Digital Commons Network^™

A Pan-Cancer Patient-Derived Xenograft Histology Image Repository With Genomic And Pathologic Annotations Enables Deep Learning Analysis, Brian S White, Xing Yi Woo, Soner Koc, Todd Sheridan, Steven B Neuhauser, Shidan Wang, Yvonne A Evrard, Li Chen, Ali Foroughi Pour, John D Landua, R Jay Mashl, Sherri R Davies, Bingliang Fang, Maria Gabriela Raso, Kurt W Evans, Matthew H Bailey, Yeqing Chen, Min Xiao, Jill C Rubinstein, Brian J Sanderson, Michael W Lloyd, Sergii Domanskyi, Lacey E Dobrolecki, Maihi Fujita, Junya Fujimoto, Guanghua Xiao, Ryan C Fields, Jacqueline L Mudd, Xiaowei Xu, Melinda G Hollingshead, Shahanawaz Jiwani, Saul Acevedo, Pdxnet Consortium, Brandi N Davis-Dusenbery, Peter N Robinson, Jeffrey A Moscow, James H Doroshow, Nicholas Mitsiades, Salma Kaochar, Chong-Xian Pan, Luis G Carvajal-Carmona, Alana L Welm, Bryan E Welm, Ramaswamy Govindan, Shunqiang Li, Michael A Davies, Jack A Roth, Funda Meric-Bernstam, Yang Xie, Meenhard Herlyn, Li Ding, Michael T Lewis, Carol J Bult, Dennis A Dean, Jeffrey H Chuang

Faculty, Staff and Students Publications

Patient-derived xenografts (PDX) model human intra- and intertumoral heterogeneity in the context of the intact tissue of immunocompromised mice. Histologic imaging via hematoxylin and eosin (H&E) staining is routinely performed on PDX samples, which could be harnessed for computational analysis. Prior studies of large clinical H&E image repositories have shown that deep learning analysis can identify intercellular and morphologic signals correlated with disease phenotype and therapeutic response. In this study, we developed an extensive, pan-cancer repository of >1,000 PDX and paired parental tumor H&E images. These images, curated from the PDX Development and Trial Centers Research Network Consortium, had a …

Barriers And Facilitators To Healthy Eating In Disadvantaged Adults Living In The Uk:: A Scoping Review, R Briazu, F Masood, Louise Hunt, Clare Pettinger, Carol Wagstaff, R Mccloy

School of Health Professions

In the UK people living in disadvantaged communities are less likely than those with higher socio-economic status to have a healthy diet. To address this inequality, it is crucial scientists, practitioners and policy makers understand the factors that hinder and assist healthy food choice in these individuals. In this scoping review, we aimed to identify barriers and facilitators to healthy eating among disadvantaged individuals living in the UK. Additionally, we used the Theoretical Domains Framework (TDF) to synthesise results and provide a guide for the development of theory-informed behaviour change interventions. Five databases were searched, (CINAHL, Embase, MEDLINE, PsycINFO, and …

Pathogenic Variants In Autism Gene Katnal2 Cause Hydrocephalus And Disrupt Neuronal Connectivity By Impairing Ciliary Microtubule Dynamics, Tyrone Despenza, Shujuan Zhao, Sheng Chih Jin, Et Al.

2020-Current year OA Pubs

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (cerebral ventriculomegaly), the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized among patients with autism spectrum disorders (ASD).

Assessment Of Patient-Derived Xenograft Growth And Antitumor Activity: The Nci Pdxnet Consensus Recommendations, Funda Meric-Bernstam, Ramaswamy Govinden, Li Ding, Ryan Fields, Et Al.

