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2025

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Optimizing Runtime Memory Size Of Smith-Waterman Algorithm For Long Sequences Alignment, Imad Qasim Habeeb, Zeyad Qasim Habeeb, Hanan Najm Abdulkhudhur Dec 2025

Optimizing Runtime Memory Size Of Smith-Waterman Algorithm For Long Sequences Alignment, Imad Qasim Habeeb, Zeyad Qasim Habeeb, Hanan Najm Abdulkhudhur

Baghdad Science Journal

Sequence alignment is used to help researchers see areas of similarity between two sequences. Hence, it is a key component of many applications, such as DNA matching, plagiarism detection, and spelling correction. The Smith-Waterman algorithm (SWA) is widely used to calculate the sequence alignment because it is guaranteed to find an optimal solution. This algorithm creates a matrix of the size n * m where the symbols n, m refers to the lengths of two sequences needed to be aligned. Therefore, it requires impersonal hardware with a large amount of main memory at runtime to align long sequences. Furthermore, it …


Collagen Type Ii-Targeting Lentiviral Gene Therapy For Mucopolysaccharidosis Iva, Betul Celik, Sampurna Saikia, Shaukat Khan, Krishna Sai Musini, Shunji Tomatsu Dec 2025

Collagen Type Ii-Targeting Lentiviral Gene Therapy For Mucopolysaccharidosis Iva, Betul Celik, Sampurna Saikia, Shaukat Khan, Krishna Sai Musini, Shunji Tomatsu

Department of Pediatrics Faculty Papers

Mucopolysaccharidosis (MPS IVA) is caused by pathogenic variations in the GALNS gene, leading to the accumulation of glycosaminoglycans in tissues and causing progressive skeletal lesions. While conventional lentiviral vectors (LVs) provide long-term stable expression, they do not deliver therapeutic levels to bone and cartilage. We hypothesized that engineering the LV envelope with a collagen type II-targeting peptide (WYRGRL) increases the binding affinity of the LVs for bone and cartilage. These modified vectors carrying the CBh and COL2A1 promoters delivered the GALNS gene to MPS IVA newborn mice via intravenous (IV) or intraarticular (IA) administration. The peptide-modified LVs exhibited markedly increased …


Loss Of The Maternal Effect Gene Nlrp2 Impairs Embryonic And Extra-Embryonic Development, Revealing A Novel Genetic Cause Of Congenital Anomalies†, Momal Sharif, Zahra Anvar, Imen Chakchouk, Sara H El-Dessouky, Roni Zemet, Eric C Kao, Wessam E Sharaf-Eldin, Ying-Wooi Wan, Zhandong Liu, Pengfei Liu, Michael Jochum, Ignatia B Van Den Veyver Dec 2025

Loss Of The Maternal Effect Gene Nlrp2 Impairs Embryonic And Extra-Embryonic Development, Revealing A Novel Genetic Cause Of Congenital Anomalies†, Momal Sharif, Zahra Anvar, Imen Chakchouk, Sara H El-Dessouky, Roni Zemet, Eric C Kao, Wessam E Sharaf-Eldin, Ying-Wooi Wan, Zhandong Liu, Pengfei Liu, Michael Jochum, Ignatia B Van Den Veyver

Duncan NRI Faculty and Staff Publications

Maternal-effect genes (MEGs) play a crucial role in early mammalian development, and their dysfunction can lead to severe embryonic and extra-embryonic abnormalities. NLRP2, a MEG that encodes a subcortical maternal complex (SCMC) protein, has been implicated in preimplantation development, but its role after implantation remains underexplored. In this study, we investigated the developmental consequences of maternal Nlrp2 loss-of-function in a maternal knockout (KO) mouse model at embryonic day 11.5. Embryos derived from Nlrp2-KO females have abnormal yolk sac vasculature, increased embryonic resorption, craniofacial abnormalities, neural tube defects, and congenital heart defects. Placental architecture is disrupted with an altered junctional zone …


Context Matching Is Not Reasoning When Performing Generalized Clinical Evaluation Of Generative Language Models, Andrew Wen, Qiuhao Lu, Yu-Neng Chuang, Guanchu Wang, Jiayi Yuan, Jiamu Zhang, Liwei Wang, Sunyang Fu, Kurt D Miller, Heling Jia, Steven D Bedrick, William R Hersh, Kirk E Roberts, Xia Hu, Hongfang Liu Dec 2025

