Digital Commons Network^™

Post-Fire Succession In An Old-Growth Coast Redwood (Sequoia Sempervirens) Forest, Mojgan Mahdizadeh, Will Russell

Faculty Research, Scholarly, and Creative Activity

In 2020, a high-intensity wildfire burned over 35,000 ha in the Santa Cruz Mountains of California, including over 1700 ha of old-growth coast redwood forest. This event created a unique opportunity to evaluate post-fire succession. We compared vegetation recovery in high versus low/moderate severity burned areas using data collected one year and four years following the fire. Random plot sampling was conducted at Big Basin Redwoods State Park to assess the regeneration of trees, shrubs, and herbaceous species. Descriptive and inferential statistical analyses were used to assess recovery over time and across burn severities. Results indicate significant increases in shrub …

Multidimensional Analysis Of B7 Homolog 3 Rna Expression In Small Cell Lung Cancer Molecular Subtypes, Carl M Gay, Taofeek K Owonikoko, Lauren A Byers, Noura J Choudhury, Sajid Ahmed, Zachary Cain, Xiaozhong Qian, Matthew Brentnall, Simon Heeke, Ming Poi, Sharon Wu, Charles M Rudin

Faculty, Staff and Student Publications

Purpose: B7 homolog 3 (B7-H3) is a promising target for antibody-drug conjugates, with ifinatamab deruxtecan demonstrating an objective response rate of 54.8% in previously treated extensive-stage small cell lung cancer (SCLC). This analysis aimed to characterize B7-H3 RNA expression with reference to SCLC molecular subtypes (SCLC-A, SCLC-N, SCLC-P, and SCLC-I) and immune-related parameters.

Experimental design: Tumor RNA expression and mutational burden for 1,721 patients with SCLC were derived from a real-world database (Caris Life Sciences). A predominant molecular subtype was assigned based on RNA expression using a gene-ratio classifier. PD-L1 expression was assessed by IHC (antibody 22C3; positive cutoff: tumor …

Genome Sequences Of Eight Fusobacterium Watanabei Sp Isolates, Martha A Zepeda-Rivera, Falk Ponath, Kaitlyn N Lewis, Rutika P Gavate, Floyd E Dewhirst, Junko Tomida, Yoshiaki Kawamura, Kaori Tanaka, Susan Bullman, Christopher D Johnston

Faculty, Staff and Student Publications

We report draft genome sequences of eight Fusobacterium watanabei clinical isolates, ranging from 1.95 to 2.09 Mbp. Analysis against the Genome Taxonomy Database indicates that F. watanabei genomes are part of the "Fusobacterium nucleatum_J" group.

Iterative Intraoperative 3t Mri (Imri)-Guided Brachytherapy: A Prospective Study On Enhancing Implantation Precision And Dosimetric Gains In Advanced Gynecologic Cancers, Shrikiriti S Rajan, Matthew S Ning, Megan Jacobson, Samantha J Simiele, Teresa Bruno, Ramez Kouzy, Kyoko Yoshida-Court, Tatiana Cisneros-Napravnik, Henry Yu, Jason Stafford, Yusung Kim, Geena Mathew, Rauda Alicia Cordova, Maliah Domingo, Anuja Jhingran, Lilie L Lin, Melissa Joyner, Travis T Sims, Lauren Colbert, Aradhana M Venkatesan, Ann Klopp

Faculty, Staff and Student Publications

Purpose: To report on primary outcomes and dosimetric results of a prospective clinical trial and protocol for use of iterative intraoperative magnetic resonance imaging (iMRI) in gynecologic brachytherapy.

