics, the diverse array of reactor formats has become increasingly important yet challenging to navigate. This review examines the evolution and characteristics of thirteen major CFPS reactor formats, from traditional batch systems to advanced platforms. The historical development of CFPS reactors from the 1960s to present day is presented. Additionally, for each format, operational principles, advantages, limitations, and notable applications are …

A Brief Guide To Statistical Analysis Of Grouped Data In Preclinical Research, Colby J Vorland, Lilian Golzarri-Arroyo, David B Allison

Children’s Nutrition Research Center Staff Publications

Clustering and nesting (C&N) arise in many preclinical studies such as when animals are group-housed, share litters, or in cell culture. Ignoring C&N undermines the validity of analyses. We explain how C&N arise and valid designs and analyses.

Defining Lipedema’S Molecular Hallmarks By Multi-Omics Approach For Disease Prediction In Women, Leon G Straub, Jan-Bernd Funcke, Nolwenn Joffin, Chanmin Joung, Sara Al-Ghadban, Shangang Zhao, Qingzhang Zhu, Ilja L Kruglikov, Yi Zhu, Paul R Langlais, Ruth Gordillo, Karen L Herbst, Philipp E Scherer

Children’s Nutrition Research Center Staff Publications

Lipedema is a chronic disease in females characterized by pathologic subcutaneous adipose tissue expansion and hitherto remains without druggable targets. In this observational study, we investigated the molecular hallmarks of lipedema using an unbiased multi-omics approach. We found adipokine dysregulation in lipedema patients participating in a cross-sectional clinical study (ClinicalTrial.gov, NCT02838277), pointing towards the adipocyte as a key player. Analyses of newly generated transcriptomic (SRA, PRJNA940039) and proteomic (ProteomeXchange, PXD058489) datasets of early- and late-stage lipedema samples revealed a local downregulation of factors involved in inflammation. Concomitantly, factors involved in cellular respiration, oxidative phosphorylation, as well as in mitochondrial …

Soft Tissue Stabilization Of Midcarpal Instability In Ehlers-Danlos Patients Using A Cadaveric Tendon Graft, Mohammed Muneer, Fadi Bouri, Kjell Van Royen, Saif Badran, Jorge I. Quintero, Tuna Ozyurekoglu

2020-Current year OA Pubs

Ehlers-Danlos syndrome (EDS) is a group of hereditary disorders that affects collagen synthesis. In the wrist, pain and midcarpal laxity may affect up to 70% of EDS patients. The mainstay treatment of midcarpal instability in patients with ligamentous injury but not EDS includes orthotics, physiotherapy, and activity modification. These methods of conservative treatment may be unsuccessful in controlling instability in the longer term. Using autologous tendon for reconstructing midcarpal instability in patients with EDS carries the risk of loosening over time due to intrinsic abnormalities in collagen metabolism. In this article, we present a novel surgical technique using a cadaveric …

Robust Photogrammetric Scalp Morphology Estimation For Functional Optical Neuroimaging, Abigail L Magee, Calamity Svoboda, Tessa G George, Alvin A Agato, Edward J Richter, Joseph P Culver, Adam T Eggebrecht

2020-Current year OA Pubs

SIGNIFICANCE: Optical functional neuroimaging relies upon accurate anatomical models to provide optimal data registration and image reconstruction.

AIM: We establish and validate a robust photogrammetric algorithm for scalp morphology that utilizes 3-dimensional (3D) imaging with a photogrammetric cap to provide individualized scalp morphology estimation through hair in the absence of magnetic resonance imaging (MRI).

APPROACH: The scalp morphology estimation uses a flexible, neoprene cap and 3D-printed photogrammetric modules with fiducials. We create a sparse scalp sampling and align the MNI152 atlas to generate the scalp morphology estimation. We used the international 10 to 20 electroencephalogram positions for alignment and calculated …

Kpna2 Promotes Osteosarcoma Progression By Regulating The Alternative Splicing Of Ddx3x Mediated By Ybx1, Li Cao, Ke Jia, B A Van Tine, Yihan Yu, Yizhong Peng, Xuanzuo Chen, Qing Pan, Wenbo Yang, Zhicai Zhang, Zengwu Shao, Wei Wu

2020-Current year OA Pubs

Osteosarcoma (OS) is a rapidly progressive primary malignant bone tumor that occurs in children and adolescents aged between 15 and 19 years and adults aged over 60 years. As alternative splicing (AS) changes caused by abnormal splicing factors contribute to tumor progression, gene expression and AS analyses were performed on 44 osteosarcoma patients to create a genome-wide co-expression network of RNA-binding proteins (RBPs), AS events, and AS genes. A gain- or loss-of-function osteosarcoma cell model was established, and an interactive network analysis and enrichment analysis were performed. Karyopherin Subunit Alpha 2 (KPNA2) negatively correlated with patient survival. KPNA2 transports splicing …

