Digital Commons Network^™

A Probabilistic View Of Protein Stability, Conformational Specificity, And Design, Jacob A. Stern, Tyler J. Free, Kimberlee L. Stern, Spencer Gardiner, Nicholas A. Dalley, Bradley Charles Bundy, Joshua L. Price, David Wingate, Dnnis Della Corte

Faculty Publications

Various approaches have used neural networks as probabilistic models for the design of protein sequences. These "inverse folding" models employ different objective functions, which come with trade-offs that have not been assessed in detail before. This study introduces probabilistic definitions of protein stability and conformational specificity and demonstrates the relationship between these chemical properties and the p(stucture|seq) Boltzmann probability objective. This links the Boltzmann probability objective function to experimentally verifiable outcomes. We propose a novel sequence decoding algorithm, referred to as “BayesDesign”, that leverages Bayes’ Rule to maximize the p(stucture|seq) objective instead of the p(seq|structure) objective common in inverse folding …

Virtual Blebbistatin: A Robust And Rapid Software Approach To Motion Artifact Removal In Optical Mapping Of Cardiomyocytes, Louis G Woodhams, Jingxuan Guo, David Schuftan, John J Boyle, Kenneth M Pryse, Elliot L Elson, Nathaniel Huebsch, Guy M Genin

2020-Current year OA Pubs

Fluorescent reporters of cardiac electrophysiology provide valuable information on heart cell and tissue function. However, motion artifacts caused by cardiac muscle contraction interfere with accurate measurement of fluorescence signals. Although drugs such as blebbistatin can be applied to stop cardiac tissue from contracting by uncoupling calcium-contraction, their usage prevents the study of excitation-contraction coupling and, as we show, impacts cellular structure. We therefore developed a robust method to remove motion computationally from images of contracting cardiac muscle and to map fluorescent reporters of cardiac electrophysiological activity onto images of undeformed tissue. When validated on cardiomyocytes derived from human induced pluripotent …

A Multicenter Analysis Of Abnormal Chromosomal Microarray Findings In Congenital Heart Disease, Benjamin J Landis, Lindsey R Helvaty, Gabrielle C Geddes, Jiuann-Huey Ivy Lin, Svetlana A Yatsenko, Cecilia W Lo, William L Border, Stephanie Burns Wechsler, Chaya N Murali, Mahshid S Azamian, Seema R Lalani, Robert B Hinton, Vidu Garg, Kim L Mcbride, Jennelle C Hodge, Stephanie M Ware

Faculty, Staff and Students Publications

Background

Chromosomal microarray analysis (CMA) provides an opportunity to understand genetic causes of congenital heart disease (CHD). The methods for describing cardiac phenotypes in patients with CMA abnormalities have been inconsistent, which may complicate clinical interpretation of abnormal testing results and hinder a more complete understanding of genotype–phenotype relationships.

Methods and Results

Patients with CHD and abnormal clinical CMA were accrued from 9 pediatric cardiac centers. Highly detailed cardiac phenotypes were systematically classified and analyzed for their association with CMA abnormality. Hierarchical classification of each patient into 1 CHD category facilitated broad analyses. Inclusive classification allowing multiple CHD types per …

Epigenetic Induction Of Smooth Muscle Cell Phenotypic Alterations In Aortic Aneurysms And Dissections, Abhijit Chakraborty, Yanming Li, Chen Zhang, Yang Li, Kimberly R Rebello, Shengyu Li, Samantha Xu, Hernan G Vasquez, Lin Zhang, Wei Luo, Guangyu Wang, Kaifu Chen, Joseph S Coselli, Scott A Lemaire, Ying H Shen

Faculty, Staff and Students Publications

BACKGROUND: Smooth muscle cell (SMC) phenotypic switching has been increasingly detected in aortic aneurysm and dissection (AAD) tissues. However, the diverse SMC phenotypes in AAD tissues and the mechanisms driving SMC phenotypic alterations remain to be identified.

