Digital Commons Network^™

Unraveling The Hidden Complexity Of Cancer Through Long-Read Sequencing, Qiuhui Li, Ayse G Keskus, Justin Wagner, Michal B Izydorczyk, Winston Timp, Fritz J Sedlazeck, Alison P Klein, Justin M Zook, Mikhail Kolmogorov, Michael C Schatz

Faculty, Staff and Students Publications

Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the genome, transcriptome, and epigenome, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long-read sequencing for both …

Proteogenomic Characterization Of Non-Functional Pancreatic Neuroendocrine Tumors Unravels Clinically Relevant Subgroups, Shunrong Ji, Lihua Cao, Jing Gao, Yang Du, Zeng Ye, Xin Lou, Fen Liu, Yehan Zhang, Junfeng Xu, Xiaohan Shi, Huan Wang, Penghao Li, Yikai Li, Hongxu Chen, Zhicheng Yang, Suizhi Gao, Wuhu Zhang, Dan Huang, Shujuan Ni, Miaoyan Wei, Fei Wang, Yan Wang, Tian Ding, Desheng Jing, Guixiong Fan, Zhiyun Gong, Renquan Lu, Yi Qin, Jie Chen, Xiaowu Xu, Pei Wang, Bing Zhang, Li Ding, Ana I Robles, Henry Rodriguez, David K Chang, Ralph H Hruban, Dong Gao, Daming Gao, Gang Jin, Hu Zhou, Jianmin Wu, Xianjun Yu

Faculty, Staff and Students Publications

The majority of neuroendocrine neoplasms in pancreas are non-functional pancreatic neuroendocrine tumors (NF-PanNETs), which exhibit a high occurrence of distant metastases with limited therapeutic options. Here, we perform a comprehensive molecular characterization of 108 NF-PanNETs through integrative analysis of genomic, transcriptomic, proteomic, and phosphoproteomic profiles. Proteogenomic analysis provides functional insights into the genomic driver alterations of NF-PanNETs, revealing a potential mediator of MEN1 alterations using Men1-conditional knockout mice. Machine-learning-based modeling uncovers a three-protein signature as an independent prognostic factor, which is validated by an independent external cohort. Proteomic and phosphoproteomic-based stratification identifies four subtypes with distinct molecular characteristics, immune microenvironments, …

Integrating Short-Read And Long-Read Single-Cell Rna Sequencing For Comprehensive Transcriptome Profiling In Mouse Retina, Meng Wang, Yumei Li, Jun Wang, Soo Hwan Oh, Yexuan Cao, Rui Chen

Faculty, Staff and Students Publications

The vast majority of protein-coding genes in the human genome produce multiple mRNA isoforms through alternative splicing, significantly enhancing the complexity of the transcriptome and proteome. To establish an efficient method for characterizing transcript isoforms within tissue samples, we conducted a systematic comparison between single-cell long-read and conventional short-read RNA sequencing techniques. The transcriptome of approximately 30,000 mouse retina cells was profiled using 1.54 billion Illumina short reads and 1.40 billion Oxford Nanopore Technologies long reads. Consequently, we identify 44,325 transcript isoforms, with a notable 38% previously uncharacterized and 17% expressed exclusively in distinct cellular subclasses. We observe that long-read …

Challenging Race-Based Health Care Discrimination: A New Private Right Of Action, Aaron Pinkett

Northwestern University Law Review

The Hippocratic Oath calls on doctors to “do no harm.” Yet we know from extensive public health research that clinicians repeatedly cause harm to Black patients by dismissing their medical concerns, misdiagnosing them, and undertreating their pain. These practices of differential treatment for Black patients have led to steadily increasing racial disparities in health care outcomes throughout the United States. Title VI of the Civil Rights Act of 1964 prohibits this type of disparate impact, but modern Supreme Court jurisprudence forecloses opportunities for affected parties to seek legal relief—despite the clearly established legislative intent of Title VI. However, another legal …

