Digital Commons Network^™

Characterization Of Water Intake And Water Conversion Ratio For Male And Female Broilers From Four Commercial Broiler Lines Reared To Eight Weeks Of Age, J.Z. Hiltz, C.W. Maynard, T.W. Tabler, M.A. Maquesda, K.M. Shafer, K.B. Nelson, M.T. Kidd, N.B. Anthony, S.K. Orlowski-Workman

Poultry Science Faculty Publications and Presentations

Increased interest and investigation into the sustainability of broiler production has led to a need for reliable and repeatable means to measure water intake and its conversion rate into salable meat. Therefore, a study was conducted to characterize the water intake and water conversion ratio (WCR) of male and female broilers from four modern broiler strains. Two of these lines represented fast growing broiler strains (FGB A and FGB B) targeting a small bird market and two represented high yielding broiler strains (HYB A and HYB B). Three replicates of 25 sexed broilers from each line were placed into 24 …

The Economics Of Us Row Crop Production With Large-Scale Autonomous Machines, Joshua Strine, Chad Fiechter, James Lowenberg-Deboer

Department of Agricultural Economics Faculty Publications

Labor challenges are underpinning large multinational farm machine manufacturers' development of autonomy solutions for their large-scale machine offerings. This study simulates a linear optimization model to examine the economics of large-scale autonomous machines for a rotational maize and soybean farm in the Midwest US. Results support the hypothesis that autonomous machines can be economically viable for farms facing severe labor shortages. However, under current technology and pricing structures, conventional mechanization remains the most profitable option for farms with reliable labor. Critical factors shaping the competitiveness of autonomy include subscription fees, field efficiency, and human supervision requirements. As these factors evolve, …

Farm Efficiency And Precision Agriculture Technology, Chad Fiechter, Brady Brewer, Jennifer Ifft, Michael Boehlje

Department of Agricultural Economics Faculty Publications

Precision agriculture technology (PAT) is often viewed as a potential driver of future efficiency gains in farming. Using within-farm variation from an unbalanced panel of Kansas farms, this study examines the impact of PAT bundles on efficiency in generating gross revenue. On average, we find little evidence that these technologies improve efficiency. However, among less efficient farms, several bundles are linked to notable efficiency gains, underscoring the importance of accounting for farm heterogeneity.

Freshwater Turtle Assemblages And Densities In Agricultural Ditches And Aquaculture Ponds Of Eastern Arkansas, Andrhea D. Massey, John D. Willson, Brett A. Degregorio

Biological Sciences Faculty Publications and Presentations

The Mississippi Alluvial Plain (MAP) of Arkansas is a landscape where many wetlands have been altered for use as aquaculture ponds or agricultural ditches. Commercial harvest of freshwater turtles within the MAP is not restricted or limited, with reported harvest numbers for 2019 alone exceeding 4000 for spiny softshell turtles (Apalone spinifera) and 39,000 for red-eared sliders (Trachemys scripta elegans). Herein, we attempt to provide baseline estimates of freshwater turtle densities and community composition in aquaculture ponds and agricultural ditches of eastern Arkansas, the habitat types most frequently trapped by commercial harvesters. We used a capture-mark-recapture approach over 3 summers …

An Open Letter To Leslie, Anne G. Kinne Phd

Journal of Conscious Evolution

This article celebrates the life and work of dear friend and mentor, Allan Leslie Combs, acknowledging his continued presence in my life. Interweaving stories of our relationship with his insights on integral consciousness, Bateson’s concept of aphanipoiesis, Varela et al.’s notion of autopoiesis, and using narrative, storytelling, and autoethnographic methodologies, I tell a tale of becoming that troubles and haunts my past. The sticky tendrils of Ancestral trauma and its transhistorical epigenetic inheritance, once acutely troublesome, are shifting due in large part to the contents of this letter. Woven together, these conscious, intersecting, and interactive lenses show how Leslie has …

