Digital Commons Network^™

Influence Of Macrophages On Vascular Invasion Of Inflammatory Breast Cancer Emboli Measured Using An In Vitro Microfluidic Multi-Cellular Platform, Manasa Gadde, Melika Mehrabi-Dehdezi, Bisrat G Debeb, Wendy A Woodward, Marissa Nichole Rylander

Faculty, Staff and Student Publications

Inflammatory breast cancer (IBC) is an aggressive disease with a poor prognosis and a lack of effective treatments. It is widely established that understanding the interactions between tumor-associated macrophages (TAMs) and the tumor microenvironment is essential for identifying distinct targeting markers that help with prognosis and subsequent development of effective treatments. In this study, we present a 3D in vitro microfluidic IBC platform consisting of THP1 M0, M1, or M2 macrophages, IBC cells, and endothelial cells. The platform comprises a collagen matrix that includes an endothelialized vessel, creating a physiologically relevant environment for cellular interactions. Through the utilization of this …

Trends And Challenges In The Utilization Of Web-Based Information Repositories For The Academicians Of University Libraries In Tamil Nadu, Vasanth R, Catherin Beula C, Balasubramanian P

Library Philosophy and Practice (e-journal)

A Web-Based Information repository is a technology used to collect and organize multimedia information such as images, text, audio, video, software, and scientific data. It improves knowledge management and provides high-speed access to the database. The researcher made an initiative to analyze the trends in information services accessed from the university library website and to analyze the satisfaction of the respondents with Web-Based Information Repositories available in the sample unit. The target population of this study is research scholars in various departments of Madurai Kamaraj University, Madurai. The questionnaire method has been used for the collection of data required. A …

Conserving Nature's Chorus: Local And Landscape Features Promoting Frog Species Richness In Farm Dams, Martino E. Malerba, Jodi J L Rowley, Peter I. Macreadie, James Frazer, Nicholas J. Wright, Nayyar Zaidi, Asef Nazari, Dhananjay Thiruvady, Don A. Driscoll

Climate Science Research Articles

Habitat loss is a key factor in the ongoing freshwater biodiversity crisis. A promising way to help tackle the rapid decline in freshwater biodiversity is to improve the potential for artificial wetlands to provide habitat for aquatic wildlife. Farm dams (also known as agricultural ponds) are among the most abundant waterbodies in agricultural landscapes and can act as “oases” against droughts for many species. Despite their prominent role in agriculture, predictive models to evaluate their ecological potential are yet to emerge. Here we use a continental-scale data set of 104,013 audio recordings from citizen scientists to identify and locate 107 …

Understanding Endangered Sawfish Through The Growth And Structure Of Their Rostral Teeth, Linh Truong, Gabe Gambleton, Jens Hegg

CURCI Student Research

Sawfish are an endangered ray with a toothy rostrum containing a large number of teeth. Largetooth sawfish are a critically endangered species worldwide. Little is known about their life history or behavior, and natural populations are too low to easily track them. Preserved rostra are more accessible to study. Measurements of the rostrum teeth and rostrum length were taken which may indicate a subspecies or sexual dimorphism in the sample. 120 sawfish rostra from the Brazil sample were quantified using ImageJ to compare rostrum size to fish age and length. Sawfish rostral teeth have repeated tubule structures within them that …

Multi-View Brain Tumor Segmentation (Mvbts): An Ensemble Of Planar And Triplanar Attention Unets, Snehal Rajput, Rupal Kapdi, Mehul Raval, Mohendra Roy

Turkish Journal of Electrical Engineering and Computer Sciences

3D UNet has achieved high brain tumor segmentation performance but requires high computation, large memory, abundant training data, and has limited interpretability. As an alternative, the paper explores using 2D triplanar (2.5D) processing, which allows images to be examined individually along axial, sagittal, and coronal planes or together. The individual plane captures spatial relationships, and combined planes capture contextual (depth) information. The paper proposes and analyzes an ensemble of uniplanar and triplanar UNets combined with channel and spatial attention for brain tumor segmentation. It investigates the significance of each plane and analyzes the impact of uniplanar and triplanar ensembles with …

A Unique Hybrid Domain Hand-Crafted Feature To Classify Colorectal Tissue Histopathological Images Using Multiheaded Cnn, Anurodh Kumar, Amit Vishwakarma, Varun Bajaj