Context Matching Is Not Reasoning When Performing Generalized Clinical Evaluation Of Generative Language Models, Andrew Wen, Qiuhao Lu, Yu-Neng Chuang, Guanchu Wang, Jiayi Yuan, Jiamu Zhang, Liwei Wang, Sunyang Fu, Kurt D Miller, Heling Jia, Steven D Bedrick, William R Hersh, Kirk E Roberts, Xia Hu, Hongfang Liu

Faculty, Staff and Student Publications

Current discussion surrounding the clinical capabilities of generative language models(GLMs) predominantly centers around multiple-choice question-answer(MCQA) benchmarks derived from clinical licensing examinations. While accepted for human examinees, characteristics unique to GLMs bring into question the validity of such benchmarks. Here, we validate five benchmarks using eight GLMs, ablating for parameter size and reasoning capabilities, validating via prompt permutation three key assumptions that underpin the generalizability of MCQA-based assessments: that knowledge is applied, not memorized, that semantic consistency will lead to consistent answers, and that situations with no answers can be recognized. While large models are more resilient to our perturbations compared …


Context Matching Is Not Reasoning When Performing Generalized Clinical Evaluation Of Generative Language Models, Andrew Wen, Qiuhao Lu, Yu-Neng Chuang, Guanchu Wang, Jiayi Yuan, Jiamu Zhang, Liwei Wang, Sunyang Fu, Kurt D Miller, Heling Jia, Steven D Bedrick, William R Hersh, Kirk E Roberts, Xia Hu, Hongfang Liu Dec 2025

Context Matching Is Not Reasoning When Performing Generalized Clinical Evaluation Of Generative Language Models, Andrew Wen, Qiuhao Lu, Yu-Neng Chuang, Guanchu Wang, Jiayi Yuan, Jiamu Zhang, Liwei Wang, Sunyang Fu, Kurt D Miller, Heling Jia, Steven D Bedrick, William R Hersh, Kirk E Roberts, Xia Hu, Hongfang Liu

Faculty, Staff and Student Publications

Current discussion surrounding the clinical capabilities of generative language models(GLMs) predominantly centers around multiple-choice question-answer(MCQA) benchmarks derived from clinical licensing examinations. While accepted for human examinees, characteristics unique to GLMs bring into question the validity of such benchmarks. Here, we validate five benchmarks using eight GLMs, ablating for parameter size and reasoning capabilities, validating via prompt permutation three key assumptions that underpin the generalizability of MCQA-based assessments: that knowledge is applied, not memorized, that semantic consistency will lead to consistent answers, and that situations with no answers can be recognized. While large models are more resilient to our perturbations compared …


(R2150) Impact Of Specialist Predator Harvesting On The Stability Of A Three-Species Food Chain Model With A Generalist Predator, S. Ganga, S. Vijaya Dec 2025

(R2150) Impact Of Specialist Predator Harvesting On The Stability Of A Three-Species Food Chain Model With A Generalist Predator, S. Ganga, S. Vijaya

Applications and Applied Mathematics: An International Journal (AAM)

In this study, the stability of a three-species food chain model comprising a prey, an intermediate specialist predator, and a top predator exhibiting generalist behavior is examined, with harvesting applied to the intermediate predator. The main objective is to investigate how variations in the harvesting rate influence system stability and the coexistence of all three species. The positivity, boundedness, and equilibrium points of the model are analyzed to ensure biological feasibility. The equilibrium point involving the prey and the top predator satisfies the criteria for both local and global asymptotic stability. The coexistence equilibrium point attains local asymptotic stability based …


Comparative Transcriptomics Reveals Novel And Differential Long-Noncoding Rna Responses Underlying Interferon-Mediated Antiviral Regulation In Porcine Alveolar Macrophages, Jiuyi Li, Oluwaseun Adeyemi, Laura C. Miller, Yongming Sang Dec 2025

Comparative Transcriptomics Reveals Novel And Differential Long-Noncoding Rna Responses Underlying Interferon-Mediated Antiviral Regulation In Porcine Alveolar Macrophages, Jiuyi Li, Oluwaseun Adeyemi, Laura C. Miller, Yongming Sang

