Digital Commons Network^™

A Review Of Literature On The Usage Of Low-Cost Sensors To Measure Particulate Matter, Amit U. Raysoni, Sai Deepak Pinakana, Esmeralda Mendez, Dawid K. Wladyka, Katarzyna Sepielak, Owen Temby

School of Earth, Environmental, & Marine Sciences Faculty Publications

With advances in technological sciences, individuals can utilize low-cost air monitoring sensors to record air quality at homes, schools, and businesses. Air quality data collected from LCSs are publicly accessible, informing the community of the air quality around them. It is important to measure local and regional particulate matter (PM) concentrations to keep the public involved, especially those with specific health concerns, such as asthma, wheezing, and seasonal allergies. The number of studies involving the use of LCSs to evaluate PM levels is increasing with more manufacturers producing ‘easy to use’ LCSs targeting the public. The goal of this review …

Spartan Daily, March 14, 2023, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2023

Volume 160, Issue 20

Acute Acat1/Soat1 Blockade Increases Mam Cholesterol And Strengthens Er-Mitochondria Connectivity., Taylor C Harned, Radu V Stan, Ze Cao, Rajarshi Chakrabarti, Henry N Higgs, Catherine C Y Chang, Ta Yuan Chang

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

Cholesterol is a key component of all mammalian cell membranes. Disruptions in cholesterol metabolism have been observed in the context of various diseases, including neurodegenerative disorders such as Alzheimer's disease (AD). The genetic and pharmacological blockade of acyl-CoA:cholesterol acyltransferase 1/sterol O-acyltransferase 1 (ACAT1/SOAT1), a cholesterol storage enzyme found on the endoplasmic reticulum (ER) and enriched at the mitochondria-associated ER membrane (MAM), has been shown to reduce amyloid pathology and rescue cognitive deficits in mouse models of AD. Additionally, blocking ACAT1/SOAT1 activity stimulates autophagy and lysosomal biogenesis; however, the exact molecular connection between the ACAT1/SOAT1 blockade and these observed benefits remain …

Tsks Localizes To Nuage In Spermatids And Regulates Cytoplasmic Elimination During Spermiation, Taichi Noda, Akane Morohoshi, Martin M Matzuk, Masahito Ikawa

Faculty, Staff and Students Publications

Spermatozoa have a streamlined shape to swim through the oviduct to fertilize oocytes. To become svelte spermatozoa, spermatid cytoplasm must be eliminated in several steps including sperm release, which is part of spermiation. Although this process has been well observed, the molecular mechanisms that underlie it remain unclear. In male germ cells, there are membraneless organelles called nuage, which are observed by electron microscopy in various forms of dense material. Reticulated body (RB) and chromatoid body remnant (CR) are two types of nuage in spermatids, but the functions of both are unknown. Using CRISPR/Cas9 technology, we deleted the entire coding …

In Vivo Functional Characterization Of Egfr Variants Identifies Novel Drivers Of Glioblastoma, Estefania Luna-Figueroa, Alexis Cervantes, Rachel Curry, Carrie A Mohila, Ganesh Rao, Ali Jalali, Gordon B Mills, Kenneth L Scott, Benjamin Deneen

Faculty, Staff and Students Publications

BACKGROUND: Glioblastoma is the most common and aggressive primary brain tumor. Large-scale sequencing initiatives have cataloged its mutational landscape in hopes of elucidating mechanisms driving this deadly disease. However, a major bottleneck in harnessing this data for new therapies is deciphering "driver" and "passenger" events amongst the vast volume of information.

METHODS: We utilized an autochthonous, in vivo screening approach to identify driver, EGFR variants. RNA-Seq identified unique molecular signatures of mouse gliomas across these variants, which only differ by a single amino acid change. In particular, we identified alterations to lipid metabolism, which we further validated through an unbiased …

Human Schistosomiasis Vaccines As Next Generation Control Tools

Faculty, Staff and Students Publications

No abstract provided.