Turkish Journal of Electrical Engineering and Computer Sciences

Early diagnosis of colorectal cancer lengthens human life and is helpful in efforts to cure the illness. Histopathological inspection is a routinely utilized technique to diagnose it. Visual assessment of histopathological images takes more investigation time, and the decision is based on the individual perceptions of clinicians. The existing methods for colorectal cancer classification use only spatial information. However, studies on the spectral domains of information are lacking in the literature. Therefore, the performance of the existing techniques is moderate. To improve the performance of colorectal cancer classification, this work proposes a unique hybrid domain hand-crafted feature formulated using scale-invariant …

Hybrid Machine Learning Model To Predict Chronic Kidney Diseases Using Handcrafted Features For Early Health Rehabilitation, Amjad Rehman, Tanzila Saba, Haider Ali, Narmine Elhakim, Noor Ayesha

Turkish Journal of Electrical Engineering and Computer Sciences

Chronic kidney diseases proliferate due to hypertension, diabetes, anemia, obesity, smoking etc. Patients with such conditions are sometimes unaware of first symptoms, complicating disease diagnosis. This paper presents chronic kidney disease (CKD) prediction model to classify CKD patients from NCKD (Non-CKD). The proposed study has two main stages. First, we found the odds ratio through logistic regression and comparison test to identify early risk factors from kidneys? MRI and differentiate CKD from NCKD subjects. In stage 2, LR, LDA, MLP classifiers were applied to predict CKD and NCKD by extracting features from MRI. The odds ratio of blood glucose random …

Classification Of Chronic Pain Using Fmri Data: Unveiling Brain Activity Patterns For Diagnosis, Rejula V, Anitha J, Belfin Robinson

Turkish Journal of Electrical Engineering and Computer Sciences

Millions of people throughout the world suffer from the complicated and crippling condition of chronic pain. It can be brought on by several underlying disorders or injuries and is defined by chronic pain that lasts for a period exceeding three months. To better understand the brain processes behind pain and create prediction models for pain-related outcomes, machine learning is a potent technology that may be applied in Functional magnetic resonance imaging (fMRI) chronic pain research. Data (fMRI and T1-weighted images) from 76 participants has been included (30 chronic pain and 46 healthy controls). The raw data were preprocessed using fMRIprep …

Deep Feature Extraction, Dimensionality Reduction, And Classification Of Medical Images Using Combined Deep Learning Architectures, Autoencoder, And Multiple Machine Learning Models, Ahmet Hi̇dayet Ki̇raz, Fatime Oumar Djibrillah, Mehmet Emi̇n Yüksel

Turkish Journal of Electrical Engineering and Computer Sciences

Accurate analysis and classification of medical images are essential factors in clinical decision-making and patient care. A novel comparative approach for medical image classification is proposed in this study. This new approach involves several steps: deep feature extraction, which extracts the informative features from medical images; concatenation, which concatenates the extracted deep features to form a robust feature vector; dimensionality reduction with autoencoder, which reduces the dimensionality of the feature vector by transforming it into a different feature space with a lower dimension; and finally, these features obtained from all these steps were fed into multiple machine learning classifiers (SVM, …

Effectiveness Of Thyme Honey In The Management Of Xerostomia In Geriatric Patients With End-Stage Renal Disease: A Randomized Controlled Clinical Trial With A Biochemical Assessment, Asmaa Ras, Dalia M. Ghalwash, Radwa R. Hussein, Suzan M. Seifallah

Dentistry

Background

Taking into consideration the value of the oral health condition in geriatric people with end-stage renal disease (ESRD) associated with xerostomia and believing that salivary stimulants or substitutes could potentially be used to manage this condition. This study aimed to evaluate the clinical effectiveness of thyme honey as oral rinse in geriatric patients with ESRD using the subjective dry mouth score as a primary objective and to assess the effect of thyme honey on the salivary nitric oxide level, salivary flow rate, and salivary ph in addition to objective dry mouth score as a secondary objective.