Lilrb4 Regulates Circadian Disruption-Induced Mammary Tumorigenesis Via Non-Canonical Wnt Signaling Pathway, Olajumoke Ogunlusi, Mrinmoy Sarkar, Kayla Carter, Arhit Chakrabarti, Devon J Boland, Tristan Nguyen, James Sampson, Christian Nguyen, Danielle Fails, Yava Jones-Hall, Loning Fu, Gus Wright, Da Mi Kim, James J Cai, Bani Mallick, Alex C Keene, Jeff R Jones, Tapasree Roy Sarkar

Faculty, Staff and Students Publications

Epidemiological studies have shown that circadian rhythm disruption (CRD) is associated with the risk of breast cancer. However, the role of CRD in mammary gland morphology and aggressive basal mammary tumorigenesis and the molecular mechanism underlying CRD-induced carcinogenesis remain unknown. To investigate the effect of CRD on aggressive tumorigenesis, a genetically engineered mouse model of aggressive breast cancer was used. The impact of CRD on the tumor microenvironment was investigated using the tumors from LD12:12 and CRD mice via scRNA-seq, flow cytometry, multiplexing immunostaining, and realtime PCR. The effect of LILRB4-immunotherapy on CRD-induced tumorigenesis was also investigated. Here we investigated …

Uncovering The Diversity Of Bats In The Mbam Minkom Massif, Cameroon: Insights Into The Importance Of Tropical Inselbergs, Amanda L. Grunwald, Terrence C. Demos, Patrick J. Atagana, Courtney M. Volk, Ara Monadjem, Franck P. Meyo Konoo, Yvette Ngueagni, R. Travis Merrill, Daniel J. Ballhorn, Luis A. Ruedas, Multiple Additional Authors

Biology Faculty Publications and Presentations

We report the results of two expeditions (2019 and 2022) to the Mbam Minkom Massif (Centre Region, Cameroon), focused on an assessment of the montane area's bat fauna. We describe bat species' richness and highlight the incredible diversity and ecological importance of this highly threatened ecosystem. Across both years, we captured a total of 36 bat species representing 21 genera and six families on Mbam Minkom Massif and in the surrounding lowland forest. Our findings include two new species records for Cameroon, and two additional records of the recently described bat, Pseudoromicia mbamminkom. We provide accounts for all captured species, …

Differential Microrna Profiling Of Blood L1cam And Bulk Extracellular Vesicles In Bipolar Disorder, Gabriel R Fries, Salahudeen Mirza, Jun Wang, Camila N C Lima, Wei Zhang, Marcela Carbajal Tamez, Giselli Scaini, Jair C Soares, Joao Quevedo

Faculty, Staff and Student Publications

Objective: This preliminary study aimed to identify microRNA (miRNA) signatures associated with bipolar disorder (BD) by profiling blood-derived extracellular vesicles (EVs) of both putative neuronal origin and from all sources.

Method: In two parallel studies of individuals with BD and controls (CON), we characterized miRNA expression profiles of blood EVs selected for L1CAM, a putative marker of neuronal origin (n = 20 BD/20 CON), as well as bulk EVs (n = 21 BD/20 CON). For each study, analyses identified miRNAs differentially expressed between groups, followed by functional interrogation and testing for associations with clinical features.

Results: Results of …

Sleep-Disordered Breathing Subtypes And Future Diet Quality In The Multi-Ethnic Study Of Atherosclerosis, Kaitlin S Potts, Cecilia Castro-Diehl, Tianyi Huang, Alexis C Wood, Jerome I Rotter, Stephen S Rich, Tamar Sofer, Susan Redline, Heming Wang

Children’s Nutrition Research Center Staff Publications

Objectives: Sleep-disordered breathing (SDB) and diet quality impact cardiometabolic disease, but few studies have examined if SDB influences diet quality. This study estimated the association between SDB subtypes (with and without sleepiness) and future diet quality in the Multi-Ethnic Study of Atherosclerosis.