Student Preferences For Active Learning And Their Beliefs, Experiences, And Knowledge, Tammy Shilling, Jerome Thayer, Anneris Coria-Navia, Heather Ferguson

Faculty Publications

Active teaching methods are believed to facilitate higher-order thinking skills and prepare allied health students for independent clinical decision-making. This quantitative, correlational study aimed to explain the relationships between student preferences for active over traditional methods and their beliefs, the frequency and positiveness of their experiences, and the extent of knowledge they have received regarding active and traditional teaching methods. Two hundred and thirty students completed a 53-item online survey. Students were enrolled in a Doctor of Physical Therapy, Masters in Speech-language Pathology, or Bachelor of Science Nursing program in one of seventeen participating institutions across a ten-state Midwest region. …

Hypermitotic Meningiomas Harbor Dna Methylation Subgroups With Distinct Biological And Clinical Features, James C Bayley, Akdes S Harmanci, Sybren L N Maas, Sandro Santagata, Tiemo Klisch, Arie Perry, Wenya Linda Bi, Felix Sahm, Akash J Patel, Stephen T Magill, David R Raleigh

Faculty, Staff and Students Publications

BACKGROUND: Meningiomas, the most common primary intracranial tumors, can be separated into 3 DNA methylation groups with distinct biological drivers, clinical outcomes, and therapeutic vulnerabilities. Alternative meningioma grouping schemes using copy number variants, gene expression profiles, somatic short variants, or integrated molecular models have been proposed. These data suggest meningioma DNA methylation groups may harbor subgroups unifying contrasting theories of meningioma biology.

METHODS: A total of 565 meningioma DNA methylation profiles from patients with comprehensive clinical follow-up at independent discovery (n = 200) or validation (n = 365) institutions were reanalyzed and classified into Merlin-intact, Immune-enriched, or Hypermitotic DNA methylation …

Impact Of Crowding On The Diversity Of Expanding Populations., Carl F. Schreck, Diana Fusco, Yuya Karita, Stephen Martis, Jona Kayser, Marie-Cécilia Duvernoy, Oskar Hallatschek

Manuscripts, Articles, Book Chapters and Other Papers

Crowding effects critically impact the self-organization of densely packed cellular assemblies, such as biofilms, solid tumors, and developing tissues. When cells grow and divide, they push each other apart, remodeling the structure and extent of the population's range. Recent work has shown that crowding has a strong impact on the strength of natural selection. However, the impact of crowding on neutral processes, which controls the fate of new variants as long as they are rare, remains unclear. Here, we quantify the genetic diversity of expanding microbial colonies and uncover signatures of crowding in the site frequency spectrum. By combining Luria-Delbrück …

Editorial: Inter-Organ Crosstalk During Exercise In Health And Disease: Extracellular Vesicles As New Kids On The Block, Kenneth Verboven, Ivan Jose Vechetti Jr

Department of Nutrition and Health Sciences: Faculty Publications

Within exercise physiology, the study of factors potentially mediating interorgan crosstalk during and after exercise is a fascinating field of research. As exercise activates a plethora of metabolic pathways in several tissues, organs and systems, examining the underlying biological mechanisms contributing to exercise related metabolic benefits is imperative. Since two decades, the skeletal muscle is known to secrete humoral factors into the circulation in response to exercise, originally described as “myokines” by Pedersen et al. (2003). These myokines are now well known and extensively studied in the field of exercise science (Pedersen and Febbraio, 2012). Interestingly, exercise also triggers other …

Large And Stable Genome Edits At The Sorghum Alpha Kafirin Locus Result In Changes In Chromatin Accessibility And Globally Increased Expression Of Genes Encoding Lysine Enrichment, J. Preston Hurst, Abou Yobi, Aixia Li, Shirley Sato, Thomas E. Clemente, Ruthie Angelovici

Department of Agronomy and Horticulture: Faculty Publications

Introduction: Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.