Methods

This was …

The Neuroimmune Regulation And Potential Therapeutic Strategies Of Optic Pathway Glioma, Khushboo Irshad, Yu-Kai Huang, Paul Rodriguez, Jung Lo, Benjamin E Aghoghovwia, Yuan Pan, Kun-Che Chang

Faculty, Staff and Student Publications

Optic pathway glioma (OPG) is one of the causes of pediatric visual impairment. Unfortunately, there is as yet no cure for such a disease. Understanding the underlying mechanisms and the potential therapeutic strategies may help to delay the progression of OPG and rescue the visual morbidities. Here, we provide an overview of preclinical OPG studies and the regulatory pathways controlling OPG pathophysiology. We next discuss the role of microenvironmental cells (neurons, T cells, and tumor-associated microglia and macrophages) in OPG development. Last, we provide insight into potential therapeutic strategies for treating OPG and promoting axon regeneration.

Cccd: Corner Detection And Curve Reconstruction For Improved 3d Surface Reconstruction From 2d Medical Images, Mriganka Sarmah, Arambam Neelima

Turkish Journal of Electrical Engineering and Computer Sciences

The conventional approach to creating 3D surfaces from 2D medical images is the marching cube algorithm, but it often results in rough surfaces. On the other hand, B-spline curves and nonuniform rational B-splines (NURBSs) offer a smoother alternative for 3D surface reconstruction. However, NURBSs use control points (CTPs) to define the object shape and corners play an important role in defining the boundary shape as well. Thus, in order to fill the research gap in applying corner detection (CD) methods to generate the most favorable CTPs, in this paper corner points are identified to predict organ shape. However, CTPs must …

Focal Modulation Network For Lung Segmentation In Chest X-Ray Images, Şaban Öztürk, Tolga Çukur

Turkish Journal of Electrical Engineering and Computer Sciences

Segmentation of lung regions is of key importance for the automatic analysis of Chest X-Ray (CXR) images, which have a vital role in the detection of various pulmonary diseases. Precise identification of lung regions is the basic prerequisite for disease diagnosis and treatment planning. However, achieving precise lung segmentation poses significant challenges due to factors such as variations in anatomical shape and size, the presence of strong edges at the rib cage and clavicle, and overlapping anatomical structures resulting from diverse diseases. Although commonly considered as the de-facto standard in medical image segmentation, the convolutional UNet architecture and its variants …

Infrared Imaging Segmentation Employing An Explainable Deep Neural Network, Xinfei Liao, Dan Wang, Zairan Li, Nilanjan Dey, Rs Simon, Fuqian Shi

Turkish Journal of Electrical Engineering and Computer Sciences

Explainable AI (XAI) improved by a deep neural network (DNN) of a residual neural network (ResNet) and long short-term memory networks (LSTMs), termed XAIRL, is proposed for segmenting foot infrared imaging datasets. First, an infrared sensor imaging dataset is acquired by a foot infrared sensor imaging device and preprocessed. The infrared sensor image features are then defined and extracted with XAIRL being applied to segment the dataset. This paper compares and discusses our results with XAIRL. Evaluation indices are applied to perform various measurements for foot infrared image segmentation including accuracy, precision, recall, F1 score, intersection over union (IoU), Dice …

Contact With Caregivers Is Associated With Composition Of The Infant Gastrointestinal Microbiome In The First 6 Months Of Life, Kyle S. Wiley, Andrew M. Gregg, Molly M. Fox, Venu Lagishetty, Curt A. Sandman, Jonathan P. Jacobs, Laura M. Glynn

Psychology Faculty Articles and Research

Objectives

Little is known about how physical contact at birth and early caregiving environments influence the colonization of the infant gastrointestinal microbiome. We investigated how infant contact with caregivers at birth and within the first 2 weeks of life relates to the composition of the gastrointestinal microbiome in a sample of U.S. infants (n = 60).

