Digital Commons Network^™

The Role Of Cybersecurity In Bioinformatics For Aviation And Aerospace Safety, Sharon L. Burton

Publications

The intersection of bioinformatics and cybersecurity is critical to ensuring the privacy, integrity, and safety of biological data [1]. Bioinformatics is an interdisciplinary field that embodies the cyber age through its reliance on sophisticated algorithms, cloud computing, and secure data management practices, reflecting the profound digital transformation across various scientific disciplines [2].

Intouch Week Of October 28, 2024, New York Medical College

InTouch

• Medical Students Run for Charity at the 2024 TCS New York City Marathon
• NYMC Goes Pink for Breast Cancer Awareness Month
• Furry Friends Bring Comfort to the College
• Faculty Spotlight: From Pupil to Professor: Alumni Lighting the Way at NYMC
• Student Spotlight: AMA Foundation Physicians of Tomorrow Scholarship Recipient

Automation, Improvement, And Sensitivity Analysis Of 3d Parameterized Maize Stalk Models, Joseph Steven Carter

Theses and Dissertations

Maize is the most grown crop in the world. Each year, 5% of maize is lost due to a phenomenon known as stalk lodging (breakage of the stalk below the ear). One of the most promising solutions to stalk lodging is to design stalks with superior geometry to increase stalk strength. Researchers have developed a 3D parameterized maize stalk model, but these models take a long time to structurally analyze and are missing important material properties. This thesis addressed these problems by developing an automated package for analyzing the 3D parameterized maize stalk model, and by measuring the longitudinal shear …

Prompting Effective Learning Pathways: Applied Behavior Analysis In Practice, Brandie Ann Kretzschmar

Walden Dissertations and Doctoral Studies

The purpose of this quantitative study was to contribute to the literature for prompting interventions in the field of applied behavior analysis (ABA). This study examined the clinical utilization of prompting strategies with verbal operant programming across currently credentialed practitioners. Evidence-based practices are well known, but clinical guidance regarding prompting strategies is still emerging. This gap is potentially related to the lack of a prompting assessment to assist practitioners in creating clients' programming. To collect data a 52-question survey was used in this ethnographic study. Data was collected from 62 respondents, with 55 overall completed surveys. Errorless learning was reported …

Dna-Binding Proteins From Mbd Through Zf To Ben: Recognition Of Cytosine Methylation Status By One Arginine With Two Conformations, Xing Zhang, Robert M Blumenthal, Xiaodong Cheng

Faculty, Staff and Student Publications

Maintenance methylation, of palindromic CpG dinucleotides at DNA replication forks, is crucial for the faithful mitotic inheritance of genomic 5-methylcytosine (5mC) methylation patterns. MBD proteins use two arginine residues to recognize symmetrically-positioned methyl groups in fully-methylated 5mCpG/5mCpG and 5mCpA/TpG dinucleotides. In contrast, C2H2 zinc finger (ZF) proteins recognize CpG and CpA, whether methylated or not, within longer specific sequences in a site- and strand-specific manner. Unmethylated CpG sites, often within CpG island (CGI) promoters, need protection by protein factors to maintain their hypomethylated status. Members of the BEN domain proteins bind CGCG or CACG elements within CGIs to regulate gene …

Developmental-Status-Aware Transcriptional Decomposition Establishes A Cell State Panorama Of Human Cancers, Yikai Luo, Han Liang

Faculty, Staff and Student Publications

Background: Cancer cells evolve under unique functional adaptations that unlock transcriptional programs embedded in adult stem and progenitor-like cells for progression, metastasis, and therapeutic resistance. However, it remains challenging to quantify the stemness-aware cell state of a tumor based on its gene expression profile.

Methods: We develop a developmental-status-aware transcriptional decomposition strategy using single-cell RNA-sequencing-derived tissue-specific fetal and adult cell signatures as anchors. We apply our method to various biological contexts, including developing human organs, adult human tissues, experimentally induced differentiation cultures, and bulk human tumors, to benchmark its performance and to reveal novel biology of entangled developmental signaling in …

Prenatal Opioid And Alcohol Exposures: Association With Altered Placental Serotonin Transporter Structure And/Or Expression, Nune Darbinian, Nana Merabova, Gabriel Tatevosian, Sandra Adele, Armine Darbinyan, Mary F Morrison, C Lindsay Devane, Sammanda Ramamoorthy, Laura Goetzl, Michael E Selzer

Faculty, Staff and Student Publications

Fetal exposures to many drugs of abuse, e.g., opioids and alcohol (EtOH), are associated with adverse neurodevelopmental problems in early childhood, including abnormalities in activity of the serotonin (5HT) transporter (SERT), which transports 5HT across the placenta. Little is known about the effects of these drugs on SERT expression. Pregnant women who used EtOH or opioids were compared to gestational age-matched controls using a structured questionnaire to determine prenatal substance exposure. Following elective pregnancy termination, placental membranous vesicles and exosomes were prepared from first and second trimester human placentas. Changes in EtOH- or opioid-exposed placental SERT expression and modifications were …

Single Nanobubble Formation On Au Nanoelectrodes And Au@Ws2 Nanoelectrodes: Voltammetric Analysis And Electrocatalysis, Xian-Zhun Luo, Xiao-Hu Chen, Yong-Xin Li

Journal of Electrochemistry

Taking advantage of the extremely small size of the gold nanodisk electrode, the single hydrogen nanobubble generated on the surface of the nanoelectrode was studied to evaluate its hydrogen evolution performance. It was found that compared with the bare gold nanodisk electrode, the bubble formation potential of the gold nanodisk electrode modified with tungsten disulfide quantum dots (WS₂ QDs) on the surface was more positive, indicating that its hydrogen evolution activity was higher. Microdynamic model analysis shows that the average standard rate constant of the rate-determining step of the hydrogen evolution reaction of gold nanoelectrodes modified with WS_{2 …}

Author Spotlight, Fei Li, Yi-Ge Zhou, Yi-Lun Ying, Yong-Xin Li, Yu Huang, Zhen Wu

Journal of Electrochemistry

No abstract provided.