Food and Animal Sciences Faculty Research

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major threat to the global swine industry. Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of antiviral immunity, but their roles in porcine alveolar macrophages (PAMs)—the primary target of PRRSV—remain poorly characterized. This study presents a genome-wide analysis of lncRNA expression in PAMs stimulated with a PRRS modified live virus (MLV) vaccine and two type I interferons, IFN-α1 and IFN-ω5. Whole-transcriptome sequencing identified over 2000 differentially expressed lncRNAs, with IFN-ω5 inducing the most extensive transcriptional reprogramming. Weighted gene co-expression network analysis (WGCNA) revealed interferon-specific lncRNA-mRNA modules, and functional enrichment showed …


The Dynamic Among The Producer, Consumer, And Predator In The Presence Of Fear, Hunting Cooperation, And Anti-Predator Behavior, Muslim Saad Jabbar, Raid Kamel Naji Dec 2025

The Dynamic Among The Producer, Consumer, And Predator In The Presence Of Fear, Hunting Cooperation, And Anti-Predator Behavior, Muslim Saad Jabbar, Raid Kamel Naji

Baghdad Science Journal

In general, the dynamic interactions that form the relationships between predators and prey within a food chain depend heavily on fear, hunting cooperation, and anti-predator defenses. These elements support species’ survival in their particular habitats, balance the ecosystem, and control the numbers of predators and prey. Therefore, a three-species food chain system consisting of producer-consumer-predator, which plays a crucial role in ecological dynamics, has been formulated mathematically. The objective is to investigate the influence of fear, hunting cooperation, and anti-predators on the dynamic behavior of the food chain system. Two types of functional responses have been utilized. The characteristics of …


Voices Of The Headland: Robinson Jeffers And The Bird Of Prey, By Alan Malnar, Eric San George Dec 2025

Voices Of The Headland: Robinson Jeffers And The Bird Of Prey, By Alan Malnar, Eric San George

Jeffers Studies

No abstract provided.


Biomechanics Of The Ribs During Respiration At The Costotransverse Joint: An In-Vivo Retrospective Pilot Study, Michael Maninang, Greg Almeter, Erik Pearson, Arvie Vitente Dec 2025

Biomechanics Of The Ribs During Respiration At The Costotransverse Joint: An In-Vivo Retrospective Pilot Study, Michael Maninang, Greg Almeter, Erik Pearson, Arvie Vitente

Rehabilitation Sciences Department Faculty Articles

Introduction: Scarce in‑vivo data describe how ribs move at the costotransverse joints during quiet breathing—knowledge critical to thoracic biomechanics and pain mechanisms. This pilot study uses four‑dimensional computed tomography (4D‑CT) to quantify, for the first time, the three‑dimensional magnitude and direction of rib motion at these joints throughout quiet respiration.

Methods: This retrospective, descriptive pilot study analyzed ten 4D‑CT scans obtained from patients undergoing thoracic imaging prior to radiation therapy. End‑expiration and end‑inspiration phases were aligned with a demons deformable‑registration algorithm. For each costotransverse joint, the three‑dimensional displacement vector, its absolute magnitude, and its components along the lateral–medial (L–M), …


Tumor Biology And Access To Care And Metastatic Breast Cancer Outcomes, Matthew R. Dunn, Sarah C. Van Alsten, Marc A. Emerson, Katherine Reeder-Hayes, Terry Hyslop, Melissa A. Troester Dec 2025

Tumor Biology And Access To Care And Metastatic Breast Cancer Outcomes, Matthew R. Dunn, Sarah C. Van Alsten, Marc A. Emerson, Katherine Reeder-Hayes, Terry Hyslop, Melissa A. Troester

Kimmel Cancer Center Faculty Papers

PURPOSE: To understand how access to care influences metastatic breast cancer burden (MBC) while accounting for molecular tumor characteristics, and identify interventions to reduce metastatic disease burden.