Methods: Patients with locally advanced cervical or vaginal cancer (FIGO stages IB2 - IVA, and stage II-IVA, respectively) undergoing pulsed dose rate (PDR) brachytherapy were enrolled in a prospective clinical trial (NCT03634267) using iterative 3T iMRI during brachytherapy implant placement. Applicator and optional interstitial needles were placed under iMRI guidance in a 3T clinical MRI scanner. Imaging, dosimetry and clinical outcomes (local control (LC), recurrence-free survival (RFS), overall survival (OS)), …

Large-Scale Crispr Screening In Primary Human 3d Gastric Organoids Enables Comprehensive Dissection Of Gene-Drug Interactions, Yuan-Hung Lo, Hudson T Horn, Mo-Fan Huang, Wei-Chieh Yu, Chia-Mei Young, Qing Liu, Madeline Tomaske, Martina Towers, Antonia Dominguez, Michael C Bassik, Dung-Fang Lee, Lei S Qi, Jonathan S Weissman, Jin Chen, Calvin J Kuo

Faculty, Staff and Student Publications

Understanding how genes influence drug responses is critical for advancing personalized cancer treatments. However, identifying these gene-drug interactions in a physiologically relevant human system remains a challenge, as it requires a model that reflects the complexity and heterogeneity among individuals. Here we show that large-scale CRISPR-based genetic screens, including knockout, interference (CRISPRi), activation (CRISPRa), and single-cell approaches, can be applied in primary human 3D gastric organoids to systematically identify genes that affect sensitivity to cisplatin. Our screens uncover genes that modulate cisplatin response. By combining CRISPR perturbations with single-cell transcriptomics, we resolve how genetic alterations interact with cisplatin at the …

Phenotypic Evaluation Of F10 Soybean Generations From Grobogan X Slamet Cross For Large Seed Size Selection, Ponendi Hidayat, Nurtiati, Zulfa Ulinnuha, Adellansyah

Jurnal Kultivasi

Soybeans are an important crop with high nutritional value and diverse uses. Current consumer and industry preference is for soybean varieties with large seeds and high productivity. To meet these demands, one effective approach is through hybridization. This study aims to evaluate the phenotype of F10 soybean line from a cross between Grobogan and Slamet for large-seeded and high-yield. The study was conducted in the screenhouse and Plant Breeding and Biotechnology Laboratory, Faculty of Agriculture, Jenderal Soedirman University. The experiment used a Randomized Complete Block Design (RCBD) with three replications, testing genotypes from Slamet x Grobogan crosses and three check …

Rna Gene Expression-Based Liquid Biopsies For Diagnosing Hepatocellular Carcinoma, Balvinder Bobbie Saarsal, Ila Chauhan, Jeevan Divakaran, Shizue Mito

School of Medicine Publications

The incidence of non-alcoholic steatohepatitis, a significant risk factor for hepatocellular carcinoma (HCC), is on the rise, highlighting the urgent need for improved diagnostic biomarkers. To date, no systematic analysis has evaluated international studies using liquid samples to assess the utilization of RNA species as biomarkers for HCC. Liquid biopsies based on RNA expression offer more specific and sensitive diagnostic biomarkers for HCC than alpha-fetoprotein (AFP). The inclusion criteria mandated English-language articles, freely available full texts, and primary research published between January 1, 2019, and May 15, 2024. Quantitative analysis was performed using the area under the receiver operating characteristic …

Alekna V. 207-217 W. 110 Portfolio Owner Llc

All Decisions

The Appellate Division, First Department, remanded this class action for trial to determine if the landlord engaged in a fraudulent scheme to deregulate apartments while receiving J-51 tax credits. The court applied the "totality of the circumstances" standard, which superseded the stricter common-law fraud standard, and held that tenants must prove the landlord "knowingly engaged" in the fraudulent scheme. The decision found no impermissible retroactive effect in applying the new standard and affirmed that managing agents can be held liable for their participation in a fraudulent scheme. The court denied the tenant's summary judgment motion and modified the lower court's …

Cortical Spectral Dynamics Of Vibrotactile Frequency Processing, Nabi Rustamov, Phillip Demarest, Zhuangyu Han, Safia Mohamud, Simon Haroutounian, Eric C Leuthardt

2020-Current year OA Pubs

While scientific research has extensively explored how the brain integrates touch and pain signals, the cerebral processing of specific vibrotactile frequencies remains poorly understood. This gap is particularly significant given clinical evidence that vibrotactile stimulation can reduce pain in both chronic pain patients and experimental settings. Our study investigated the cortical electrophysiological correlates of peripheral vibrotactile stimulation across different frequencies in healthy volunteers, with a focus on frequency-dependent patterns of neuronal activation. While electroencephalogram (EEG) was recorded, healthy participants received vibrotactile stimulation (high-frequency burst stimulation with different inter-burst intervals) to the left index fingertip at frequencies corresponding to established neural …