2020-Current year OA Pubs

Although patient-derived xenografts (PDX) are commonly used for preclinical modeling in cancer research, a standard approach to in vivo tumor growth analysis and assessment of antitumor activity is lacking, complicating the comparison of different studies and determination of whether a PDX experiment has produced evidence needed to consider a new therapy promising. We present consensus recommendations for assessment of PDX growth and antitumor activity, providing public access to a suite of tools for in vivo growth analyses. We expect that harmonizing PDX study design and analysis and assessing a suite of analytical tools will enhance information exchange and facilitate identification …

Media Optimization Techniques For Microalgae Through Technological Advancements: A Mini Review, Khairul A. Radzun, Hasan M. Agha, Nur Farrahim F. Abdullah, Mas I. Ahmad, Igor Ivanovski, Amjad A. Mohammed, Abdulmutalib Alabeed Alkamil

AUIQ Complementary Biological System

Microalgae have been classified as the most primitive plant species and the ability to grow rapidly makes it very suitable for biomass cultivation by using different technologies over the past years. Microalgal biomass can be used for various productions such as biofuels, food, supplements, and more as it is categorized as environmentally friendly throughout the cultivation process. Nutrients play one of the most important roles in cultivating microalgae besides other factors such as temperature, pH, salinity, inorganic carbon, oxygen, light intensity, and carbon dioxide availability. The technology has become much more advanced in cultivating microalgae for maximizing lipid or biomass …

Orca Annual Report 2023-24, Msu Orca

Steeplechase: An ORCA Student Journal

Quick Facts about ORCA, Academic Year 23-24

• 10 slots filled for Posters-at-the-Capitol with projects from the College of Education and Human Services, the College of Humanities and Fine Arts, the Hutson School of Agriculture, and the Jones College of Science, Engineering & Technology
• 264 student presentations delivered during both Scholars Weeks with support from over 100 individual faculty members
• 28 grants awarded totaling over $21,000
• 15 items published in Steeplechase: An ORCA Student Journal

Review: Protection Of Wooden Structures With Nano-Titanium Dioxide Coating, Zienab Zienab A. Ahmed1*, And M. M. Mosallem2

Journal of Engineering Research

Wood is widely used for various purposes with good performance. Wood works as the main material for furniture, monuments, decorations and constructions. which has the close relationship with human. Durability of wood is important in ensuring an appropriate life for the structure being designed. Wooden construction deteriorates easily due to UV radiation and weather conditions. Many of wood types need a preservative treatment. Several compounds are available for chemical protection, but not all are completely safe for human health. New technologies with low environmental impact and economically feasible are developed, which improves the life cycle of wood. Titanium dioxide is …

Improved Efficiency And Sensitivity Analysis Of 3-D Agent-Based Model For Pain-Related Neural Activity In The Amygdala, Kayla Kraeuter, Carley Reith, Benedict J. Kolber, Rachael Miller Neilan

Spora: A Journal of Biomathematics

Neuropathic pain is caused by nerve injury and involves brain areas such as the central nucleus of the amygdala (CeA). We developed the first 3-D agent-based model (ABM) of neuropathic pain-related neurons in the CeA using NetLogo3D. The execution time of a single ABM simulation using realistic parameters (e.g., 13,000 neurons and 22,000+ neural connections) is an important factor in the model’s usability. In this paper, we describe our efforts to improve the computational efficiency of our 3-D ABM, which resulted in a 28% reduction in execution time on average for a typical simulation. With this upgraded model, we performed …

The Effect Of Chemical Coagulant Dosages On The Removal Of Turbidity From Wastewater, Estabraq Ali Hameed, Rodhan Abdullah Salih, Ali Mohammed Saleh, Hussein M. Issa, Mahmod A. Abdulqader

AUIQ Complementary Biological System

This research aims to compare different coagulants, which are alum, ferric chloride, and polyaluminum chloride, in treating turbidity in water. The objective is to determine the optimal dosage of each coagulant for the removal of visible turbidity at levels of 400, 85, 70, and 40 NTU, respectively. The study also considers the (pH) levels resulting from the addition of coagulants, measures the percentage of remaining materials from the used coagulant (sulfates from alum, chloride from ferric chloride, and chlorides from polyaluminum chloride). A 1000 l tank and its components were controlled by adding the desired pollutants (clay and plant impurities) …

Consequences Of Global Climate Change On Biodiversity And Food Security: A Mini Review, Hasan M. Agha, Abdulmutalib Alabeed Alkamil, Rana Tariq Yahya, Amjad Abdulhadi Mohammed, Zaid Tahseen Ali, Muneer Mohammed Saleh Alsayadi