Hindsight Is 20/20: Epilepsy Is Not One-Size-Fits-All, Raika Kim

Northwestern University Law Review

For many, epilepsy is one of the first conditions that come to mind when thinking of a disability, and for good reason: over 50 million people in the world live with epilepsy. Yet misunderstandings about epilepsy have perpetuated social stigma surrounding the disability for centuries. Ableist beliefs led to the passage of laws in the 1900s condoning—and in some cases, requiring—sterilization of individuals with epilepsy and restriction of their right to marry. Even today, state driving laws, justified as promoting public safety, categorically prevent anyone diagnosed with epilepsy from driving unless they are seizure free for an arbitrary, nonuniform period …

The Impact Of Paternal Obesity On Placental Development And Function During Pregnancy, Delaney G. Wolfe, Delaney G. Wiolfe

Department of Nutrition Student Projects

Paternal obesity is a rising concern in conception and reproductive health, with increasing evidence suggesting its impact on pregnancy outcomes. While maternal obesity's effects on fetal development and placental function are well-documented, the role of paternal obesity remains less understood. The placenta, crucial for nutrient exchange and fetal development, can be disrupted by inflammation, oxidative stress, and epigenetic modifications, potentially leading to long-term health implications for both maternal and fetal health. Understanding the paternal influence on placental development is essential for improving pregnancy outcomes and offspring
health. This study aims to investigate the relationship between paternal obesity on placental function …

Gender Myths & Colonial Lies, Sophie Camilleri

Honors Papers and Posters

The gender binary is deeply ingrained in today's society, despite a general lack of knowledge on where this system originates from. It is crucial to counter misinformation stemming from propaganda and fear campaigns surrounding the gender binary. This research sheds light on the oppressive roots of gender, as well as its role in the colonization of marginalized individuals around the globe. This paper will make connections to present day systems of oppression and the long-term effects of colonization on Black and Hispanic women.

Climate Exceptionalism In Court, Zachary D. Clopton, David A. Dana

Northwestern University Law Review

Across a range of cases, fossil fuel companies, government actors, and some judges have conceded that climate change is an exceptional phenomenon, only to argue that its exceptional nature is a reason to keep climate change out of court. These parties and judges thus seek to avoid the adjudication of climate cases on the merits, even when the neutral application of existing law would provide for jurisdiction in these cases. We term this phenomenon “climate jurisdiction exceptionalism.”

This Article provides a comprehensive account of climate jurisdiction exceptionalism, focusing on two main threads: Article III standing and state court jurisdiction. First, …

Region-Specific Roles Of Oviductal Motile Cilia In Oocyte/Embryo Transport And Fertility†, Deirdre M Scully, Tian Xia, Guzel R Musina, Michaela A Mccown, Kohei Umezu, Bonnie K Kircher, Richard R Behringer, Irina V Larina

Faculty, Staff and Students Publications

The physiological and clinical importance of motile cilia in reproduction is well recognized; however, the specific role they play in transport through the oviduct and how ciliopathies lead to subfertility and infertility are still unclear. The contribution of cilia beating, fluid flow, and smooth muscle contraction to overall progressive transport within the oviduct remains under debate. Therefore, we investigated the role of cilia in the oviduct transport of preimplantation eggs/embryos using a combination of genetic and advanced imaging approaches. We show that the region of the oviduct where cumulus-oocyte complex circling occurs, around the time of fertilization, is correlated with …

Pilot First-In-Human Ccr2 Pet/Ct To Detect Abdominal Aortic Aneurysm Wall Instability, Santiago Elizondo-Benedetto, Deborah Sultan, Ryan Wahidi, Mahdjoub Hamdi, Mohamed S Zaghloul, Shahab Hafezi, Batool Arif, Laura K Mcdonald, Kitty Harrison, Dakkota Thies, Gyu Seong Heo, Hannah Luehmann, Lisa Detering, J Westley Ohman, Zachary J Wanken, Luis A Sanchez, Joseph E Ippolito, Jie Zheng, Robert J Gropler, Richard Laforest, Yongjian Liu, Mohamed A Zayed

2020-Current year OA Pubs

No abstract provided.