People’S Plate: The Recipe For Equitable Food Distribution, Bayleigh Nicole Thurston

Theses

Food insecurity remains a pressing issue in the United States that disproportionately affects vulnerable populations, leaving millions without access to nutritious meals. In 2023 alone, over 50 million people turned to food assistance programs for additional support1. While traditional nutrition programs like food banks and soup kitchens provide a vital service to many communities, they often lack the capacity to address the multifaceted nature of hunger. The social stigma and alienation associated with seeking food assistance become of little concern when organizations are grappling with daunting challenges of limited resources, logistical hurdles, and the need to provide quality, nutritious meals. …

Evaluation Of Color, Water Content, And Antioxidant Properties Of Wood Ear Mushroom With Nano Edible Coating, Packaging, And Storage Temperature, Aulia Afifah Rachman, Jajang Sauman Hamdani, Kusumiyati

Jurnal Kultivasi

Wood ear mushrooms are often consumed in Asia and Tropical America for their jelly-like texture, health, and freshness. However, they are easily damaged due to microbes and poor postharvest handling, which affects quality. The combination of nano edible coating, packaging, and storage temperature offers a solution to these issues. This study aims to evaluate the effect of nano edible coating, packaging, and storage temperature on the color (L*, a*, and b*), water content, and antioxidant properties (total phenolic and flavonoid) of wood ear mushrooms. The study was conducted at the Horticulture Laboratory, Faculty of Agriculture, Universitas Padjadjaran. The experimental design …

Understanding The Interplay Between The Digital And The Physical In Shared Augmented Reality Gaming: Probing Through Urban Legends, Jiangnan Xu, Sanzida Mojib Luna, Garreth W. Tigwell, Nicolas Lalone, Michael Saker, Samuli Laato, John Dunham, Yihong Wang, Alan Chamberlain, Konstantinos Papangelis

Articles

Shared Augmented Reality (Shared AR) is an emerging technology that enables multiple users to interact synchronously within a collocated AR environment. Yet, there is limited research on the group interactions and dynamics in Shared AR, particularly in the context of gaming. To address this gap, we investigate Shared AR group interactions using a phone-based Shared AR mobile game called Urban Legends. Through in-situ observations, focus groups, and one-on-one interviews with 22 participants, we examine how users collaborate and communicate within the game. Our findings reveal that while verbal communication predominates, non-verbal cues are often overlooked by collocated participants, and …

Effect Of Eco-Enzyme Application On Soil Nutrient And Plant Productivity Of Green Mustard-Peanut In Inceptisol, Idris Abd Rachman, Buhari Umasugi, Krishna Aji, Nurul Fahira A Hakim, Adnan Sofyan, Asrul Dedy Ali Hasan

Jurnal Kultivasi

Appropriate land management has a long-term impact on soil performance and is believed to improve soil fertility. This study investigated the effect of eco-enzymes on soil nutrients and plant productivity of green mustard-peanut in inceptisol. The research was conducted from February to April 2025. The experiment used a randomized block design (RBD) consisting of 5 treatments and replicated 3 times, so that there were 15 units, including N0 = without Eco-enzyme, N1 = Eco-enzyme 2cc/L. N2= Eco-enzyme 4cc/L, N3= Eco-enzyme 6cc/L, and N4= Eco-enzyme 8cc/L. The commodities used were green mustard (Brassica juncea L) and peanut (Arachis hypogaea Linn). Soil …

Enhancing Sustainable Rice Production Through Organic Plus Fertilizer In Irrigated Paddy Fields, Oviyanti Mulyani, Emma Trinurani Sofyan, Ania Citraresmini, Benny Joy, Anne Yuliana Husen

Jurnal Kultivasi

Sustainable rice farming is increasingly threatened by declining soil fertility, excessive reliance on chemical fertilizers, and environmental degradation from intensive agricultural practices. There is an urgent need for innovative organic fertilizer products that combine organic materials with macro and micronutrient enhancements to restore soil health effectively. This research aimed to evaluate the effect of organic plus fertilizer (OPF) as a sustainable soil amendment to improve soil nutrient status, increase paddy productivity, and enhance overall soil health. The experiment was conducted using a Randomized Block Design (RBD) with nine treatments: one recommended OPF dose, six combinations of NPK (75 – 100%) …

Career: Flavones As Safe, Sustainable Additives To Tune Biodegradable Plastic Stability, Kyle Moor

Funded Research Records

No abstract provided.