METHODS: We examined the transcriptomic and epigenomic dynamics of aortic SMC phenotypic changes in mice with angiotensin II-induced AAD by using single-cell RNA sequencing and single-cell sequencing assay for transposase-accessible chromatin. SMC phenotypic alteration in aortas from patients with ascending thoracic AAD was examined by using single-cell RNA sequencing analysis.

RESULTS: Single-cell RNA sequencing analysis revealed that aortic stress induced the transition of …

Senate Executive Committee Minutes September 18, 2023, Bronx Community College Senate Executive Committee

BCC Governance Archives

Minutes for the meeting of the Senate Executive Committee on September 18, 2023.

Dietary Patterns Of Children From The Amazon Region Of Ecuador: A Descriptive, Qualitative Investigation, Kristin N. Murphy, Lisa Boyce, Eduardo Ortiz, Marcela Santos, Gloria Balseca

Human Development and Family Studies Faculty Publications

Many young children in Ecuador suffer from high rates of malnutrition and stunting that affect their long-term growth and development. Little is known about the dietary patterns of children from the Amazon region who experience some of the highest rates of stunting (height-for-age) within Ecuador. Semi-structured interviews were conducted with 50 mothers of young children living in the Ecuadorian Amazon. In addition to descriptions of overall dietary patterns, three themes emerged from the interviews relating to strengths mothers have in feeding their children healthy diets: knowledge, autonomous and independent children, and supportive and responsive parenting. Five themes were found relating …

Genetic Improvement Of Tocotrienol Content Enhances The Oxidative Stability Of Canola Oil, Min Deng, Hao Chen, Wei Zhang, Edgar B. Cahoon, Yongming Zhou, Chunyu Zhang

Center for Plant Science Innovation: Faculty Publications

Background: Tocotrienols and tocopherols, which are synthesized in plastids of plant cells with similar functionalities, comprise vitamin E to serve as a potent lipid-soluble antioxidant in plants. The synthesis of tocopherols involves the condensation of homogentisic acid (HGA) and phytyl diphosphate (PDP) under the catalysis of homogentisate phytyltransferase (HPT). Tocotrienol synthesis is initiated by the condensation of HGA and geranylgeranyl diphosphate (GGDP) mediated by homogentisate geranylgeranyl transferase (HGGT). As one of the most important oil crops, canola seed is regarded as an ideal plant to efficiently improve the production of vitamin E tocochromanols through genetic engineering approaches. However, only …

The Utah Statesman, September 18, 2023, Utah State University

The Utah Statesman

Weekly student newspaper of Utah State University in Logan.

The Rider (2023-09-18), Natalie Lapsley

The Rider Archives

Vol.9 No.4

Pathways To Success: Unleashing Experiential Learning In Higher Education For Aspiring Law Enforcement Professionals, Leonard A. Averhoff

Seton Hall University Dissertations and Theses (ETDs)

This generic qualitative inquiry (GQI) explores experiential learning in higher education for students interested in law enforcement careers. Through interviews and focus group discussions, the study aimed to uncover insights into the perceptions and experiences of students engaging in a university student security program (USSP). The USSP allows full-time students to work as uniformed, unarmed paid employees of the university’s police department providing various law enforcement type functions. The research identified five themes that emerged from the data analysis: exposure, career development, training, leadership, and personal growth.

The theme of exposure highlighted the importance of hands-on learning, allowing students to …

Comments Of American Economic Liberties Project On 2023 Draft Merger Guidelines, Robert H. Lande, Erik Peinert

All Faculty Scholarship

The American Economic Liberties Project (“Economic Liberties”) is a nonprofit research and advocacy organization dedicated to understanding and addressing the problem of concentrated economic power in the United States. We submit this comment with Professor Robert H. Lande, the Venable Professor of Law Emeritus at the University of Baltimore School of Law, in response to the Draft Merger Guidelines proposed by the Department of Justice Antitrust Division and the Federal Trade Commission (together, “the Agencies”). Economic Liberties and Professor Lande write together in support of the Agencies’ efforts to improve the Merger Guidelines, last updated in 2010, to match the …