METHODS: The Carolina Breast Cancer Study is a population-based cohort with invasive breast cancer (diagnosed 2008-2013). Both de novo metastasis (stage IV at diagnosis) and distant recurrence were evaluated (12 years of follow-up. Tumor data were from medical records, pathology reports, and RNA expression data. Social variables and access to care were from participant surveys. Generalized linear models were used to estimate associations of biological and access characteristics with MBC; Cox models were …


Lightweight Assembly Workpiece Detection Algorithm Based On Improved Yolov8, Shuheng Wu, Yongkui Liu, Lin Zhang, Yingying Xiao, Lihui Wang Dec 2025

Lightweight Assembly Workpiece Detection Algorithm Based On Improved Yolov8, Shuheng Wu, Yongkui Liu, Lin Zhang, Yingying Xiao, Lihui Wang

Journal of System Simulation

Abstract: To address the issues of low recognition accuracy and slow detection speed with existing deep learning-based object detection algorithms for robotic automatic assembly tasks, a lightweight assembly workpiece object detection algorithm based on YOLOv8 was proposed. The PConv was introduced to improve the C2f module, and a new Faster_C2f module was designed to enhance the detection speed of the model. The SIoU loss function was employed to optimize the location prediction accuracy of the CIoU loss function and improve the localization accuracy of small targets. The high-level screening-feature fusion pyramid networks (HS-FPN) structure was used to improve the Neck …


Isolation And Molecular Characterization Of Shiga Toxin Producing Genes Stx1and Stx2 From The Captive Migratory Birds Of Lahore, Romana Zulfiqar, Hamid Ullah, Bushra Nisar Khan, Muhammad Habib Ur Rehman, Hoor Ul Ain, Alishba Zaheer, Samrah Hussain, Aazba Naeem Dec 2025

Isolation And Molecular Characterization Of Shiga Toxin Producing Genes Stx1and Stx2 From The Captive Migratory Birds Of Lahore, Romana Zulfiqar, Hamid Ullah, Bushra Nisar Khan, Muhammad Habib Ur Rehman, Hoor Ul Ain, Alishba Zaheer, Samrah Hussain, Aazba Naeem

Journal of Bioresource Management

A total of 240 cloacal and fecal swabs were collected from 25 avian species, including ducks, swans, geese, pheasants, guinea fowl, parrots, cranes, and crows. Samples were cultured on Sorbitol MacConkey Agar, and presumptive Escherichia coli isolates were confirmed using morphological, biochemical, and molecular methods. Shiga toxin–producing E. coli (STEC) was identified through PCR detection of stx1 and stx2 genes, followed by sequencing. Antibiotic susceptibility testing was performed using the Kirby–Bauer disc diffusion method against streptomycin, ceftriaxone, ciprofloxacin, azithromycin, and tetracycline. Only four STEC isolates were recovered, resulting in an overall prevalence of 1.66 % (4/240). Positive cases were detected …


A Method Of Heuristic Human-Llm Collaborative Source Search, Yi Chen, Sihang Qiu, Zhengqiu Zhu, Yatai Ji, Yong Zhao, Rusheng Ju Dec 2025

A Method Of Heuristic Human-Llm Collaborative Source Search, Yi Chen, Sihang Qiu, Zhengqiu Zhu, Yatai Ji, Yong Zhao, Rusheng Ju

Journal of System Simulation

Abstract: Traditional source search algorithms are prone to local optimization, and source search methods combining crowdsourcing and human-AI collaboration suffer from low cost-efficiency due to human intervention. In this study, we proposed a lightweight human-AI collaboration framework that utilized multi-modal large language models (MLLMs) to achieve visual-language conversion, combined chain-of-thought (CoT) reasoning to optimize decision-making, and constructed a heuristic strategy that incorporated probability distribution filtering and a balance between exploitation and exploration. The effectiveness of the framework was verified by experiments. The human-AI alignment heuristic strategy with large language model adaptation design provides a new idea to reduce manual …


Emotive Immersion: Eeg-Driven Ai Art In Immersive Visual Spaces (Full Dome), Yuming Chen, Gianni Corino Dec 2025

Emotive Immersion: Eeg-Driven Ai Art In Immersive Visual Spaces (Full Dome), Yuming Chen, Gianni Corino

School of Art, Design and Architecture

This paper proposes a rethinking of the “Future Screen” through the integration of affective computing, generative AI, and immersive spatial display. As an advanced screen paradigm, the full dome environment transcends flat, passive interfaces and enables dynamic, multisensory, and emotionally adaptive media experiences (Von Chamier-Waite, 2013). Building on this potential, the research presents Coids, an interactive dome installation. In this work, real-time emotional states are captured using EEG-based emotion recognition. These inputs dynamically shape AI-generated visuals within a shared immersive setting.Drawing on theories of immersion, presence, AI generated visuals and affect, the study explores how physiological data, even from low-resolution …