Rapid: Data Collection On Roadway Vehicle Abandonment In The Fast-Moving Los Angeles Wildfire Evacuations, Sarah Grajdura

Funded Research Records

No abstract provided.

Career: Algebra And Representation Theory For Non-Semisimple Topological Field Theory, Matthew Young

Funded Research Records

No abstract provided.

Baby Open Brains: An Open-Source Dataset Of Infant Brain Segmentations, Eric Feczko, Dimitrios Alexopoulos, Christopher D Smyser, Et Al.

2020-Current year OA Pubs

Reproducibility of neuroimaging research on infant brain development remains limited due to highly variable processing approaches. Progress towards reproducible pipelines is limited by a lack of benchmarks such as gold-standard brain segmentations. These segmentations are limited by the difficulty of infant brain segmentations, which require extensive neuroanatomical knowledge and are time-consuming in nature. Addressing this, we constructed the Baby Open Brains (BOBs) Dataset, an open source resource of manually curated and expert reviewed infant brain segmentations. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic …

Multimodal Spatial Transcriptomic Characterization Of Mouse Kidney Injury And Repair, Qiao Xuanyuan, Haojia Wu, Hemalatha Sundaramoorthi, Pierre Isnard, Changfeng Chen, Waleed Rahmani, Benjamin D Humphreys

2020-Current year OA Pubs

The transition from acute kidney injury to chronic kidney disease is characterized by significant changes in the cellular composition and molecular interactions within the kidney. Utilizing high-resolution Xenium and whole transcriptome Visium spatial transcriptomics platforms, we analyze over a million cells on 12 male mouse kidneys across six stages of renal injury and repair. We define and validate 20 major kidney cell populations and delineate distinct cellular neighborhoods through this multimodal spatial analysis. We further reveal a specific fibro-inflammatory niche enriched in failed-repair proximal tubule cells, fibroblasts, and immune cells, with conserved neighborhood gene signatures across mouse and human. Within …

Hybrid Reference Genome Assembly For The Archetypal Leishmania (Viannia) Guyanensis Bearing The Dsrna Totivirus Lrv1, Peter J Myler, Gowthaman Ramasamy, Wesley C Warren, Deborah E Dobson, Stephen M Beverley

2020-Current year OA Pubs

We report a high-quality hybrid genome assembly and annotation for a

Genetic Deletion Of The Sodium Phosphate Cotransporter Napi2a Ameliorates Heart Failure In Mice, Hiroko Yamauchi-Sawada, Benjamin D Humphreys, Et Al.

2020-Current year OA Pubs

Apical membrane sodium transporters in renal proximal tubules, such as sodium-glucose co-transporter 2, are attractive therapeutic targets for the treatment of heart failure (HF). Sodium-phosphate co-transporter 2a (NaPi2a) is predominantly expressed in the apical membrane of proximal tubular epithelia and functions to reabsorb filtered phosphate and sodium. It currently remains unclear whether the inhibition of NaPi2a attenuates HF. We found that NaPi2a deficiency improved the cardiac phenotypes of the HF models of transverse aortic constriction (TAC) and doxorubicin (Dox) cardiotoxicity. Natriuretic and phosphaturetic effects were observed in NaPi2a-KO mice under normal conditions, resulting in low serum phosphate and fibroblast growth …

The Genetic Architecture Of Cervical Length Is Shared With Spontaneous Preterm Birth Risk, Hope M Wolf, Bradley T Webb, Jerome F Strauss 3rd, Adi L Tarca, Roberto Romero, Sonia S Hassan, Shawn J Latendresse, Tinnakorn Chaiworapongsa, Stanley Berry, Nardhy Gomez-Lopez, Piya Chaemsaithong, Timothy P York

2020-Current year OA Pubs

BACKGROUND: Sonographic cervical length is a powerful predictor of maternal risk for spontaneous preterm birth (sPTB). Twin and family studies have established a maternal genetic heritability for sPTB ranging from 13 to 20%, however, there is no corresponding estimate for the heritability of mid-trimester cervical length, or an understanding of how genetic factors contribute to cervical changes across pregnancy.