Methods: Probable SDB was characterized by self-reported physician-diagnosed sleep apnea (PDSA) or habitual snoring and subtyped by presence or absence of sleepiness. A food frequency questionnaire measured diet 1.6 years before, and 7.8 years after SDB assessment. Diet quality was measured with the Alternate Healthy Eating Index-2010 (AHEI). Mean differences in AHEI at follow-up by SDB subtypes were …

Cutting Edge Developments In Bone Oncology – Highlights From The Cancer And Bone Society 2024 Annual Meeting, Deanna N Edwards, Shreya Patel, Gabriel M Pagnotti

Faculty, Staff and Student Publications

The 2024 Annual Conference of the Cancer and Bone Society (CABS), held jointly with the Bone Research Society at the University of Sheffield, highlighted the Society's enduring mission to advance understanding of cancer-bone interactions through collaboration, mentorship, and scientific excellence. Established from the early Cancer Induced Bone Disease meetings and re-emerging as an independent body in 2016, CABS continues to serve as a global community bridging basic, translational, and clinical research. This year's meeting featured a comprehensive scientific program spanning tumor-bone biology, therapeutic innovation, and microenvironmental regulation. Clinical sessions emphasized the evolution of bone-targeted treatments such as bisphosphonates, denosumab, and …

The Microstructure Of Metastatic Bone Lesions Suggests Tumor Mediated Alterations In Bone Mineralization, Hanwen Fan, Zhan Xu, Carla Berrospe Rodriguez, Noah Dover, Andrei Demkov, Morgan Lilly, Guillermo Aguilar, Larry J Suva, Xiang H-F Zhang, Yuxiao Zhou

Faculty, Staff and Students Publications

Breast, prostate and lung cancer cells frequently metastasize to bone, leading to disruption of the bone microstructure. This study utilized mechanical testing coupled with micro-CT imaging, digital volume correlation (DVC), and atomic force microscopy (AFM) nanomechanical testing to examine the mechanical property variations in mouse long bones (tibia) with metastatic lung cancer cell involvement, spanning from the whole-bone scale to the microstructural level. In addition, we also investigated how metastatic invasion alters the morphology of hydroxyapatite nanocrystals in bone at the nanometer scale. The biochemical composition within metastatic lesions was assessed using Raman spectroscopy and correlated with AFM mechanical testing …

Genetic Variations In Extracellular Matrix Degradation Pathways Linking To Major Depressive Disorder: Evidence From A Large-Scale Genetic Association Study, Halliru Zailani, Daniel Tzu-Li Chen, Sheng-Che Lin, Jia-Hau Lee, Mei-Ling Li, Jane Pei-Chen Chang, Kuan-Pin Su

BioMedicine

Dysregulation of extracellular matrix (ECM) degradation pathways has been increasingly implicated in major depressive disorder (MDD), yet its genetic basis remains unclear. This study investigated the relationship between ECM-related genetic polymorphisms and MDD susceptibility. In a case-control study, we analyzed 317 MDD patients and 1,268 sexmatched controls from the Taiwan Biobank (TWB). Genomic DNA was analyzed using the Affymetrix TWB array, targeting single nucleotide polymorphisms (SNPs) in 140 ECM degradation genes (Reactome database). Full-model association tests identified significant SNPs, validated with 5,000 max(T) permutations and adjusted via logistic regression for age, body mass index, education level, and marital status. We …

Neuroprotection Of Paeoniflorin As Antidepressant Candidate, Yuh-Fung Chen, Yi-Jui Chen, Jai-Sing Yang, Min-Min Lee, Huei-Yann Tsai

BioMedicine

Background: Depression is one of the common mental disorders worldwide, and currently used antidepressants have undesirable effects; therefore, the development of new antidepressants without side effects is urgently needed. Paeoniflorin (PF) exhibits various pharmacological activities, including anti-inflammatory, antioxidant, and neuroprotective effects. NMDA receptors in the hippocampus play a vital role in the pathophysiology of depression. Due to the scarcity of reports on the neuroprotection of PF on NMDA-induced excitotoxicity in the hippocampus, the present study aims to investigate the effects of PF on NMDA-mediated EPSP and calcium influx in the hippocampus to evaluate the potential of PF as an antidepressant. …