Animal Board Invited Review: Practical Applications Of Genomic Information In Livestock, D. P. Berry, Matthew L. Spangler

Department of Animal Science: Faculty Publications

Access to high-dimensional genomic information in many livestock species is accelerating. This has been greatly aided not only by continual reductions in genotyping costs but also an expansion in the services available that leverage genomic information to create a greater return-on-investment. Genomic information on individual animals has many uses including (1) parentage verification and discovery, (2) traceability, (3) karyotyping, (4) sex determination, (5) reporting and monitoring of mutations conferring major effects or congenital defects, (6) better estimating inbreeding of individuals and coancestry among individuals, (7) mating advice, (8) determining breed composition, (9) enabling precision management, and (10) genomic evaluations; genomic …

A Naturally Derived Watercress Flower-Based Phenethyl Isothiocyanate-Enriched Extract Induces The Activation Of Intrinsic Apoptosis Via Subcellular Ultrastructural And Ca2+ Efflux Alterations In An In Vitro Model Of Human Malignant Melanoma, Sotiris Kyriakou, Louiza Potamiti, Nikoletta Demosthenous, Tom Amery, Kyle Stewart, Paul G. Winyard, Rodrigo Franco, Aglaia Pappa, Mihalis I. Panayiotidis

School of Veterinary and Biomedical Sciences: Faculty Publications

The aim of the current study was to (i) extract isolated fractions of watercress flowers enriched in polyphenols, phenethyl isothiocyanate and glucosinolates and (ii) characterize the anticancer mode of action of non-lethal, sub-lethal and lethal concentrations of the most potent extract fraction in primary (A375) and metastatic (COLO-679) melanoma cells as well as non-tumorigenic immortalized keratinocyte (HaCaT) cells. Cytotoxicity was assessed via the Alamar Blue assay, whereas ultrastructural alterations in mitochondria and the endoplasmic reticulum were determined via transmission electron microscopy. Mitochondrial membrane depolarization was determined using Mito-MP dye, whereas apoptosis was evaluated through the activation of caspases-3, -8 and …

Exploring Nonprofit Views On Water Management And Conservation Strategies, Jillian Marie Farley

Dissertations and Theses

Valuing water resources presents a multitude of methodological and theoretical challenges, including economics, biodiversity, and cultural significance. Information is not readily available on the individuals working every day on water resource management and how they navigate such a complex topic. This project is designed to help all parties better understand the opinions of individuals working for nonprofit organizations and Watershed Councils in the State of Oregon about current methods of water resource conservation. The results reflect respondents’ personal views on the process and practices of valuing water and are designed to prompt deeper discussions between the organizations, communities, and policymakers. …

September 18, 2023

The Gavel Gazette

No abstract provided.

The Echo: September 18, 2023, Taylor University

2023-2024 (Volume 111)

No abstract provided.

Neighborhood Disadvantage And Neural Correlates Of Threat And Reward Processing In Survivors Of Recent Trauma, E. Kate Webb, Timothy D. Ely, Grace E. Rowland, Lauren A.M. Lebois, Sanne J.H. Van Rooij, Steven E. Bruce, Tanja Jovanovic, Stacey L. House, Francesca L. Beaudoin, Xinming An, Thomas C. Neylan, Gari D. Clifford, Sarah D. Linnstaedt, Laura T. Germine, Kenneth A. Bollen, Scott L. Rauch, John P. Haran, Alan B. Storrow, Christopher Lewandowski, Paul I. Musey, Phyllis L. Hendry, Sophia Sheikh, Christopher W. Jones, Brittany E. Punches, Robert A. Swor, Jose L. Pascual, Mark J. Seamon, Elizabeth M. Datner, Claire Pearson, David A. Peak, Roland C. Merchant, Robert M. Domeier, Niels K. Rathlev, Paulina Sergot, Leon D. Sanchez, Ronald C. Kessler, Karestan C. Koenen, Samuel A. Mclean, Jennifer S. Stevens, Kerry J. Ressler, Nathaniel G. Harnett

Department of Emergency Medicine Faculty Papers

IMPORTANCE: Differences in neighborhood socioeconomic characteristics are important considerations in understanding differences in risk vs resilience in mental health. Neighborhood disadvantage is associated with alterations in the function and structure of threat neurocircuitry.