Spreading Depolarization And Seizures: End Of The Beginning, Or Beginning Of The End?, Isamu Aiba, Jeffrey L Noebels

Faculty, Staff and Students Publications

Like Janus, the Roman god of beginnings, transitions, and endings, spreading depolarizations (SDs) can be depicted with two faces: one looking backward, waving a symbolic farewell to the end of a cortical seizure; the other forward looking, opening a darker door for a fatal wave in the brainstem that ends life. There is good agreement on the distinct electrical nature of both events, but neither role is yet proven in patients. SD is a slow-moving wave of cellular depolarization that steadily silences neuronal networks and depresses EEG amplitude, whereas seizures represent fast, intermittent synchronization of neural networks with highly variable …

Cryptic Species Diversity Within The Andes Frog Phrynopus Juninensis (Shreve, 1938) From Peru, Sam Voss

John Wesley Powell Student Research Conference

The frog genus Phrynopus resides in Peru's upper montane forest and supra-treeline grasslands. It is characterized by its lack of a tympanum, narrow digits, and usual lack of dentigerous process of vomers. The genus includes 37 distinct species that reproduce with terrestrial eggs. Previous molecular research revealed that the genus Phrynopus contains a new undescribed species previously thought to be Phrynopus juninensis. Phrynopus juninensis is characterized by its large size, strong supratympanic fold, and unique coloration; it is distributed in the Cordillera Oriental in Central Peru between 3420-3850 m in elevation. Its snout-vent length ranges between 22.0 to 30.6 mm …

Ingestion Of Cyanobacteria (Vulcanococcus Sp.) By The Rotifer Plationus Patulus, Aug Ningombam

John Wesley Powell Student Research Conference

Rotifers are small (≤ 1 mm) aquatic animals that live in freshwater and marine environments where they act as both predator and prey and serve as important members of food webs. Rotifers consume different forms of particulate foods and, depending on the species, may ingest bacteria, protists, phytoplankton, and other zooplankton. Recent increases in global temperature coupled with fertilizer runoff from agricultural and municipal lands have resulted in increases in the distribution and abundance of cyanobacteria in freshwater environments; under certain conditions cyanobacteria populations can experience explosions (blooms) where cell concentrations can exceed 105 / mL. We evaluated the ability …

Robust Inner Knuckle Print Recognition System Using Densenet201 And Inceptionv3 Models, Haitham Salman Chyad, Tarek Abbes

Iraqi Journal for Computer Science and Mathematics

Texture features and stability have generated significant interest in biometric recognition. The inner knuckle print is distinctive and difficult to fake, making it extensively used in individual identification, criminal investigation, and various other domains. In recent years, the rapid progress of deep learning technology has created new prospects for internal knuckle recognition. This paper proposes a robust inner-knuckle-print recognition system (RIKP-RS) depending on two deep learning (DL) models. This paper focuses on the key components of the inner surface of the hand namely the little finger, ring finger, middle finger, index finger, and thumb finger that are used for human …

Solving Multidimensional Fractional Telegraph Equation By Using Yang Hussein Jassim Method, Naser Rhaif Swain, Hassan Kamil Jassim

Iraqi Journal for Computer Science and Mathematics

This study employs the Young Hussein Jassim (YHJ)technique to examine the exact solutions of the space-time telegraphequation analytically (ST-TE). The YHJ approach is an innovative andappealing hybrid transformation integration method, effectivelycombining the HJ and Young methods. Through a simplified iterativeprocess with minimal computational requirements, this approach quicklyprovides convergent, sequential solutions. The reliability of the methodis demonstrated by applying it to two case studies of the ST-TE withinthe framework of the Tania derivative, which includes the definition ofnon-singular kernel functions. The study also includes extensivecomparisons between approximate, exact, and relevant literature-basedsolutions to assess the technique's accuracy andeffectiveness. Graphical representations illustrate the …

A Lightweight U-Net Model For Accurate Skin Lesion Segmentation, Fallah H. Najjar, Karrar A. Kadhim, Farhan Mohamed, Mohd Shafry Mohd Rahim, Asniyani Nur Haidar Abdullah