Prophylactic Effect Of Omega-3 Polyunsaturated Fatty Acids Monotherapy In Preventing Recurrent Major Depressive Disorder: A Randomized Controlled Trial, Ikbal Andrian Malau, Cheng-Ho Chang, Wei-Jen Chen, Wen-Chun Liu, Halliru Zailani, Hsien-Feng Liao, Jane Pei-Chen Chang, Wei-Che Chiu, Kuan-Pin Su

BioMedicine

Background: Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have demonstrated efficacy as adjunctive treatment for MDD. In fact, fewer studies assessed the prophylactic properties of n-3 PUFAs as monotherapy on the recurrence of MDD.

Aims: This study aimed to assess the prophylactic effect of n-3 PUFAs monotherapy against recurrent MDD.

Methods: We conducted a 6-month randomized controlled trial to assess the prophylactic effect of n-3 in preventing recurrent MDD. We assigned 60 remitted MDD patients to the n-3 group (n = 30) and placebo (n = 30). Furthermore, we assessed the difference in depression severity and MDD recurrence based on the …

Tai Chi For Cardiovascular Wellness: Integrating An Ancient Practice Into Modern Therapeutic Approaches, Chun-Han Cheng, Wen-Rui Hao, Huan-Yuan Chen, Po-Yuan Chen, Ju-Chi Liu, Tzu-Hurng Cheng

BioMedicine

Tai Chi, a traditional Chinese martial art characterized by gentle, fluid movements and deep breathing, has gained increasing recognition for its cardiovascular health benefits. This study investigated the integration of Tai Chi into contemporary cardiovascular health practices, focusing on its physiological and psychological effects. The slow, controlled movements characteristic of Tai Chi contribute to enhanced cardiovascular fitness, decreased blood pressure, and improved vascular function, while simultaneously alleviating stress and fostering emotional well-being. Through a review of clinical studies and trials, this study underscores the efficacy of Tai Chi in cardiovascular rehabilitation programs and its accessibility as a community-based intervention. Additionally, …

Circadian Rhythms And Neuroendocrine Dysregulation In Adhd: Therapeutic Insights From Omega-3 Fatty Acids, Ayesha Zafar Iqbal, Patricia Marest Suwindi, Sunny Yin-Shan Chen, Lindsay Liang-Tien Cho, Kuan-Pin Su, Jane Pei-Chen Chang

BioMedicine

Attention-deficit hyperactivity disorder (ADHD) is a common neurodevelopmental condition often accompanied by circadian rhythm disturbances, particularly delayed sleep phase. These involve superchiasmatic nucleus (SCN) dysregulation, altered melatonin secretion, and hypothalamic–pituitary–adrenal (HPA) axis activity, which may be exacerbated by artificial light exposure. Genetic studies further implicate circadian mechanisms, linking ADHD with polymorphisms in clock genes such as PER and CLOCK.

Nutraceuticals, particularly omega-3 polyunsaturated fatty acids (n-3 PUFAs), have been proposed as modulators of circadian rhythms. N-3 PUFAs are essential for brain health and may influence melatonin synthesis and sleep–wake regulation. Preclinical and clinical findings suggest that supplementation can improve cognitive …

The Integrative Role Of Melatonin In Psychiatric Disorders: A Systematic Review Of Evidence From Circadian Biology, Lifestyle Medicine, And Psychoneuroimmunology, Ho Bao Chau Le, Kollawat Somsri, Thansita Bhunyakarnjanarat, Nattiya Hirankarn, Asada Leelahavanichkul

BioMedicine

Melatonin, a hormone produced by the pineal gland, is known for regulating circadian rhythms and has emerging therapeutic potential in psychiatric disorders. This systematic review examines evidence from clinical and preclinical studies to assess melatonin’s efficacy in the following conditions: depression, anxiety, bipolar disorder, and schizophrenia. Beyond its role in circadian regulation, melatonin exhibits antioxidative, anti-inflammatory, and immunomodulatory properties, which intersect with nutrition, lifestyle medicine, and psychoneuroimmunology (PNI).