AUIQ Complementary Biological System

A thriving eco-system and abundant species diversity are crucial for all forms of life on Earth. Whether or not the climate remains stable has a direct impact on biodiversity and the ecosystem services that are provided by that diversity. There is a strong correlation between biodiversity and food security, and this is influencing how the impact of biodiversity on climate change is felt. Changes in the duration of the growth season for plants, the distribution of arable lands, and the availability of high-quality water are all ways in which climate change impacts agriculture. There will be numerous positive effects on …

Evaluation Of Bnp, Upa And Wint5a In Four Stages Of Iraqi Patients With Heart Failure, Raghda Faris Salim, Wafaa Raji Alfatlawi, Muhammed A.H. Aldabagh

AUIQ Complementary Biological System

Heart disease is classified as one of the most serious and widespread diseases in the world, presenting major challenges to public health and leading to high mortality rates. A comprehensive understanding of its causative factors, along with early recognition of signs and symptoms, is essential to achieve rapid diagnosis and promote preventive measures. This research conducted on 100 Iraqi patients divided into four stages according to the criteria of the American College of Cardiology, where each stage includes 25 patients suffering from heart disease. Their ages ranges (40 -75) years. A comparative analysis was performed with 50 healthy individuals serving …

The Importance, Issues And Challenges Of Large Mammal's Conservation In Malaysia, Hasan M. Agha, Abdulmutalib Alabeed Alkamil, Suqi Wang, Abbas Ismayilov, Amjad Abdulhadi Mohammed

AUIQ Complementary Biological System

Malaysia's biodiversity is one of the most important factors that have made the country a habitat for numerous species. Where the tropical climate and rainforests provide an ideal habitat for numerous plants and animals. Massive mammals are among the most important creatures found in Malaysia, and the Malaysian peninsula is home to unique species of mammals. Due to the modification of their living environment, urban development, urban expansion, and population growth have significantly reduced the number of these mammals. Damage to habitats and a decline in large mammal populations have had far-reaching consequences for the ecosystem, with the potential for …

Beyond The Scalpel: Understanding Acute Kidney Problems After Heart Surgery, Navakanth Raju Ramayanam, Sarad Pawar Naik Bukke, Hari Babu Ramenani, Saira Patan, Niranjan Ponna, Supriya Pilliboina, Sahanaz Pinjari, Sri Sathyavathi D., Narayana Goruntla, Tadele Mekuriya Yadesa

AUIQ Complementary Biological System

Acute renal injury (ARI) post cardiac surgery leads to substantial difficulty in going about the treatment, that often results in aggravated morbidity and mortality rates. Through this manuscript, we have the opportunity to cover a basic assessment of ARI complexity, including comorbidities which have been categorized as preoperative, intraoperative, and postoperative factors. The risk of all these ailments may also increase which is due to advanced age and comorbidities such as diabetes and hypertension and may lead to procedures like cardiopulmonary bypass (CPB) and duration of cardiopulmonary bypass. The cardiac procedures under discussion like the Coronary artery bypass surgery (CABG) …

Conversion Of Chicken Rice Waste Into Char Via Hydrothermal, Pyrolysis, And Microwave Carbonization Processes: A Comparative Study, Mahmod A. Abdulqader, Muhammad Akromin Suliman, Tabit Abas Ahmed, Ruihong Wu, Aiman. M. Bobaker, Tiyasha Tiyasha, Mohamed A. Yassin, Nabil Al-Areeq

AUIQ Complementary Biological System

This study aims to convert chicken rice waste (CRW) to chars by hydrothermal carbonatization (HTC), pyrolysis (PY), and microwave irradiation (MW) processes. The operating parameters affecting the HTC process (range of temperatures 120, 140, 160, 180, and 200 °C) for hydro-char production, while the pyrolysis (range of temperatures 400, 500, 600, and 700 ^°C) for pyro-char production, and microwave irradiation (range of microwave power 200, 400, 600, and 800 W) for micro-char production were investigated. Comparative studies of the physicochemical properties of produced chars were investigated by Brunauer-Emmett-Teller (BET), X-ray diffraction (XRD), Fourier transform infrared (FTIR), and scanning electron …