Iraqi Journal for Computer Science and Mathematics

In this paper, a new lightweight U-Net deep learning-based neural network designed for the segmentation of skin lesions is proposed. Segmentation of skin lesions is the most critical step in computer-aided dermatology diagnosis for the early detection of melanoma and other diseases. However, we address the difficulty related to the precise definition of the lesion margins with an eye on the computation cost. We have demonstrated the state-of-the-art performance of DeepSkinSeg in most metrics on dermoscopic images using the PH2 and Human Against Machine (HAM10000) datasets. The metrics of the DeepSkinSeg model were robustness measured as the Intersection over Union …

Optimizing Transcutaneous Spinal Cord Stimulation: An Exploratory Study On The Role Of Electrode Montages And Stimulation Intensity On Reflex Pathway Modulation, Shirin Madarshahian, Michael Trakhtorchuck, Tatiana Guerrero, Kristin Gustafson, James Harrop, Caio Matias, M. J. Mulcahey, Alessandro Naopli, Alex Vaccaro, Mijail Serruya

Farber Institute for Neuroscience Faculty Papers

Transcutaneous spinal cord stimulation (tSCS) is a promising non-invasive method to improve motor function in individuals with spinal cord injury (SCI) by enhancing spinal reflex pathways. This study aimed to investigate the effects of different tSCS electrode placement montages and targeted spinal levels on neurophysiological responses such as spinally evoked motor responses (sEMRs), dorsal root reflex activation, and muscle recruitment in individuals with SCI and healthy controls to optimize stimulation strategies for motor recovery. Five participants (three individuals with SCI and two controls) underwent transcutaneous spinal cord stimulation using various electrode montages, target spinal level stimulation, and single- and paired-pulse …

Giving Day 2025 Generates $1.3 Million For Ole Miss, Tina H. Hahn

University of Mississippi News

OXFORD, Miss. – When the last online donation came through on Wednesday (April 9) for Giving Day 2025, 2,685 donors had combined to give $1.34 million to bolster the University of Mississippi.

The Effect Of Topping And Various Cytokinin-Based Plant Growth Regulators Applications On Immature Liberica Coffee Growth, Yudithia Maxiselly, Joshua Samuel, Cucu Suherman

Jurnal Kultivasi

The growth of Liberica coffee in the 2-year immature plant phase can be improved by applying cytokinin-based plant growth regulators (PGRs) and topping. Toppings applied to plants can inhibit apical dominance, while cytokinin PGRs such as 6-Benzylaminopurine (BAP) and coconut water can stimulate plant shoot growth. This research aims to determine the effect of topping and PGR application on the vegetative growth of Liberica coffee plants. This experiment was carried out at the Ciparanje experimental field, Universitas Padjadjaran, West Java, with an elevation of ± 750 meters above sea level from March to June 2024. The experimental design used a …

The Effect Of Soil Conditioner And Growth Booster On The Agronomic Characters And Number Of Nodules Of Black Soybean, Tien Turmuktini, I Putu Rahmat Santoso, Lia Amalia, Nunung Sondari, Elly Roosma Ria, Yenny Muliani, Endang Kantikowati, Tualar Simarmata

Jurnal Kultivasi

Soil Conditioner & Growth Booster (SCGB) is a potion that was made to be used as a soil conditioner and plant growth promoter. SCGB is made from organic matter, biological fertilizers, soil ameliorants, and microelements. This research aims to determine the best dosage of SCGB on the agronomic characters, effective nodules, and black soybean variety ‘Detam-1’ yield. This research was conducted in the experimental field of the Faculty of Agriculture, Winaya Mukti University, Sumedang, Indonesia. This experiment used a simple randomized block design (RBD) with six treatments (0, 3, 6, 9, 12, 15 kg/ha) and repeated 4 times. The observation …

Heterologous Expression Of Maize-Derived Antimicrobial Peptide Zmes4 In Escherichia Coli For Potential Plant Pathogen Control, Suseno Amien, Dadi Nurdiana, Noor Istifadah, Noladhi Wicaksana, Haifanisa Salsabila