METHODS: This study was based on a prospective longitudinal cohort of (N = 5,160) Black/African American women who underwent serial sonographic examination of the uterine cervix during pregnancy and were genotyped via next-generation low-pass whole genome sequencing.

RESULTS: Bivariate genetic correlations …

Artificial Intelligence Algorithm Predicts Response To Immune Checkpoint Inhibitors, Faisal Fa'ak, Nicolas Coudray, George Jour, Milad Ibrahim, Irineu Illa-Bochaca, Shi Qiu, Adalberto Claudio Quiros, Ke Yuan, Douglas B Johnson, David L Rimm, Jeffrey S Weber, Aristotelis Tsirigos, Iman Osman

2020-Current year OA Pubs

PURPOSE: Cancer treatment has been revolutionized by immune checkpoint inhibitors (ICI). However, a subset of patients do not respond and/or they experience significant adverse events. Attempts to integrate reliable biomarkers of ICI response as part of standard care have been hampered by limited generalizability. We previously reported our supervised machine learning (ML) model in a retrospective cohort of metastatic melanoma.

EXPERIMENTAL DESIGN: In this study, we expanded our testing to include larger cohorts of patients with melanoma accrued at several sites, including patients enrolled in clinical trials in both adjuvant and metastatic settings. We examined pretreatment hematoxylin and eosin slides …

From Livestream To Table: Psychological Drivers Of Purchase Intention In Restaurant Livestreaming, Qingchuo Zhang, Rong Huang, Qian Chen, Jinhua Zhang

Plymouth Business School

Purpose – Restaurant livestreaming, where consumers interact with real-time digital content that promotesphysical dining experiences, has emerged as a distinctive form of digital marketing. It integrates onlineengagement with offline consumption in a novel way.Design/methodology/approach – Thisstudy builds upon the stimulus-organism-response (S-O-R) framework.It incorporates insights from flow theory and perceived value theory to examine how emotional immersion andcognitive evaluation influence consumer purchase intentions in the context of restaurant livestreaming.A structural model is then tested using survey data collected from 482 livestream consumers.Findings – Using a sequential mixed methods design, this study first identifies key environmental stimuli throughin-depth interviews. These stimuli include …

A Fluorescence Lifetime-Based Flim-Timer For Measuring The Protein Turnover Of Transcription Factor Nrf2 In Live Cells, Dina Dikovskaya, Claudia Bento-Pereira, Kanade Shiga, Andrea Corno, Maureen Higgins, Rachel Toth, Adrian T. Saurin, Albena T. Dinkova-Kostova

Peninsula Medical School

Measuring protein turnover in cells has been greatly assisted by fluorescent timers (FT). However, FT quantification requires relatively high fluorescence intensity samples, prohibiting their use for proteins with low or non-uniform expression like transcription factor Nrf2, the master regulator of redox homeostasis. To visualise changes in stability/turnover of Nrf2, we constructed a genetically encoded tag combining sfGFP and mCherry and used intensity-independent Fluorescence Lifetime Imaging (FLIM) to measure Förster Resonance Energy Transfer (FRET) within the tag (named FLIM-timer). We show that the ability of mCherry to act as a FRET-acceptor develops as the protein matures, allowing the use of FLIM-FRET …

“Of Their Women We Hear Less”: Pride And Prejudice In The Tale Of ‘Aldarion And Erendis.’, Sara Brown