Sex Differences In The Association Of Vascular Risk And Apoe Genotype With Cognitive Decline And Dementia: Evidence From A U.S. Longitudinal Study, Longjian Liu, Jintong Hou, Saishi Cui, Xiaopeng Zhao, Zuolu Liu, J. Craig Longenecker, Nathalie S May, Jin Jun Luo, Rose Ann Dimaria-Ghalili, Howard J. Eisen Dec 2025

Sex Differences In The Association Of Vascular Risk And Apoe Genotype With Cognitive Decline And Dementia: Evidence From A U.S. Longitudinal Study, Longjian Liu, Jintong Hou, Saishi Cui, Xiaopeng Zhao, Zuolu Liu, J. Craig Longenecker, Nathalie S May, Jin Jun Luo, Rose Ann Dimaria-Ghalili, Howard J. Eisen

Division of Cardiology Faculty Papers

BACKGROUND: Sex differences in the association between vascular factors and cognitive outcomes remain unclear. We aimed to investigate the associations of blood pressure metrics (hypertension, systolic blood pressure [SBP), pulse pressure, ankle and brachial pressures, and ankle to brachial pressure index [ABI]) with the risk of cognitive decline and dementia.

METHODS: We conducted a population-based longitudinal analysis using data from the Atherosclerosis Risk in Communities (ARIC) study (begun in 1987-1989) in the United States. We analyzed a total of 12,268 participants aged 45-64 years who had validated exposure measurements, cognitive function tests (first administrated 1990-1992), and followed up for incidence …


Estimating Prey Capture Attempts And Activity Costs In Foraging Emperor Penguins (Aptenodytes Forsteri) Using Integrated Biologging Data, Taylor Rose Azizeh Dec 2025

Estimating Prey Capture Attempts And Activity Costs In Foraging Emperor Penguins (Aptenodytes Forsteri) Using Integrated Biologging Data, Taylor Rose Azizeh

Master's Theses

To forage efficiently in patchy and unpredictable prey landscapes, marine predators must optimize energy intake while minimizing costs. Central place foragers like emperor penguins face greater energetic constraints during demanding periods of high investment like chick-rearing. I used high-resolution tri-axial acceleration, depth, and GPS data from 25 birds from two feeding seasons (2019 and 2022) to quantify prey capture attempts and a proxy for energy expenditure (overall dynamic body acceleration; ODBA) across dive types (epipelagic, mesopelagic, benthic), phases (descent, bottom, ascent), and over time at-sea. While prey capture attempts per minute did not differ when looking across dive types alone, …


Anti-Saccade Error Rates Are Associated With Somatic Depressive Symptoms In Cocaine Use Disorder, Constanza De Dios, Heather E Webber, Margaret C Wardle, Jin H Yoon, Michelle A Patriquin, Jessica N Vincent, Joy M Schmitz, Scott D Lane Dec 2025

Anti-Saccade Error Rates Are Associated With Somatic Depressive Symptoms In Cocaine Use Disorder, Constanza De Dios, Heather E Webber, Margaret C Wardle, Jin H Yoon, Michelle A Patriquin, Jessica N Vincent, Joy M Schmitz, Scott D Lane

Faculty, Staff and Student Publications

Background: Inhibitory control deficits are associated with cocaine use disorder (CUD) development and maintenance. Additionally, drug use and inhibitory control can be negatively affected by depressive symptoms, including somatic factors like sleep disturbance and fatigue.

Aim: The current study assessed the relationship between inhibitory control and depressive symptoms among individuals initiating CUD treatment. We examined associations among anti-saccade response inhibition performance, total scores on the Beck Depression Inventory-II (BDI-II), and individual BDI-II items.