Methods

Skin-to-skin and physical contact with caregivers at birth and early caregiving environments were surveyed at 2 weeks postpartum. Stool samples were collected from infants at 2 weeks, 2, 6, and 12 months of age and underwent 16S rRNA sequencing as a proxy …

Addressing The Challenges Of Establishing Quality Wastewater Or Non- Sewered Sanitation-Based Surveillance, Including Laboratory And Epidemiological Considerations, In Malawi., Rochelle H. Holm, Ruth Nyirenda, Ted Smith, Petros Chigwechokha

Faculty and Staff Scholarship

Learning from clinical laboratories, wastewater or environmental (including non-sewered sanitation) environmental microbiology laboratories can be established in resource-limited settings that focus on pathogen detection and pandemic prevention. Transparent discussions on the laboratory challenges and adaptations required for this can help meet the future requirements of health research and surveillance. This report aims to describe the challenges encountered when setting up a wastewater or environmental laboratory for multipathogen surveillance in Malawi, a resource-limited setting, as well as the lessons learnt. We identified nine unifying themes: what to monitor, human resource capacity, indicators of data quality, equipment availability, supply of consumable goods, …

Early Season Monitoring Of Tarnished Plant Bug, Lygus Lineolaris, In Wild Hosts Using Pheromone Traps, Justin George, James P Glover, Gadi V P Reddy, Chris Johnson, David R Hall

Faculty, Staff and Student Publications

Simple Summary

The tarnished plant bug, Lygus lineolaris (Hemiptera: Miridae), is a polyphagous pest and causes severe economic damage to cotton crops. Managing the weedy field edges is important in preventing early-season infestations of L. lineolaris in cotton to prevent damage to the squares and other fruiting structures. Scouting fields for L. lineolaris is time- and labor-intensive, and end-user variability associated with field sampling can lead to inaccuracies. Insect traps that combine visual cues and pheromones are more accurate, sustainable, and economically feasible in contrast to traditional insect detection methods. In this study, we investigated the application of red or …

Super-Enhancer Hijacking Drives Ectopic Expression Of Hedgehog Pathway Ligands In Meningiomas, Mark W Youngblood, Zeynep Erson-Omay, Chang Li, Hinda Najem, Süleyman Coșkun, Evgeniya Tyrtova, Julio D Montejo, Danielle F Miyagishima, Tanyeri Barak, Sayoko Nishimura, Akdes Serin Harmancı, Victoria E Clark, Daniel Duran, Anita Huttner, Timuçin Avşar, Yasar Bayri, Johannes Schramm, Julien Boetto, Matthieu Peyre, Maximilien Riche, Roland Goldbrunner, Nduka Amankulor, Angeliki Louvi, Kaya Bilgüvar, M Necmettin Pamir, Koray Özduman, Türker Kilic, James R Knight, Matthias Simon, Craig Horbinski, Michel Kalamarides, Marco Timmer, Amy B Heimberger, Ketu Mishra-Gorur, Jennifer Moliterno, Katsuhito Yasuno, Murat Günel

Faculty, Staff and Students Publications

Hedgehog signaling mediates embryologic development of the central nervous system and other tissues and is frequently hijacked by neoplasia to facilitate uncontrolled cellular proliferation. Meningiomas, the most common primary brain tumor, exhibit Hedgehog signaling activation in 6.5% of cases, triggered by recurrent mutations in pathway mediators such as SMO. In this study, we find 35.6% of meningiomas that lack previously known drivers acquired various types of somatic structural variations affecting chromosomes 2q35 and 7q36.3. These cases exhibit ectopic expression of Hedgehog ligands, IHH and SHH, respectively, resulting in Hedgehog signaling activation. Recurrent tandem duplications involving IHH permit de novo chromatin …

The Gut Microbiome As A Biomarker And Therapeutic Target In Hepatocellular Carcinoma, Betul Gok Yavuz, Saumil Datar, Shadi Chamseddine, Yehia I Mohamed, Michael Lapelusa, Sunyoung S Lee, Zishuo Ian Hu, Eugene J Koay, Hop S Tran Cao, Prasun Kumar Jalal, Carrie Daniel-Macdougall, Manal Hassan, Dan G Duda, Hesham M Amin, Ahmed O Kaseb

Faculty, Staff and Student Publications

The microbiome is pivotal in maintaining health and influencing disease by modulating essential inflammatory and immune responses. Hepatocellular carcinoma (HCC), ranking as the third most common cause of cancer-related fatalities globally, is influenced by the gut microbiome through bidirectional interactions between the gut and liver, as evidenced in both mouse models and human studies. Consequently, biomarkers based on gut microbiota represent promising non-invasive tools for the early detection of HCC. There is a growing body of evidence suggesting that the composition of the gut microbiota may play a role in the efficacy of immunotherapy in different types of cancer; thus, …