Jurnal Kultivasi

ZmES4 is a plant-derived antimicrobial peptide (AMP) from maize that shows promise as a biocontrol agent against plant pathogenic organisms. In the context of growing challenges in sustainable agriculture, AMPs like ZmES4 represent innovative alternatives to chemical pesticides. This study focuses on the structural characterization and heterologous expression of the ZmES4 peptide in Escherichia coli (E. coli). The gene encoding ZmES4 was obtained from the maize female gametophyte (NCBI Reference Sequence: NM_001112150.3) and cloned into the pET24d(+) expression vector using NcoI and XhoI restriction sites. Transformation into E. coli BL21 (DE3) cells enabled recombinant expression upon induction with isopropyl β-D-1-thiogalactopyranoside …

Evaluation Of Thermotherapy On Potato Tubers To Control Tuber-Borne Nematodes, Meloidogyne Spp, Wawan Kurniawan, Supramana, Abdul Munif, Giyanto

Jurnal Kultivasi

Root knot nematodes (Meloidogyne spp.) are significant plant-parasitic nematodes frequently transmitted through potato tubers and are a major factor contributing to the decline in both crop quality and yield. This study aims to evaluate the effectiveness of thermotherapy for eliminating Meloidogyne spp. from potato tubers and its impact on sprouting viability. Thermotherapy was conducted by immersing potato tubers and second-stage juveniles (J2) of Meloidogyne spp. in water at temperatures of 50 °C, 52.5 °C, 55 °C, and 60 °C for durations ranging from 5 to 75 minutes, depending on the treatment. Parameters observed included the mortality rate of Meloidogyne spp. …

The Antimicrobial Resistance-Water-Corporate Interface: Exploring The Connections Between Antimicrobials, Water, And Pollution, Jason P Burnham

2020-Current year OA Pubs

Antibiotic resistance is a public health emergency, with ten million deaths estimated annually by the year 2050. Water systems are an important medium for the development and dissemination of antibiotic resistance from a variety of sources, explored in this perspective review. Hospital wastewater and wastewater systems more broadly are breeding grounds for antibiotic resistance because of the nature of their waste and how it is processed. Corporations from various sectors contribute to antibiotic resistance in many direct and indirect ways. Pharmaceutical factory runoff, agricultural antibiotic use, agricultural use of nitrogen fertilizers, heavy metal pollution, air pollution (atmospheric deposition, burning of …

Abstract Book (Pdf), School Of Medicine

Medicine Research Day

The collection of abstracts for all three sections of the 2025 Medicine Research Day organized by session (Translational Research, Quality Improvement, Clinical Vignettes) then alphabetical by last name of the primary author.

Microlocal Litigation For A Mass Tort World, Sarah L. Swan

DePaul Law Review

No abstract provided.

Physicists As Environmental Experts, Rachel Rothschild

DePaul Law Review

No abstract provided.

Between Science And Administration: Regulatory Epistemology, Corporate Influence, And Endocrine-Disrupting Chemicals, Colleen Lanier-Christensen

DePaul Law Review

No abstract provided.

Industrywide Corruption In Three American Industries, Stephan Landsman

DePaul Law Review

No abstract provided.

Farm Until It’S Gone: Industrial Animal Agriculture And The Limits Of Law, Douglas A. Kysar

DePaul Law Review

No abstract provided.

The Fractography Of Bone: Impact Of Flat Bone And The Story It Tells, Abigail Hoffmeister, Chase Freeman, Brandon Mendoza, Nathaniel Fitch, Annie Markarian, Jack Tran, Joshua Lau, Nicholas Tran

Seaver College Research And Scholarly Achievement Symposium

Fractography as a method for fracture analysis has been applied widely to materials that range from glass to ceramics and polymers of varying compositions. Very limited research has been done, however, to apply this knowledge of fractography and fracture patterns to bone. With the goal of telling the story of how a bone was broken, this research focuses on observing known patterns of fracture in polymers, and applying these patterns to bone. For the purposes of this research, porcine scapulae were acquired, dissected from surrounding tissue, and broken using a standardized weight drop at varying heights. The fractured bone was …