Methods: N = 101 patients enrolled in a clinical trial for CUD completed drug-specific anti-saccade and depression (BDI-II) measures prior to treatment. Generalized linear models tested the …


Volumetric Video With Skateboarders: Creative Opportunities Of Working With An Emerging Screen Technology Beyond The Studio, Dani Landau, Diego Zamora Dec 2025

Volumetric Video With Skateboarders: Creative Opportunities Of Working With An Emerging Screen Technology Beyond The Studio, Dani Landau, Diego Zamora

School of Art, Design and Architecture

Volumetric video is an emerging moving image technology in which each pixel is recorded witha location in three dimensions. Volumetric videos are normally created in studios using rigs made upof multiple cameras with LiDAR sensors and computers that combine the moving images. We tookthis technology out of the studio to explore variations of this technique in public skateparks. We foundthat as the technology is still in developing stages there are creative constraints: the lidar cameras sense at a limited distance to the subject, the image is of a relatively low resolution, and there are often glitches in theimage. In our …


Hybrid Pre-Trained Models With Machine Learning Classifier For Skin Cancer Classification, Toqa A. Sadoon, Asaad F. Qasim, Mohammed Khalaf, Ali M. Hasan Dec 2025

Hybrid Pre-Trained Models With Machine Learning Classifier For Skin Cancer Classification, Toqa A. Sadoon, Asaad F. Qasim, Mohammed Khalaf, Ali M. Hasan

Baghdad Science Journal

Classification of skin lesions can be challenging because of the subtle variation on the skin surface due to the appearance of these lesions. In the other hand, the digital dermoscopy has been widely used by dermatologist to diagnose cancer. For accurate detection, the clinicians should have a lot of experiences, but human nature is prone to error, forgetfulness, tension, and speed in diagnosis, all of which can affect the accuracy of detection. For these reasons, automated skin lesion classification has been used by many researchers to help dermatologists in making the right and accurate decision during diagnosis. A preprocessing image …


Exploring The Therapeutic Potential Of Fermented Apple Juice And Sidr Leaves Powder On Gut Microbiota Modulation And Neuropathy Relief In Diabetic Rats, Bakenam Ali Mohamed, Alyae M.S. Gabal, Gehan M. Morsy Dec 2025

Exploring The Therapeutic Potential Of Fermented Apple Juice And Sidr Leaves Powder On Gut Microbiota Modulation And Neuropathy Relief In Diabetic Rats, Bakenam Ali Mohamed, Alyae M.S. Gabal, Gehan M. Morsy

Baghdad Science Journal

Diabetes and its complications, particularly diabetic neuropathy, represent major health risks. This study investigated the potential of natural nutrients and bioactive compounds specifically fresh and fermented apple juice and sidr leaf powder to improve gut microbiota and alleviate neuropathy in diabetic rats. Seventy adult male Sprague–Dawley rats (180 ± 20 g) were assigned to six groups (11 rats each), while the diabetic control group (15 rats). Diabetes was induced by feeding a high-sucrose, high-fat (HSHF) diet and administering streptozotocin (45 mg/kg, intraperitoneally) during the 4th week. The groups included: healthy control; diabetic control; diabetic rats receiving fresh or fermented …


Distinct Populations Of Lung Capillary Endothelial Cells And Their Functional Significance, Joel James, Dan Yi, Zhiyu Dai, Et Al. Dec 2025

Distinct Populations Of Lung Capillary Endothelial Cells And Their Functional Significance, Joel James, Dan Yi, Zhiyu Dai, Et Al.

2020-Current year OA Pubs

The role of the lung's microcirculation and capillary endothelial cells in normal physiology and the pathobiology of pulmonary diseases is obviously vital. The recent discovery of molecularly distinct aerocytes and general capillary (gCaps) endothelial cells by single-cell transcriptomics (scRNAseq) advanced the field in understanding microcirculatory milieu and cellular communications. However, increasing evidence from different groups indicated the possibility of a more heterogeneous nature of lung capillaries. Therefore, we investigated enriched lung endothelial cells by scRNAseq and identified five novel populations of gCaps with distinct molecular signatures and roles. Our analysis suggests that two major populations of gCaps that express Scn7a(Na


Visualizing The Effect Of Process Pause On Virus Entrapment During Constant Flux Virus Filtration, Wenbo Xu, Xianghong Qian, Hironobu Shirataki, Daniel Straus, Sumith Ranil Wickramasinghe Dec 2025

Visualizing The Effect Of Process Pause On Virus Entrapment During Constant Flux Virus Filtration, Wenbo Xu, Xianghong Qian, Hironobu Shirataki, Daniel Straus, Sumith Ranil Wickramasinghe