Metabolomic Phenotype Of Hepatic Steatosis And Fibrosis In Mexican Children Living With Obesity, Nayely Garibay-Nieto, Karen Pedraza-Escudero, Isabel Omaña-Guzmán, María José Garcés-Hernández, Eréndira Villanueva-Ortega, Mariana Flores-Torres, José Luis Pérez-Hernández, Mireya León-Hernández, Estibalitz Laresgoiti-Servitje, Juan Carlos Lopez-Alvarenga

School of Medicine Publications

Background and Objectives: Metabolic-dysfunction-associated steatotic liver disease or MASLD is the main cause of chronic liver diseases in children, and it is estimated to affect 35% of children living with obesity. This study aimed to identify metabolic phenotypes associated with two advanced stages of MASLD (hepatic steatosis and hepatic steatosis plus fibrosis) in Mexican children with obesity.

Materials and Methods: This is a cross-sectional analysis derived from a randomized clinical trial conducted in children and adolescents with obesity aged 8 to 16 years. Anthropometric and biochemical data were measured, and targeted metabolomic analyses were carried out using mass spectrometry. …

Extracellular Vesicles In Triple–Negative Breast Cancer: Immune Regulation, Biomarkers, And Immunotherapeutic Potential, Kaushik Das, Subhojit Paul, Arnab Ghosh, Saurabh Gupta, Tanmoy Mukherjee, Prem Shankar, Anshul Sharma, Shiva Keshava, Subhash C. Chauhan, Vivek Kumar Kashyap

School of Medicine Publications

Triple–negative breast cancer (TNBC) is an aggressive subtype accounting for ~10–20% of all human BC and is characterized by the absence of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) amplification. Owing to its unique molecular profile and limited targeted therapies, TNBC treatment poses significant challenges. Unlike other BC subtypes, TNBC lacks specific molecular targets, rendering endocrine therapies and HER2–targeted treatments ineffective. The chemotherapeutic regimen is the predominant systemic treatment modality for TNBC in current clinical practice. However, the efficacy of chemotherapy in TNBC is variable, with response rates varying between a wide range …

Open Structure And Gating Of The Arabidopsis Mechanosensitive Ion Channel Msl10, Jingying Zhang, Grigory Maksaev, Peng Yuan

2020-Current year OA Pubs

Plants are challenged by drastically different osmotic environments during growth and development. Adaptation to these environments often involves mechanosensitive ion channels that can detect and respond to mechanical force. In the model plant Arabidopsis thaliana, the mechanosensitive channel MSL10 plays a crucial role in hypo-osmotic shock adaptation and programmed cell death induction, but the molecular basis of channel function remains poorly understood. Here, we report a structural and electrophysiological analysis of MSL10. The cryo-electron microscopy structures reveal a distinct heptameric channel assembly. Structures of the wild-type channel in detergent and lipid environments, and in the absence of membrane tension, capture …

Metabolomic Phenotype Of Hepatic Steatosis And Fibrosis In Mexican Children Living With Obesity, Nayely Garibay-Nieto, Karen Pedraza-Escudero, Isabel Omaña-Guzmán, María José Garcés-Hernández, Eréndira Villanueva-Ortega, Mariana Flores-Torres, José Luis Pérez-Hernández, Mireya León-Hernández, Estibalitz Laresgoiti-Servitje, Berenice Palacios-González, Juan Carlos López-Alvarenga, Mauricio Lisker-Melman, Felipe Vadillo-Ortega

2020-Current year OA Pubs

No abstract provided.

Substitution Of Maxillary Central Incisor With Forced Eruption Of Impacted Maxillary Canine, Wei-Lun Lim, Huei-Mei Tsai, Yu-Ling Cheng, Yuen-Yung Tsang, Ming-Jeaun Su, Chia-Yi Pan

Taiwanese Journal of Orthodontics

This case report describes the orthodontic management of missing teeth and rehabilitation needs in a 26-year-old woman. Several missing teeth on her maxillary anterior esthetic zone, a poor prognosed left mandibular first molar and a missing right mandibular first molar was also found. The treatment plan included extraction of the unrestorable maxillary left incisor, surgical exposure and forced eruption of the impacted maxillary left canine. While on the lower arch, protraction of mandibular second and third molars was planned. A good functional occlusion was achieved after 42 months treatment duration. The transposed impacted maxillary left canine was orthodontically extruded and …