Phospho-Rpa2 Predicts Response To Platinum And Parp Inhibitors In Homologous Recombination-Proficient Ovarian Cancer, Angela Schab, Amanda Compadre, Rebecca Drexler, Megan Loeb, Kevin Rodriguez, Joshua Brill, Carmen Sandoval, Brooke Sanders, Lindsay Kuroki, Carolyn Mccourt, Andrea R. Hagemann, Premal Thaker, David Mutch, Matthew Powell, Ian S. Hagemann, Lulu Sun, Priyanka Verma, Elena Lomonosova, Dineo Khabele, Mary M. Mullen, Et Al.

2020-Current year OA Pubs

BACKGROUNDTreatment of tubo-ovarian high-grade serous carcinoma (HGSC) includes cytoreductive surgery, platinum-based chemotherapy, and often poly(ADP-ribose) polymerase (PARP) inhibitors. While homologous recombination (HR) deficiency is a well-established predictor of therapy sensitivity, over 50% of HR-proficient HGSCs also exhibit sensitivity. Currently, there are no biomarkers to identify which HR-proficient HGSCs will be sensitive to standard-of-care therapy. Replication stress may serve as a key determinant of response.METHODSWe evaluated phospho-RPA2-T21 (p-RPA2) foci via immunofluorescence as a biomarker of replication stress in formalin-fixed, paraffin-embedded HGSC samples collected at diagnosis from patients treated with platinum chemotherapy (discovery cohort, n = 31; validation cohort, n = 244) …

Reference Range Determination For The Sflt-1/Plgf Ratio In A Diverse Cohort Of Pregnant Women In The United States, Antonio F Saad, David M Haas, Eugene Chang, Scott A Shainker, Miriah Denbo, Michelle Silasi, George Saade, Sarosh Rana, Tetsuya Kawakita, Luis D Pacheco, Jennifer Powers Carson, Angela Dietl, Deirdre Allegranza, Ge Guo, David Stamilio

2020-Current year OA Pubs

BACKGROUND: The serum soluble fms-like tyrosine kinase-1 (sFlt-1) to placental growth factor (PlGF) ratio is an established tool for predicting preeclampsia in many countries but is not widely adopted in the United States. This study aimed to determine reference ranges for the Elecsys® sFlt-1/PlGF ratio and the sFlt-1 and PlGF immunoassays (Roche Diagnostics International Ltd) in a diverse US population of healthy pregnant women.

METHODS: This was a prospective, noninterventional sample and data collection study performed between November 2022 and November 2023 at 9 collection sites and one measurement site in the United States. Evaluable women were ≥18 years old, …

Evaluation Of Internally Cooled Radiofrequency Ablation Targeting Multiple Shoulder Nerves For Chronic Shoulder Pain Relief And Function Restoration: A Prospective Study, Mitsukuni Yoshida, Peter K Park, Loc V Thang

2020-Current year OA Pubs

OBJECTIVE: Shoulder pain is a prevalent musculoskeletal disorder, affecting up to 70% of adults over their lifetimes. Recently, radiofrequency ablation (RFA) has gained attention as a treatment for joint pain. This study aims to evaluate the efficacy of internally cooled RFA (icRFA) in alleviating shoulder pain and improving both qualitative and quantitative measures of shoulder function.

DESIGN: Prospective cohort study.

SUBJECTS: Patients with chronic shoulder pain (n = 35) who responded positively to diagnostic blocks of the suprascapular nerve (SSN), axillary nerve (AN), and lateral pectoral nerve (LPN).

METHODS: Patients underwent icRFA targeting the SSN, AN, and LPN. Treatment response …

Increasing Birth-Dose Hepatitis B Vaccination In Nigeria: Qualitative Analysis Of Data From A Crowdsourcing Open Call, Sonam J Shah, Maria Afadapa, Nkiruka Obodoechina, Olufunto A Olusanya, Temitope Ojo, Dawit Alemu, Juliet Iwelunmor, Et Al.

2020-Current year OA Pubs

BACKGROUND: Despite World Health Organization and Nigerian recommendations for hepatitis B birth-dose (HepB-BD) vaccination, only one-third of Nigerian newborns receive timely HepB-BD vaccination, This study identified facilitators to increasing HepB-BD vaccination based on data from a crowdsourcing open call in Nigeria.

METHODS: Our team conducted an open call across Nigeria for teams to submit ideas on how to increase HepB-BD vaccination. Independent judges evaluated the submissions based on predefined criteria. We analyzed textual data from the top 29 entries using iterative coding and thematic analysis within a socioecological model to identify priority facilitators.

RESULTS: The open call received 362 total …