The review finds that melatonin improves sleep quality, restores circadian balance, and modulates stress-related neuroimmune pathways. It also supports neuroplasticity and reduces oxidative stress, contributing to resilience against psychosocial and environmental stressors. …

From Rhythm To Resilience: The Interplay Of Circadian Rhythm, Melatonin, Lifestyle, Nutrition In Psychoneuroimmunology (Pni), Jane Pei-Chen Chang, Kuan-Pin Su

BioMedicine

Emerging evidence reveals that circadian rhythm, melatonin signaling, nutrition, and inflammation are intricately intertwined in shaping both mental and physical health. Circadian disruptions and lifestyle imbalances contribute to neuroinflammation, mood dysregulation, and cardiometabolic dysfunction, as seen in attention-deficit/hyperactivity disorder (ADHD), major depressive disorder (MDD), metabolic syndrome,and cardiovascular diseases. This special issue highlights interdisciplinary research that integrates circadian biology, nutrition, and psychoneuroimmunology (PNI) toward personalized and preventive psychiatry. Featured studies explore circadian and melatonin mechanisms in ADHD and MDD, the therapeutic and prophylactic potential of omega-3 polyunsaturated fatty acids (n-3 PUFAs), the neuroprotective potentical of paeoniflorin, and the role of extracellular …

Climate And Non-Genetic Effects On Goat Milk Quality And Casein Prediction Using Machine Learning, Ibrahima Mahamane Abdourhamane, Dilek Arsoy

The Thai Journal of Veterinary Medicine

Milk quality is becoming more and more crucial for farmers with the increasing use of component-based pricing systems in the sector. This study aimed to investigate the effects of climate-related and non-genetic factors on goat milk quality on the island of Northern Cyprus and to predict casein content using machine learning techniques. An analysis was performed on 21,695 goat milk samples collected between 2012 and 2018. Somatic cell count (SCC), standard plate count (SPC), and key milk components such as protein, casein, lactose, and fat were evaluated for different seasons, regions, farm sizes, and raw milk types. Five machine learning …

Stage- And Smoking-Associated Microrna Expression In Lung Adenocarcinoma, Min Huang, Yimin Ge, Huiqin Chen, Caimiao Wei, David Cogdell, Cristina Ivan, Meng Chen, Wei Zhang, George A Calin, Ming Guo

Faculty, Staff and Student Publications

Background: Altered expression of microRNAs (miRNAs) is implicated in lung carcinogenesis, but little research has investigated the association of miRNA alterations with lung cancer stage or smoking status. To identify such alterations in lung adenocarcinoma, we conducted miRNA profiling.

Methods: Lung adenocarcinoma specimens and paired nonneoplastic lung tissues from 58 patients who had received no preoperative therapy and underwent tumor resection from 1991 to 2006 were collected from tumor tissue banks. Thirty (52%) of the tumors were stage I and 28 (48%) stage II or higher. Twenty-five (43%) patients were nonsmokers and 33 (57%) were smokers. To identify miRNAs of …

The Environmental Integration - An Introduction To The Sustainability Of The Urban Heritage Of Nubia (Applied To Gharb Suhail), Ahmed Mohamed Said Elsaadany

Mansoura Engineering Journal

The Nubia region is an important historical and cultural place, as it is distinguished by a unique architectural heritage. The influence of the surrounding environment on the designs of buildings and structures in this region is evident. Traditional architecture arose spontaneously over long periods of time, but it was essentially based on correct scientific concepts. The architecture of Nubia in southern Egypt, which is located on the banks of the Nile River, was a mud architecture that used natural building materials from the environment influenced by Ancient Egyptian architecture, some influences from Islamic architecture represented in privacy and courtyard in …

Toward Resilience In Broadacre Agriculture: A Methodological Review Of Remote Sensing In Crop Productivity, Phenology, And Environmental Stress Detection, Jenny Shen, Hai Wang, Hasnein Tareque

Agriculture Research Articles

Highlights

What are the main findings?