Journal of Tolkien Research

In discussing J.R.R. Tolkien’s Second Age “Tale of the Mariner’s Wife,” past scholars have used descriptors such as ‘resentful’, ‘strong-willed’, ‘unhappy’ – even ‘misandrist’. There can be no doubt that this is a story of a deeply unhappy marriage between two people with irreconcilable differences, to use the modern parlance of the divorce courts, but it would also be true to say that Erendis seems to come out of the narrative with a more sullied reputation than her husband. In fact, Aldarion appears to have everything he could have wanted, such as his freedom to sail and an heir for …

Passive Precision Alignment For Thin-Panel Deployable Space Systems, Jake Sutton, Trevor Carter, Brooklyn Olson, David Wing, Fisk Lungreen, Larry Howell, Nathan Usevitch, Spencer Magleby, Mark Stephen

Small Satellite Conference

Optical satellite performance improves with increased surface area, which enhances light capture and sensor input. Deployable mechanisms allow satellites to remain compact during launch and expand in orbit but the large relative motion during deployment makes it difficult to achieve precision alignment in the final deployed state. This study focuses on designing passive hinges in rigid-panel origami-based deployable satellites for optical applications. A novel kinematic coupling method is developed, incorporating magnets, compact Lamina Emergent Torsional (LET) joints, and principles from Maxwell couplings. This system autonomously achieves alignment without motorized actuation. The design process involved iterative testing of ten two-panel hinge …

A Ka Band High Data Rate Transmitter For Leo Satellites Design And System Simulation, Jean-Hervé Corre, Ronan Foubert, Thomas Dehaene, Hugo Hartmann, Yann Prigent, Bertrand Lechevalier

Small Satellite Conference

This paper addresses the design of a high-throughput Ka-band transmitter for LEO satellites. This article particularly focuses on RF and microwave subsystems and system simulation.

The purpose of this transmitter (named KaLLISTO) is to operate the downlink from a LEO satellite to a ground station. High data rates are required to meet the expressed demand from satellite operators to enable much more data volume downlink. The equipment is the latest state-of-the-art qualified COTS based design. This design is perfectly adapted to New-Space programs, where cost effectiveness, performance and reliability are key factors. The allocated band goes from 25.5 to 27GHz …

Stari: Starlight Acquisition And Reflection Toward Interferometry, John D. Monnier, James Cutler, Michael Meyer, Caden Burkhardt, Akshat Dubey, Jacob Klingler, Raven St. Clair, Shivani Sunil, Daniil Voloshin, Leonid Pogorelyuk, Melissa Flores, Albert Ostoja-Starzewski, Simone D'Amico, Ethan Foss, Prachet Jain, Antonio Rizza, E. Glenn Lightsey, Althea Noonan, Kerri Cahoy, Gautam Vasisht

Small Satellite Conference

We introduce the NASA-funded mission STARI (STarlight Acquisition and Reflection toward Interferometry). We plan to demonstrate the first transfer of starlight between two separate spacecraft, a key technology step towards long-baseline interferometry. Consisting of two propulsive 6U CubeSats flying in Low Earth Orbit separated by ∼100 meters, STARI will reflect a small beam of starlight from the Chief spacecraft toward the Deputy spacecraft, where the light will be collected by an off-axis parabola and focused into a single-mode fiber. With the use of differential Global Positioning System (GPS), visual LED beacons and fast-steering-mirrors (FSMs), we aim for continuous high-throughput fiber …

Spacecraft-Initiated Scheduling Of Ground Stations: On-Orbit Results From Techedsat-11, Adam Gannon, Timothy Recker, Lucas Shalkhauser, Rachel Dudukovich, Janette Briones, Alejandro Salas, Malachi Mooney-Rivkin, Marcus Murbach

Small Satellite Conference

The commonplace practice of manually scheduling communications is challenged by complex and often unpredictable data needs of modern spacecraft. Automation has clear benefits to improve timeliness and efficiency of space communications. In this work we describe and experimentally demonstrate a suite of software which automates the process of scheduling contacts for satellite communications. Service is scheduled based on a spacecraft’s needs and contacts execute automatically without a human in the loop. Requests for service originate onboard the spacecraft, traverse a low-rate control channel to reach a terrestrial server, and are fulfilled by ground station assets. This work describes an experiment …