Designing A Model For Conservation Agricultural Extension In Western Iran, Mosayeb Gholami, Amirhossien Alibaygi, Abdolhamid Papzan

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

Conservation agriculture is seen as a new solution to environmental degradation and unsusainable water and soil resources. Since the adoption rate for conservation agriculture in Iran is not high, there is a need to design an extension model in this field. The aim of this study was to design an extension model for conservation agriculture in Kermanshah Province, located in the west of Iran. The study involved two groups: experts in conservation agriculture selected via purposeful sampling with a wide range of expertise, and farmers from Ravansar and Sonqor townships in Kermanshah Province, selected through a multistage clustering technique. The …

Utilizing Collaborating Biomedical Deep Model For Diagnosis Of Ultrasonography Tumor Images, Maytham N. Meqdad, Seifedine Kadry

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

Artificial intelligence models are the most common methods of diagnosing various diseases today. In the meantime, the use of deep learning for faster diagnosis with less error, which is usually less expensive than other methods, is noteworthy. However, these methods are expensive due to the problems of accessing data, including care data such as hospitals and clinics. This article presents a novel federated learning-based approach for ultrasound mammography image classification. In this method, the clients possess their own datasets and are trained to use them. Then, the server, with the help of the trained clients, obtains the best parameters for …

Mitigating Care Provider Turnover For Children With Developmental Disabilities, Abigail Equinoa

Occupational Therapy Student Capstones

No abstract provided.

Math 75: Introduction To Linear Algebra, Sarah K. Merz

Pacific Open Texts

This text is intended to use in a first course of Linear Algebra with a prerequisite of Calculus 1. Topics covered include systems of linear equations, matrix operations and inverses, linear transformations, Markov chains, determinants, eigenvalues and eigenvectors, diagonalization, vector geometry, projections and planes, homogeneous coordinates, subspaces, spanning sets, linear independence, orthogonality, fundamental subspaces, and least squares.

Humanities Center Annual Report 2023-24, Humanities Center, University Of San Diego

Humanities Center Annual Reports

No abstract provided.

Immigrant-Origin Students At The University Of Southern Maine [Report], Marina Chakmakchi Mppm, Ll.M.

Global Talent Navigator

Document providing the full report. Consists of 62 pages plus appendices.

Executive Summary and Highlights

The University of Southern Maine (USM) is uniquely positioned to serve as a regional educational hub for New Americans. USM helps New Americans to achieve their educational goals, become self-sufficient, and thrive in Maine’s communities. This report and its findings aim to guide future endeavors in attracting and retaining immigrant-origin students. The proposed recommendations will foster an inclusive campus, ultimately contributing to the well-being of the entire student population at USM. This report attempts to offer system improvements to effectively address the needs of immigrant-origin …

Implementation Of A Mindfulness Approach To Emotional Regulation In A Public High School., Kaelin Cherise Shay

Doctor of Nursing Practice Papers

According to the Gallup and Walton Family Foundation-State of American Youth Survey for 2023, schools in the United States received an average grade of C+ when it comes to supporting their students’ mental health, highlighting a potential area for improvement in the school system (Wilcoxon & Marken, 2023). This quality improvement project aimed to teach high school students about emotional regulation using a mindfulness platform and evidence-based techniques designed for the school environment. The sessions focused on improving the students’ understanding of emotions and emotional regulation and helping them apply techniques to regulate emotions in a healthy manner.

This project …

Sustainability Spotlight, Hanley Sustainability Institute, University Of Dayton

Hanley Sustainability Institute Newsletter

No abstract provided.

Air Force Institute Of Technology Research Report 2022, Air Force Institute Of Technology

AFIT Documents

This report summarizes the research activities of the Air Force Institute of Technology's Graduate School of Engineering and Management, as well as AFIT's research centers. It describes research interests and faculty expertise; list student theses/dissertations; identifies research sponsors and contributions; and outlines the procedure for contacting entities within the Institution.