• Remote sensing methodologies for crop performance monitoring were systematically reviewed across the themes of productivity, phenology, and environmental stress.
• Advances and challenges were identified within individual themes and in their integration toward holistic monitoring.

What are the implications of the main findings?

• Emerging integration approaches offer pathways beyond monitoring toward decision-support systems for broadacre agriculture.
• Future directions of advancing resilience-focused applications of remote sensing are proposed.

Abstract

Large-scale rainfed cropping systems (broadacre agriculture) face intensifying climate and resource stresses that undermine yield stability and farm livelihoods. Remote sensing (RS) offers critical tools for improving …

The Tamads2-Tatbl21 Module Enhances Wheat Resistance To Stripe Rust By Activating Tagkl-Mediated Immunity, Shijia Zhao, Hao Chu, Yanan Lu, Jiaqi Chen, Xu Wang, Guangxiang Tian, Mingjing Zhang, Pengyu Song, Yanhui Zhang, Guihua Bai, Gangming Zhan, Zhensheng Kang, Wenming Zheng, Zhengqing Fu, Na Liu

Faculty Publications

Wheat stripe rust (Puccinia striiformis f. sp. tritici, Pst) poses a catastrophic threat to global food security. While MADS-box transcription factors regulate development and abiotic stress, their roles in plant-pathogen immunity remain enigmatic. In this study, we identified TaMADS2, a Pst-induced MADS-box gene, as a positive regulator of wheat resistance. Functional analyses demonstrated that TaMADS2 overexpression significantly enhanced Pst resistance, whereas its knockdown rendered wheat more susceptible. Further investigation revealed that TaMADS2 interacts with trichome birefringence-like protein 21 (TaTBL21) to activate glycerol kinase-like (TaGKL) expression. Silencing TaGKL in wild-type or TaMADS2-overexpressing lines …

Benchmarking Dna Foundation Models For Genomic And Genetic Tasks, Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu

School of Medicine Faculty Publications

The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph, and GROVER) across diverse genomic and genetic tasks including sequence classification, gene expression prediction, variant effect quantification, and topologically associating domain (TAD) region recognition, using zero-shot embeddings. Our analysis reveals that mean token embedding consistently and significantly improves sequence classification performance, outperforming other pooling strategies. Model performance varies among tasks and datasets; while general purpose DNA foundation models showed competitive performance in pathogenic variant identification, they were less …

Workplace Policy And Associated Factors Of Minimum Acceptable Diet Practices: An Online Survey Among Working Mothers In Indonesia, Fadhila Iswi Deandra, Judhiastuty Februhartanty, Muchtaruddin Mansyur

Kesmas

Working mothers in Indonesia may influence complementary feeding practices, particularly their ability to ensure that their infants properly meet the minimum acceptable diet (MAD). In this cross-sectional study, an online survey was distributed through various online platforms where participants were recruited using convenience sampling. The questionnaire covered sociodemographic factors, workplace policies, and infant and young child feeding (IYCF) practices. Descriptive and logistic regression analyses were conducted. A total of 394 working mothers participated, of which over 90% of the respondents reported meeting minimum dietary diversity, minimum milk frequency, minimum milk feeding frequency, and MAD indicators as assessed with a standardized …

Emission Characterization And Health Risk Assessment Of Volatile Organic Compounds From Automotive Painting In Thailand, Vanitchaya Kultan, Sarawut Thepanondh, Jutarat Keawboonchu, Nattaporn Pinthong, Wissawa Malakan