Methods: A single consensus …

How Do Classroom-Turnover Times Depend On Lecture-Hall Size?, Joseph Benson, Mariya Bessonov, Korana Burke, Simone Cassani, Maria-Veronica Ciocanel, Daniel B. Cooney, Alexandria Volkening

Publications and Research

Academic spaces in colleges and universities span classrooms for 10 students to lecture halls that hold over 600 people. During the break between consecutive classes, students from the first class must leave and the new class must find their desks, regardless of whether the room holds 10 or 600 people. Here we address the question of how the size of large lecture halls affects classroom-turnover times, focusing on non-emergency settings. By adapting the established social-force model, we treat students as individuals who interact and move through classrooms to reach their destinations. We find that social interactions and the separation time …

Large And Stable Genome Edits At The Sorghum Alpha Kafirin Locus Result In Changes In Chromatin Accessibility And Globally Increased Expression Of Genes Encoding Lysine Enrichment, J. Preston Hurst, Abou Yobi, Aixia Li, Shirley Sato, Thomas E. Clemente, Ruthie Angelovici, David R. Holding

Department of Agronomy and Horticulture: Faculty Publications

Introduction: Sorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.

Methods: A single consensus …

Relationship Between Treatment Comorbidities And Hiv Viral Suppression Among People Who Live With Aids In Johannesburg., Nwogo Immaculata Ekeji, Tolulope A. Osoba, Hebatullah Tawfik, Mehdi Agha

Journal of Social, Behavioral, and Health Sciences

HIV has globally infected over 37.9 million people, of which 28.2 million (73%) are on antiretroviral treatment, and 66% of those on treatment are virally suppressed. In South Africa, however, low rate of viral suppression (47%) among people living with HIV is a major health problem that has continued to fuel HIV prevalence. A cross-sectional quantitative research design was used to investigate the relationship between treatment comorbidities and viral suppression among HIV-infected adults aged 18–49 who were diabetic, had cancer, or tuberculosis in Johannesburg. HIV Care Continuum formed the theoretical framework for this research. An existing HIV-infected patient de-identifiable dataset …

The Thin Line Between Conventional Dendritic Cells (Cdcs) And Group 3 Innate Lymphoid Cells (Ilc3s) In The Gut, Alina Ulezko Antonova, José Luís Fachi, Susan Gilfillan, Marco Colonna

2020-Current year OA Pubs

Dendritic cells (DCs) express major histocompatibility complex class II (MHC-II) and are best known for proficiently presenting antigens to T cells, thereby eliciting specific adaptive T cell responses. Moreover, conventional DCs (cDCs) are specifically adept at handling intestinal antigens. Relatively recent discoveries and investigations have proven the existence of a new group of innate lymphocytes that reside in tissues like the intestine. They lack specific antigen receptors and can express MHC-II. These group 3 innate lymphoid cells (ILC3s) comprise a subset of heterogeneous innate lymphocytes that mirror the phenotype and functions of T-helper cells and act in the first line …

Enzalutamide-Induced Signatures Revealed By Epigenetic Plasticity Using Single-Cell Multi-Omics Sequencing In Prostate Cancer, Huihui Fan, Jinze Li, Astrid M Manuel, Zhongming Zhao

Faculty, Staff and Student Publications

Prostate cancer is morphologically and molecularly heterogeneous, which poses obstacles for early diagnosis and treatment. Advancements in understanding the heterogeneity of prostate cancer will help navigate through these challenges and ultimately benefit patients. In this study, we integrated single-cell sequencing for transposase-accessible chromatin and whole transcriptome in prostate cancer cell lines, aiming to decode the epigenetic plasticity upon enzalutamide (ENZ) treatment. By comparing the cell populations representing early-treatment response or resistance to the initial tumor cells, we identified seven signature gene sets; they present consistent trends of chromatin closing co-occurred with down-regulated genes during early response and chromatin opening with …