Air Force Institute Of Technology Research Report 2021, Air Force Institute Of Technology

AFIT Documents

This report summarizes the research activities of the Air Force Institute of Technology's Graduate School of Engineering and Management, as well as AFIT's research centers. It describes research interests and faculty expertise; list student theses/dissertations; identifies research sponsors and contributions; and outlines the procedure for contacting entities within the Institution.

Summer 2024, Augustana College, Rock Island Illinois

Augustana Magazine

No abstract provided.

Temporal Variations In Aboveground Biomass, Nutrient Content, And Ecological Stoichiometry In Young And Middle-Aged Stands Of Chinese Fir Forests, Zhiqiang Li, Can Mao, Qinxiang Wu, Yuanying Peng, Jun Wang, Bin Zhang, Sheng Zhang, Ziaocui Liang, Wende Yan, Xiaoyong Chen

Faculty Authors and Creators Reception

Understanding the ecological dynamics of forest ecosystems, particularly the influence of forest age structure on soil carbon (C), nitrogen (N), and phosphorus (P) content, is crucial for effective forest management and conservation. This study aimed to investigate the nutrient storage and ecological stoichiometry across different-aged stands of Chinese fir forests. Soil samples were collected from various depths (0–15 cm, 15–30 cm, and 30–45 cm) across four age groups of Chinese fir forests (8-year-old, 12-year-old, 20-year-old, and 25-year-old) in the Forest Farm, Pingjiang County, China. Soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP) were measured, and their stoichiometries …

Grns Associated With Soybean Nodules Occupied By High- And Low-Capacity Nitrogen-Fixing Rhizobia, Ramandeep Kaur

Agronomy, Horticulture and Plant Science Dataset Collection

This dataset is a supplementary file for the graduate thesis.

File type: xlxs
File size: 61.2 MB

How Will Climate Change-Induced Increases In Wildfire Frequency Affect Soil Microbial Communities?, Bahar Saadaie Jahromi, David Karowe

Waldo Library Student Exhibits

As climate change progresses, wildfires will become more common, increasing their impact on soil microbial ecosystems. This research examines how increased fire frequency affects soil microbial communities and whether effects differ for communities associated with different tree species. Soil samples were collected from under five individuals of four tree species within each of four 1-ha plots that had experienced fire from 24 to 111 years ago. Samples were analyzed for microbial DNA using next generation sequencing techniques in order to explore the influence of fire return interval and tree species on microbial diversity and community structure. Correlations were also examined …

Learning From Oversampling: A Systematic Exploitation Of Oversampling To Address Data Scarcity Issues In Deep Learning- Based Magnetic Resonance Image Reconstruction, Ibsa Kumara Jalata, Reeshad Khan, Ukash Nakarmi

Computer Science and Computer Engineering Faculty Publications and Presentations

Data acquisitions in Magnetic Resonance Imaging (MRI) are inherently slow due to sequential acquisition protocol. Image reconstruction from under-sampled data is posed as an inverse problem in traditional model-based learning paradigms. Recent data-centric learning frameworks such as deep learning (DL) frameworks are data hungry, and demand a large, labeled training data sets. To address the lack of large training datasets, in MRI reconstructions, researchers approach the problem in two ways: (1) unsupervised method where the model is trained without the presence of fully sampled data. (2) using a method that efficiently use the limited dataset for training purpose. In this …

National Parks Field Journal, Isadora Davis

Art and Design Student Scholarship and Projects

A handwritten, richly illustrated field journal by Binghamton University art major Isadora Davis, recording a trip through national parks in the American West via SUNY Broome's BIO 217: Ecology of National Parks. Davis uses colored pencil drawings and pressed botanical specimens to record landscapes, birds, mammals, and plant life in Grand Teton, Yellowstone, Wind Cave, and Badlands National Parks, as well as Custer State Park. Davis's sketches and diagrams visually explore how to decode past landscapes from current formations, while her written entries explain species diversity, animal behavior, and the mechanisms causing geological formations and geothermal events. Part memoir of …