Kesmas

The automotive industry is a significant source of volatile organic compound (VOC) emissions, particularly from solvent-based painting processes. This study evaluated VOC characteristics and distribution to assess associated health risks for workers and communities at varying distances from automotive painting facilities in Thailand, focusing on stacks and wastewater treatment plants that handle solvent-containing wastewater. The findings revealed aromatic compounds were predominant (66% of the total emissions), followed by oxygenated VOCs (26%). The stacks mainly emitted aromatics such as toluene and ethylbenzene, whereas the wastewater released oxygenated VOCs, particularly methyl isobutyl ketone and methyl ethyl ketone. The exposure concentrations in each …

Developmental Stage-Dependent Transcriptomic Responses To Neonatal Intraventricular Hemorrhage, Elizabeth Wallace-Anthony, Miriam Zamorano, Hemendra J Vekaria, Braden B Oldham, Kiara P Umpornpun, Scott D Olson, Stefano Berto, Brandon A Miller

Faculty, Staff and Student Publications

Neonatal intraventricular hemorrhage (IVH) is a major complication of preterm birth, yet how developmental stage influences the brain's response to injury remains unclear. We performed single-nucleus RNA sequencing on rat brains 24 h after IVH at postnatal day 2 (PND2) or day 5 (PND5) to define transcriptional responses across cell types. We identified 42 distinct cell populations and found that PND5 brains exhibited a markedly stronger immune and inflammatory response to IVH, with a threefold increase in differentially expressed genes compared to PND2. Microglia were the most perturbed cell type at both stages, showing increased oxidative stress and polarization toward …

Radiologist-Validated Automatic Lumbar T1-Weighted Spinal Mri Segmentation Tool Via An Attention U-Net Algorithm, Aryan Kalluvila, Ethan Wang, Michael C Hurley, Colbey Freeman, Jason M Johnson

Faculty, Staff and Student Publications

Background/Objectives: Spinal MRI segmentation has become increasingly important with the prevalence of disc herniation and vertebral injuries. Artificial intelligence can help orthopedic surgeons and radiologists automate the process of segmentation. Currently, there are few tools for T1-weighted spinal MRI segmentation, with most focusing on T2-weighted imaging. This paper focuses on creating an automatic lumbar spinal MRI segmentation tool for T1-weighted images using deep learning.

Methods: An Attention U-Net was employed as the main algorithm because the architecture has shown success in other segmentation applications. Segmentation loss functions were compared, focusing on the difference between BCE and MSE loss. Two board-certified …

Benchmarking Dna Foundation Models For Genomic And Genetic Tasks, Haonan Feng, Lang Wu, Bingxin Zhao, Chad Huff, Jianjun Zhang, Jia Wu, Lifeng Lin, Peng Wei, Chong Wu

Faculty, Staff and Student Publications

The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-Ph, and GROVER) across diverse genomic and genetic tasks including sequence classification, gene expression prediction, variant effect quantification, and topologically associating domain (TAD) region recognition, using zero-shot embeddings. Our analysis reveals that mean token embedding consistently and significantly improves sequence classification performance, outperforming other pooling strategies. Model performance varies among tasks and datasets; while general purpose DNA foundation models showed competitive performance in pathogenic variant identification, they were less …

Red Midge Larvae Are An Invertebrate Alternative Diet To Beef Liver For Planarian Husbandry, Jonah Pacis , '25, Danielle Ireland, Evangeline Coffinas, Jerome Sheehan, Kate Sun , '27, Eva-Maria S. Collins

Biology Faculty Works

Freshwater planarians are an emerging model for toxicology and neuroscience because of their amenability to rapid behavioral screening and remarkable ability to regenerate a cephalized nervous system. As invertebrates, planarians can help reduce the use of vertebrates in research; however, laboratories typically maintain planarians on diets of homogenized organic beef or chicken liver, raising ethical concerns with feeding a vertebrate diet. Organic liver is difficult to obtain, and preparation methods vary, introducing intra- and interlaboratory variability. Here, we show that Dugesia japonica planarians can be maintained for over a year on commercially available red midge larvae (RML), a natural prey …