Renal Cell Carcinoma Unclassified With Medullary Phenotype In A Patient With Neurofibromatosis Type 2, Sanila Sarkar, Whitney Throckmorton, Racheal Bingham, Pavlos Msaouel, Giannicola Genovese, Priya Rao, Cynthia E Herzog

Faculty, Staff and Student Publications

We present, to our knowledge, the first reported case of germline neurofibromatosis Type 2 (NF2) associated with renal cell carcinoma unclassified with medullary phenotype (RCCU-MP) with somatic loss by immunohistochemistry of the SMARCB1 tumor suppressor gene located centromeric to NF2 on chromosome 22q. Our patient is a 15-year-old with germline neurofibromatosis Type 2 (NF2) confirmed by pathogenic mutation of c.-854-??46+??deletion. Her NF2 history is positive for a right optic nerve sheath meningioma, CNIII schwannoma requiring radiation therapy and post gross total resection of right frontotemporal anaplastic meningioma followed by radiation. At age 15 she developed new onset weight loss and …

T-Cell Receptor Repertoire Sequencing In The Era Of Cancer Immunotherapy, Meredith L Frank, Kaylene Lu, Can Erdogan, Yi Han, Jian Hu, John V Heymach, Alexandre Reuben

Faculty, Staff and Student Publications

T cells are integral components of the adaptive immune system, and their responses are mediated by unique T-cell receptors (TCR) that recognize specific antigens from a variety of biological contexts. As a result, analyzing the T-cell repertoire offers a better understanding of immune responses and of diseases like cancer. Next-generation sequencing technologies have greatly enabled the high-throughput analysis of the TCR repertoire. On the basis of our extensive experience in the field from the past decade, we provide an overview of TCR sequencing, from the initial library preparation steps to sequencing and analysis methods and finally to functional validation techniques. …

Genetic Architecture Of Spatial Electrical Biomarkers For Cardiac Arrhythmia And Relationship With Cardiovascular Disease, William J Young, Jeffrey Haessler, Jan-Walter Benjamins, Linda Repetto, Jie Yao, Andrew R Harper, Sophie Garnier, Stefan Van Duijvenboden, Antoine R Baldassari, Maria Pina Concas, Thuyvy Duong, Luisa Foco, Jonas L Isaksen, Hao Mei, Raymond Noordam, Casia Nursyifa, Anne Richmond, Meddly L Santolalla, Colleen M Sitlani, Negin Soroush, Sébastien Thériault, Stella Trompet, Stefanie Aeschbacher, Fariba Ahmadizar, Alvaro Alonso, Jennifer A Brody, Archie Campbell, Adolfo Correa, Dawood Darbar, Antonio De Luca, Jean-François Deleuze, Christina Ellervik, Christian Fuchsberger, Anuj Goel, Christopher Grace, Xiuqing Guo, Torben Hansen, Susan R Heckbert, Rebecca D Jackson, Jan A Kors, Maria Fernanda Lima-Costa, Allan Linneberg, Peter W Macfarlane, Alanna C Morrison, Pau Navarro, David J Porteous, Peter P Pramstaller, Alexander P Reiner, Lorenz Risch, Ulrich Schotten, Xia Shen, Gianfranco Sinagra, Elsayed Z Soliman, Monika Stoll, Eduardo Tarazona-Santos, Andrew Tinker, Katerina Trajanoska, Eric Villard, Helen R Warren, Eric A Whitsel, Kerri L Wiggins, Dan E Arking, Christy L Avery, David Conen, Giorgia Girotto, Niels Grarup, Caroline Hayward, J Wouter Jukema, Dennis O Mook-Kanamori, Morten Salling Olesen, Sandosh Padmanabhan, Bruce M Psaty, Cristian Pattaro, Antonio Luiz P Ribeiro, Jerome I Rotter, Bruno H Stricker, Pim Van Der Harst, Cornelia M Van Duijn, Niek Verweij, James G Wilson, Michele Orini, Philippe Charron, Hugh Watkins, Charles Kooperberg, Henry J Lin, James F Wilson, Jørgen K Kanters, Nona Sotoodehnia, Borbala Mifsud, Pier D Lambiase, Larisa G Tereshchenko, Patricia B Munroe