Biomedical Engineering Faculty Publications and Presentations

Virus filtration is an essential unit operation used to validate clearance of adventitious virus during the manufacture of biopharmaceutical products such as monoclonal antibodies. Obtaining at least a 10,000-fold reduction in virus particles in the permeate is challenging as monoclonal antibodies are about half the size of the virus particles. Minute virus of mice, FDA-recommended model adventitious virus, was labeled with a fluorescent dye. Laser scanning confocal microscopy was used to determine the location of virus entrapment within the virus filtration membrane. Three different hollow fiber membranes made of regenerated cellulose and polyvinylidene fluoride were tested. Feed streams consisted of …


Multivariate Optimization Of Nonlinear Response Functions Using Central Composite Design, Hussein M. Hussein, Bassma H. Elwakil, Esraa Abdelhamid Moneer, Sara H. Akl, Yahya H. Shahin Dec 2025

Multivariate Optimization Of Nonlinear Response Functions Using Central Composite Design, Hussein M. Hussein, Bassma H. Elwakil, Esraa Abdelhamid Moneer, Sara H. Akl, Yahya H. Shahin

Almaaqal Journal of Sustainability and Emerging Technology

This study addresses critical challenges in multivariate optimization by: (1) developing efficient strategies for optimizing nonlinear response functions in high-dimensional parameter spaces, (2) quantifying comparative performance of traditional versus statistical design methodologies, (3) establishing mathematical frameworks for parameter interactions, and (4) validating results through comprehensive statistical analysis. A dual-phase optimization framework combined One-Variable-At-a-Time (OVAT) screening with Central Composite Design-based Response Surface Methodology (CCD-RSM). Five parameters were evaluated using rotatable CCD (α= 2.378) with 50 design points. Statistical analysis included analysis of variance (ANOVA), regression modeling, interaction quantification, and cross-validation. CCD-RSM demonstrated superior performance with model predictability improving from …


Optimizing Bioethanol Production Using Design Of Experiments For Sustainable Biofuel Development, Hussein M. Hussein, Yahya H. Shahin, Ihab A. Moneam Dec 2025

Optimizing Bioethanol Production Using Design Of Experiments For Sustainable Biofuel Development, Hussein M. Hussein, Yahya H. Shahin, Ihab A. Moneam

Almaaqal Journal of Sustainability and Emerging Technology

This study presents a statistically optimal approach for bioethanol production from sugarcane bagasse (SCB) using alkaline pretreatment, enzymatic hydrolysis, and fermentation processes. To maximize cellulose yield, four extraction parameters—solvent type, concentration, temperature, and time—were optimized using a Taguchi statistical model. The Taguchi-optimized extraction yields 11.3% increased cellulose recovery relative to cellulose recovered via non-optimized extraction methods (i.e., alkaline treatment with 6% NaOH at 90 °C for 3 hours). This yielded 45.20% cellulose (w/w), with 37.80% weight loss (predicted weight loss was 36.94%). Statistical analysis of extraction results verified solvent type (p = 0.0022) and temperature (p = 0.0007) to be …


Synthesis Of Biogenic Silver Nanoparticles From Apricot Kernel Extracts For The Colorimetric Determination Of Gold, Ayça Gi̇rgi̇n, Hi̇lal Akbiyik, Buse Tuğba Zaman, Omid Nejati, Ayça Bal Öztürk, Gülten Çeti̇n, Sezgi̇n Bakirdere Dec 2025

Synthesis Of Biogenic Silver Nanoparticles From Apricot Kernel Extracts For The Colorimetric Determination Of Gold, Ayça Gi̇rgi̇n, Hi̇lal Akbiyik, Buse Tuğba Zaman, Omid Nejati, Ayça Bal Öztürk, Gülten Çeti̇n, Sezgi̇n Bakirdere

Turkish Journal of Chemistry

Gold is abundant in nature, however, precise and reliable analytical methods for its detection are required stemming from its increasing prevalence in environmental, biological, and industrial systems, as well as the growing interest in understanding its function in living organisms and its effects on human health. This study investigates the use of biogenically synthesized silver nanoparticles (AgNPs) for the preconcentration and determination of gold ions prior to determination by UV-Vis spectrophotometry. AgNPs were synthesized by reducing silver nitrate through the use of an apricot kernel extract as both reducer and stabilizer agent. The colloidal yellowish AgNPs interacted with gold ions, …


Efektivitas Pemberian Buah Pisang Raja Untuk Menurunkan Kelelahan Kerja Pada Operator Sewing Umkm Garmen X Karanganyar, Virginia Bernardine Gavra Prachristma Sujudi, Tyas Lilia Wardani, Rizqy Kartika Sari Dec 2025