Distribution Of Different Skeletal And Dental Relations Among Orthodontic Patients In Recent 5 Years: A Retrospective Study, Zong-Zhe Tsai, Morton Chang, Yu-Chuan Tseng

Taiwanese Journal of Orthodontics

The prevalence of malocclusion differs significantly from race to race. The cause of malocclusion could be multifactorial. Previous studies have demonstrated quantitative information on skeletal and dental relations in different countries. This study focuses on patients who had received orthodontic data collection and analysis in a specific medical center. Skeletal relation and Angle’s dental classification of male and female were statisticized and analyzed. Skeletal relation of Class I was 45.4%, Class II was 29.5%, and Class III was 25.1%. Angle’s dental classification of Class I was 39.3%; Class II was 30.8%; Class III was 29.9%. There was a statistically significant …

Shooter, Rhys G. Mcvay

Night Flight: Online Literary Journal

This is a story about community, love, passion, chasing dreams, guilt and shame. The true story of my experience with a school shooting at my high school.

Molecular Event In Hrp Apoptosis, Laura Valdez

Research Colloquium

Background: Human retinal pericytes (HRP) are contractile cells providing support for endothelial cells of capillaries, essential in the regulation of retinal vasculature. Early stages of DR are characterized by the loss of HRP, leading to angiogenesis. Our preliminary studies identified monocyte-derived macrophages secrete TGF-β1, inducing the expression and secretion of a TGFβ1-Induced, pro-apoptotic BIGH3 protein leading to apoptosis of HRP. Based on a preliminary study in renal cells (unpublished data), CTP with an RGD domain is released from BIGH3 by proteolysis leading to renal cell apoptosis. In the present study, we employed Western Blots to determine if a similar molecular …

Irbp In Diabetic Retinopathy – Cell Culture & Ophthalmic Pathology Studies, Laura Valdez

Research Colloquium

Background: Interphotoreceptor-Retinoid-Binding-Protein (IRBP) is restricted to the subretinal space by the external limiting membrane and RPE zonulae occludens. Its expression is reduced in diabetic retinopathy (DR) and increased expression is protective. Hypoxia decreases viable conelike photoreceptors (661W) but increased VEGF, suggesting a role of photoreceptors in proliferative DR (PDR) (Rodriguez et al, Arch Clin Exp. Ophthal 3:23,2021). Here, we investigated the effects of high glucose and VEGF on IRBP expression by 661W and rod-like Y79 cells and distribution of IRBP and albumin in human globes with PDR and NPDR.

Methods:  661W and Y79 cells were cultured in DMEM or RPMI …

Investigation Of Operational Conditions For The Removal Of Methylene Blue By Fenton Reaction, Aya Tolpa, Mohamed Elsamadony, Hafez Afifi, Mohamed Gar Alalm

Journal of Engineering Research

Fenton reaction has been concerned by many researchersdue to easy operation and effective degradation of bioresistantorganics. This study aims to investigate the effect ofthe operational conditions on the effectiveness of Fenton’sprocess for the decolorization of methylene blue.The influenceof methylene blue, pH, dose of H2O2 , ferrous sulfateconcentration from the wastewater were studied. Experimentshave shown that highly affect by the value of pH, Laboratoryexperiment conducted in the lab proved that pH should bebetween 3 - 4 to give the best results, It also proved that theincreasing of the dose of both hydrogen peroxide and ferroussulfate enhanced the removal efficiency of MB.

Statistical Verification Of 2d-To-3d Conversion Of Size And Number Density Of Particles, Ahmed Elkholy, Wael Rady, Mahmoud Ahmadein

Journal of Engineering Research

Particle/grain size and their number density arecommonly characterized in two dimensions (2D) from planaroptical or SEM micrographs of polished samples. Accurateconversion of such quantities into the three dimensional (3D)values are necessary for prediction of material properties.Several contradicting conversion correlations are available inliterature. The main objective of the current works it to verifysome of them. For this purpose, geometrical (3D) models ofrandomly distributed mono-size spheres were constructed andsliced at different planes. The particle count and their size werevariated within the same control volume. The statisticalinvestigations of the date suggested a (2D)-to-(3D) conversionfactor of 1.152377 ± 0.009427, which is very close to …