Faculty, Staff and Student Publications

The 3-dimensional spatial and 2-dimensional frontal QRS-T angles are measures derived from the vectorcardiogram. They are independent risk predictors for arrhythmia, but the underlying biology is unknown. Using multi-ancestry genome-wide association studies we identify 61 (58 previously unreported) loci for the spatial QRS-T angle (N = 118,780) and 11 for the frontal QRS-T angle (N = 159,715). Seven out of the 61 spatial QRS-T angle loci have not been reported for other electrocardiographic measures. Enrichments are observed in pathways related to cardiac and vascular development, muscle contraction, and hypertrophy. Pairwise genome-wide association studies with classical ECG traits identify shared genetic …

The “Science Of Social Justice”: An Interdisciplinary Theoretical Framework Grounded In Neuroscience, Education, And Anthropology Towards Healing Intergenerational Trauma, Sará King

Journal of Contemplative Inquiry

The Science of Social Justice (SSJ) is a theoretical framework for healing intergenerational trauma which stems from the impact of the historical and lived embodied experience of systemic oppression. It explores the theoretical assertion that social justice and well-being are one and the same thing. This paper explores neuroeducational and anthropological research on the relationship between empathy, emotions, and awareness to analyze how embodied and contemplative practices such as yoga and meditation are examples of awareness-based interventions that can serve as the means of promoting embodied social justice. In this paper the Systems-Based Awareness Map (SBAM) is introduced as a …

Gullah Geechee Visuality As Protest Art, Contemplative Practice, And Anti-Racist Pedagogy, Kathy J. Brown

Journal of Contemplative Inquiry

This article centers two fabric assemblage pieces I created in response to the Black Lives Matter protests of the summer 2020: the first piece made specifically in response to the murder of Breonna Taylor. In 2021, I completed the second piece—her male counterpart—created with similar methodology and materiality, in recognition of the long history of Black men who lost their lives and or were/are impacted by police brutality, specifically Sgt. Issac Woodard. I believe that as a proverbial Black collective we continue to be linked, in equal parts, by both collective memory and concurrent triumphs. Here, as critical arts-based research, …

Rhythms And Archetypes Of Contemplation: An Afro-Boricua Experience, Anthony Cruz Pantojas

Journal of Contemplative Inquiry

A critical appropriation of the prophetic imagination can orient us to emergent strategies for a more interdependent commons. Given the precarious times of the Anthropocene in which we are living, a contemplative hermeneutic that responds to enduring oppressive relational practices is necessary. This reflective treatise expounds on three archetypes that underpin the exploration of an Afro-Caribbean experience that is also a contemplative practice: the Barril de Bomba, Bomba, and Flamboyán. I argue these archetypes as poetics can orient us to new relational possibilities.

Meditation Time In The Classroom: Mindfulness Dosage And Undergraduate Psychological Distress, Kelsey Evans-Amalu, Becky Beucher, Shiva Jahani, Suat Babayigit

Journal of Contemplative Inquiry

Objectives: The present study examined the differences in participants’ individual psychological distress over four points in time while they received instructions on a guided mindfulness meditation practice differing in practice time between the two groups (20 minutes or 5 minutes). The study took place in an undergraduate yoga course at a large metropolitan university in the Southeastern United States. Data were collected over the four points in time during one continuous semester using the Outcome Questionnaire-45.2 (OQ-45.2) (Lambert et al., 2004; Tabet et al., 2019). Methods: The purpose of this 15-week quantitative study was to compare the differences in individual …

A New Wave Of The Overdose Epidemic Arises During The Covid-19 Pandemic, Tolga Suvar Md, Asokumar Buvanendran Md, Stephen Music Do, Wilson M. Compton Md, Mpe

Advances in Clinical Medical Research and Healthcare Delivery

Abstract

Objective:

The goal of this manuscript is to highlight the notoriety of the overdose epidemic which has been masked by the Coronavirus pandemic.