Efektivitas Pemberian Buah Pisang Raja Untuk Menurunkan Kelelahan Kerja Pada Operator Sewing Umkm Garmen X Karanganyar, Virginia Bernardine Gavra Prachristma Sujudi, Tyas Lilia Wardani, Rizqy Kartika Sari

National Journal of Occupational Health and Safety

Work fatigue is a common problem that can reduce productivity and increase the risk of workplace accidents. At UMKM Garmen X Karanganyar, the lack of supplementary food intake causes energy deficits and fatigue among workers. This condition underlies the research to analyze the effectiveness of giving banana raja (Musa paradisiaca L.) as an additional snack in reducing work fatigue among sewing operators at UMKM Garmen X Karanganyar. The research was conducted using a true experimental method with a pre-test and post-test design with a control group. 42 sewing operators were selected from 47 workers using simple random sampling, divided into …


Novel Spectrophotometric Method For The Determination Of Paclitaxel Through Complex Formation With Osmium, Basima A.A.Saleem, Salim A. Mohammed, Amer Th. Al-Taee Dec 2025

Novel Spectrophotometric Method For The Determination Of Paclitaxel Through Complex Formation With Osmium, Basima A.A.Saleem, Salim A. Mohammed, Amer Th. Al-Taee

Turkish Journal of Chemistry

Paclitaxel (Pac) is an important anticancer bioactive compound, and the availability of an accurate and robust analytical method for its quantification is of utmost importance. In this investigation, a novel, direct, and reliable spectrophotometric method has been proposed for the estimation of Pac via a complex formation reaction with osmium (Os). The method was based on the reaction of Pac with Os tetroxide, which produced a yellowish-brown complex. The resulting complex is soluble in water and displays a maximum absorption peak at 482 nm. The reaction conditions, including reactant concentration, pH, temperature, and reaction time, were optimized to obtain the …


Α-Glycosidase Activity Of Novel Coumarin–Triazole–Coumarin Dyads, Ersi̇n Şi̇ri̇n, Esra Sevi̇mli̇, Gökçe Seyhan, Burak Barut, Yunus Kaya, Baybars Köksoy Dec 2025

Α-Glycosidase Activity Of Novel Coumarin–Triazole–Coumarin Dyads, Ersi̇n Şi̇ri̇n, Esra Sevi̇mli̇, Gökçe Seyhan, Burak Barut, Yunus Kaya, Baybars Köksoy

Turkish Journal of Chemistry

Novel coumarin–triazole–coumarin dyads were synthesized and characterized, and their α-glycosidase inhibitory activities were evaluated spectrophotometrically. Compound 4e exhibited the most pronounced inhibitory effect, with an IC50 value of 38.98 ± 0.77 μM. The IC50 values for 4d and 4a were 93.55 ± 1.70 μM and 95.04 ± 3.55 μM, respectively. The Lineweaver–Burk plot showed that 4e inhibited α-glycosidase in a mixed type. In addition, the Ki value obtained from the Dixon plot was 19.95 ± 0.15 μM for α-glycosidase.


Efficient Recovery Of Y3+ From Aqueous Media Using Mdlm Technique:Transport Behavior And Kinetic Modeling, Volkan Demi̇rel, Ramazan Donat, Hacer Şensöz Dec 2025

Efficient Recovery Of Y3+ From Aqueous Media Using Mdlm Technique:Transport Behavior And Kinetic Modeling, Volkan Demi̇rel, Ramazan Donat, Hacer Şensöz

Turkish Journal of Chemistry

This study investigates the extraction behavior of Y³⁺ ions using a Multi-Dropped Liquid Membrane (MDLM) system that employs di(2-ethylhexyl) phosphoric acid (D₂EHPA) as the carrier ligand. The focus is on the system’s ability to transport ions between aqueous phases selectively. The extracted complex was analyzed spectrophotometrically via ultraviolet–visible (UV–Vis) measurements after complexation with 0.05% Arsenazo III. The aim of this study was to determine the influence of the optimum D₂EHPA carrier concentration, together with the pH and temperature conditions of the donor and acceptor phases, on the system’s extraction performance. Accordingly, a series of extraction experiments was performed at different …