OBJECTIVE: To investigate associations of neighborhood disadvantage with white and gray matter and neural reactivity to positive and negative stimuli in the context of trauma exposure.

DESIGN, SETTING, AND PARTICIPANTS: In this cross-sectional study, survivors of trauma who completed sociodemographic and posttraumatic symptom assessments and neuroimaging were recruited as part of the Advancing Understanding of Recovery After Trauma (AURORA) study between September 2017 and June 2021. Data …

Cultural Competence In Nursing School Curricula, Mayra P. Toney

Dissertations

The purpose of this study was to determine the benefit of both classroom instruction and an immersive clinical experience for the development of cultural competence skills among student nurses. The 3-D Model for Culturally Congruent Care was the framework used for this quantitative descriptive correlational study. The premise of the model is to draw upon the knowledge that culturally competent care derives from the healthcare provider and client level, an essential factor to the delivery of culturally competent healthcare. A convenience sample of 74 student nurses from two separate cohorts enrolled in a diploma-based program were asked to complete the …

Targeted Single-Cell Proteomic Analysis Identifies New Liquid Biopsy Biomarkers Associated With Multiple Myeloma, Sonia M Setayesh, Libere J Ndacayisaba, Kate E Rappard, Valerie Hennes, Luz Yurany Moreno Rueda, Guilin Tang, Pei Lin, Robert Z Orlowski, David E Symer, Elisabet E Manasanch, Stephanie N Shishido, Peter Kuhn

Faculty, Staff and Student Publications

Multiple myeloma (MM) is accompanied by alterations to the normal plasma cell (PC) proteome, leading to changes to the tumor microenvironment and disease progression. There is a great need for understanding the consequences that lead to MM progression and for the discovery of new biomarkers that can aid clinical diagnostics and serve as targets for therapeutics. This study demonstrates the applicability of utilizing the single-cell high-definition liquid biopsy assay (HDSCA) and imaging mass cytometry to characterize the proteomic profile of myeloma. In our study, we analyzed ~87,000 cells from seven patient samples (bone marrow and peripheral blood) across the myeloma …

Richard Schaffer Oral History, Richard Schaffer, Lorenzo Spaccarelli

Raymond College

No abstract provided.

The Effect Of Slow-Release Milk Replacer Feeding On Health And Behaviour Parameters In Dairy Breed Calves, Lea Krump, Ríona G. Sayers, Katie Sugrue, Emer Kennedy, Jim O'Mahony, Gearoid Sayers

Department of Biological Sciences Publications

The aim of this research paper was to evaluate the effect of a slow-release milk replacer on health and behaviour of neonatal dairy calves. This was done with the potential benefits to welfare during transport in mind. A total of 15 calves were randomly divided into three groups of 5, namely, a control group fed twice in 24 h with 3 l of a conventional milk replacer, a slow-release group fed once in 24 h with 2 l of conventional milk replacer and 1 litre of a specialised micro-encapsulated feed and an enriched-replacer group fed once in 24h with 3L …

Seacoast Sips Of Science Brings Unh Research To The Community, Beth Potier

UNH Today Archive

No abstract provided.

Correlative Imaging Of Three-Dimensional Cell Culture On Opaque Bioscaffolds For Tissue Engineering Applications, Mone’T Sawyer, Josh Eixenberger, Olivia Nielson, Jacob Manzi, Cadré Francis, Raquel Montenegro-Brown, Harish Subbaraman, David Estrada

Materials Science and Engineering Faculty Publications and Presentations

Three-dimensional (3D) tissue engineering (TE) is a prospective treatment that can be used to restore or replace damaged musculoskeletal tissues, such as articular cartilage. However, current challenges in TE include identifying materials that are biocompatible and have properties that closely match the mechanical properties and cellular microenvironment of the target tissue. Visualization and analysis of potential 3D porous scaffolds as well as the associated cell growth and proliferation characteristics present additional problems. This is particularly challenging for opaque scaffolds using standard optical imaging techniques. Here, we use graphene foam (GF) as a 3D porous biocompatible substrate, which is scalable, reproducible, …