Methods:

A thorough literature review of PubMed and the latest statistics from the Centers for Disease Control and Prevention (CDC) was performed for the most relevant and updated data regarding overdose deaths.

Conclusion:

The global health crisis known as the Coronavirus Disease 2019 (COVID-19) pandemic collided with the opioid epidemic in March of 2020, with devastating consequences for the United States. By overwhelming the healthcare system, the pandemic impacted patients who require continued mental health services, …

Racial Disparities In Access To Pain Management Services During Covid Pandemic At An Urban Safety-Net Hospital, Mohammad Ghorbanhoseini, Akhil Venkat Uppalapati, Allen Yang, Rafael Ortega, Eduard Vaynberg

Advances in Clinical Medical Research and Healthcare Delivery

Background: Race has been identified as one of the great divisions of mankind, associated with differences in healthcare access in the US. The COVID pandemic has shed light on a variety of disparities, including access to pain management services.

Method: All the adult patients who were referred to the pain clinic at Boston Medical Center (BMC) from December 2019- December 2020 were included in this study. A total of 2023 cases (1243 White Race and 790 People of Color) were recruited.

Result: Patients of WR received care at a younger age. COVID-19 increased the average age of WR by 2.5 …

Graves' Disease And Major Histocompatibility Complex Class Ii: A Meta-Analysis Of Hla-Dq And Hla-Drb1, Dylan Thibaut, Connor Sweeney, Shannon South, Mohamed Hussein

Advances in Clinical Medical Research and Healthcare Delivery

Background: Human leukocyte antigen (HLA) class II has shown potential in determining prognosis, understanding medication reactions, and predicting onset of Graves’ disease. The aim of this study is to further investigate the association between Graves’ disease and HLA class II, specifically HLA-DQ and HLA-DR, via meta-analysis to find HLAs that can be further examined for prognostic reasons.

Methods: Statistical analysis was performed to determine if variants of HLA-DQA1, HLA-DQB1, or HLA-DRB1 were associated with significantly altered odds of Graves’ disease. A minimum of three studies pertaining to a particular HLA was required for inclusion. Studies were excluded if …

Prospective Insight Into The Role Of Benzyl Propylene Glycoside As A Modulator Of The Cgas-Sting Signaling Pathway In The Management Of Nonalcoholic Fatty Pancreas Animal Model, Reda Albadawy, Amany Helmy Hasanin, Sara H. A. Agwa, Shaimaa Hamady

Faculty Journal Articles

No abstract provided.

Keynote: Enduring Purpose, Perpetual Evolution, Nicholas Poole

IATUL 2023 Slides

Keynote presentation

In this keynote presentation, CILIP CEO Nick Poole explores the enduring values and ethics at the heart of librarianship and how these are helping to define the role of librarians and information professionals in our digital future.

Conceptual Framework Of Information Retrieval System In The Field Of Gastroenterology And Hepatology, Masoud Mohammadi, Fatemeh Sheikhshoaei

IATUL 2023 Slides

No abstract provided.

Drought Affects Sex Ratio And Growth Of Painted Turtles In A Long-Term Study In Nebraska, Larkin A. Powell, Ellen P. Dolph, Charrissa R. Neil

School of Natural Resources: Faculty Publications

Climate forecasts suggest the Great Plains of North America have increased risk of droughts during global warming. Environmental factors have potential to influence turtle populations in aquatic habitats through temperature-dependent sex determination and influences on food availability. Long-term studies are critical to evaluate the influence of climatic variation on turtles. We used a 12-year set of mark-recapture data collected from painted turtles (Chrysemys picta, n = 162) in a pond in Keith County, Nebraska during 2005–2016 to assess variation in sex ratio and growth dynamics. Southwest Nebraska experienced two periods of drought during our study (Palmer Hydrologic Drought …