Learning Science: Physical And Life Sciences In Curricula Across U.S. Schools Of Nursing, Valerie C. Sauda

Dissertations

Nursing educators are being challenged to provide curriculum that meets the changing healthcare environment and demand for creative, innovative nurses to assist in transforming healthcare into the future (Benner, Sutphen, Leonard, & Day, 2010; Institute Of Medicine, 2011). The liberal education provided within a baccalaureate of science in nursing (BSN) degree program provides a diversity of courses within the curriculum, including courses in the natural, physical, mathematical, and social sciences (American Association of Colleges of Nursing [AACN], 2008). Although nursing programs have included science courses in curriculum since the early 1900s (Nutting & Dock, 1907), there is lack of nursing …

Recommended Editions (1/3)

The International Journal of Ecopsychology (IJE)

Introduction to Recommended Editions (1/3)

1) Open Semiotics (Vols. 1-4) Amir Biglari (Ed.)

2) The Reliability of UFO Witness Testimony, Vicente-Juan Ballester-Olmos and Richard W. Heiden, (Eds.)

The Deep Ecology Movement

The International Journal of Ecopsychology (IJE)

There are two great streams of environmentalism in the latter half of the twentieth century. One stream is reformist, attempting to control some of the worst of the air and water pollution and inefficient land use practices in industrialized nations and to save a few of the remaining pieces of wildlands as "designated wilderness areas." The other stream supports many of the reformist goals but is revolutionary, seeking a new metaphysics, epistemology, cosmology, and environmental ethics of person/planet. This paper is an intellectual archeology of the second of these streams of environmentalism, which I will call deep ecology.

Editorial Postscript

The International Journal of Ecopsychology (IJE)

No abstract provided.

Intouch Week Of September 18, 2023, New York Medical College

InTouch

• The CDM Hosts Groundbreaking For New Simulation and Educational Facility
• GSBMS Hosts Biennial Ph.D. Lab Coat Ceremony
• NYMC Goes Gold for Childhood Cancer Awareness Month
• Women in Medicine Book Discussion What We Bring to the Practice of Medicine: Perspectives from Women Physicians
• Founder's Dinner 2023
• The Office of Student Mental Health and Wellness Prioritizes Student Well-Being

Agricultural Sustainability In The Age Of Deep Learning: Current Trends, Challenges, And Future Trajectories, Mona Mohamed

Sustainable Machine Intelligence Journal

Agriculture stands as the essential foundation of human sustenance, confronting the dual challenge of providing for a burgeoning global populace while safeguarding the integrity of the natural environment. This comprehensive review paper undertakes an exhaustive exploration of the continually evolving sphere of agricultural sustainability, traversing the multifaceted terrain of present-day trends, technological innovations, and the promising trajectories that lie ahead. From the vantage point of precision agriculture and climate-smart methodologies to the strategic integration of deep learning technologies, it offers a comprehensive examination of pioneering approaches that are redefining the agricultural domain. Within, it elucidates the intrinsic relationship between agriculture …

Retraction Note: Mir20a/106a-Wtx Axis Regulates Rhogdia/Cdc42 Signaling And Colon Cancer Progression, Gui-Fang Zhu, Yang-Wei Xu, Jian Li, Hui-Lin Niu, Wen-Xia Ma, Jia Xu, Pei-Rong Zhou, Xia Liu, Dan-Li Ye, Xiao-Rong Liu, Tao Yan, Wei-Ke Zhai, Zhi-Jun Xu, Chun Liu, Lei Wang, Hao Wang, Jia-Mao Luo, Li Liu, Xuan-Qi Li, Suiqun Guo, Hui-Ping Jiang, Peng Shen, Hui-Kuan Lin, Di-Hua Yu, Yan-Qing Ding, Qing-Ling Zhang

Faculty, Staff and Student Publications

No abstract provided.