Platinum Nanoparticle-Based Collision Electrochemistry For Rapid Detection Of Breast Cancer Mcf-7 Cells, Fu-Xing Qin, Ming-Ke Li, Hui-Long Zhou, Wei Wen, Xiu-Hua Zhang, Sheng-Fu Wang, Zhen Wu

Journal of Electrochemistry

Cancer metastasis is the leading cause of death in cancer patients worldwide and one of the major challenges in treating cancer. Circulating tumor cells (CTCs) play a pivotal role in cancer metastasis. However, the content of CTCs in peripheral blood is minimal, so the detection of CTCs in real samples is extremely challenging. Therefore, efficient enrichment and early detection of CTCs are essential to achieve timely diagnosis of diseases. In this work, we constructed an innovative and sensitive single-nanoparticle collision electrochemistry (SNCE) biosensor for the detection of MCF-7 cells (human breast cancer cells) by immunomagnetic separation technique and liposome signal …

Highly Sensitive Detection Of Strontium Ions Using Metal-Organic Frameworks Functionalized Solid-State Nanochannels, Xu-Gang Wang, Zheng-Xu He, De-Fang Ding, Xue-Qin Luo, Li Dai, Wei-Qi Zhang, Qun Ma, Yu Huang, Fan Xia

Journal of Electrochemistry

Strontium-90, a highly radioactive isotope, accumulates within the food chain and skeletal structure, posing significant risks to human health. There is a critical need for a sensitive detection strategy for Strontium-90 in complex environmental samples. Here, solid-state nanochannels, modified with metal-organic frameworks (MOF) and specific aptamers, were engineered for highly sensitive detection of strontium ion (Sr²⁺). The synergistic effect between the reduced effective diameter of the nanochannels due to MOF and the specific binding of Sr²⁺ by aptamers amplifies the difference in ionic current signals, enhancing detection sensitivity significantly. The MOF-modified nanochannels exhibit highly sensitive detection of …

Evaluating Indoor Air Quality In Residential Environments: A Study Of Pm2.5 And Co2 Dynamics Using Low-Cost Sensors, Kabir Bahadur Shah, Dylan Kim, Sai Deepak Pinakana, Mkhitar A. Hobosyan, Armando Montes, Amit U. Raysoni

School of Earth, Environmental, & Marine Sciences Faculty Publications

Indoor air quality (IAQ) poses a significant public health concern, and exposures to high levels of fine particulate matter (PM2.5) and carbon dioxide (CO2) could have detrimental health impacts. This study focused on assessing the indoor air pollutants in a residential house located in the town of Mission, Hidalgo County, South Texas, USA. The PM2.5 and CO2 were monitored indoors: the kitchen and the bedroom. This investigation also aimed to elucidate the effects of household activities such as cooking and human occupancy on these pollutants. Low-cost sensors (LCSs) from TSI AirAssure™ were used in this study. They were deployed within …

Cardiovascular Findings In Klippel-Feil Syndrome: A Systematic Review, Abbigail Niewchas, Salma Alkhatib, Christopher Stewart, Mitchell Fisher, Randall Hansen, Alex Otto, Kent Mcintire, Suporn Sukpraprut-Braaten

Student Publications

Klippel-Feil syndrome (KFS) is a congenital disease defined by an abnormal fusion between cervical vertebrae. Due to the rarity of the disorder, its prevalence, along with its pathogenesis and associated conditions, remains to be clearly defined. The aim of this review is to summarize the findings of all case reports of KFS in PubMed over the last 10 years that describe cardiovascular disease, defects, or abnormalities. A total of 43 articles containing 46 reports were included from the 157 case reports considered. Cases were reviewed for commonality in biological sex and vertebral fusion and level using the Samartzis classification system …

Scale-Dependent Drivers Of Air-Sea Co2 Flux Variability, Amanda R. Fay, Dustin Carroll, Galen A. Mckinley, Dimitris Menemenlis, Hong Zhang

Faculty Research, Scholarly, and Creative Activity

In climate studies, it is crucial to distinguish between changes caused by natural variability and those resulting from external forcing. Here we use a suite of numerical experiments based on the ECCO-Darwin ocean biogeochemistry model to separate the impact of the atmospheric carbon dioxide (CO2) growth rate and climate on the ocean carbon sink — with a goal of disentangling the space-time variability of the dominant drivers. When globally integrated, the variable atmospheric growth rate and climate exhibit similar magnitude impacts on ocean carbon uptake. At local scales, interannual variability in air-sea CO2 flux is dominated by climate. The implications …

Bipolar Ionization Did Not Reduce Airborne Bacteria In A Lecture Hall, David A. Kormos, Nishit J. Shetty, Elliott T. Gall, Aaron J. Prussin, Amy Pruden, Linsey C. Marr

Mechanical and Materials Engineering Faculty Publications and Presentations

Ionization treatment of indoor air has attracted attention for its potential to inactivate airborne pathogens and reduce disease transmission, yet its real-world effectiveness remains unverified. We evaluated the impact of an in-duct, bipolar ionization system on airborne particles, including culturable bacteria, in a lecture hall. The ionizer was off with variable fan speed for 1 week, on with variable fan speed for a second week, and on with high and constant fan speed for a third week. We measured ion concentrations and aerosol particle concentrations, and we collected bioaerosol samples for analysis of 16S rRNA gene copies representing total bacteria …

Using A Natural Capital Risk Register To Support The Funding Of Seagrass Habitat Enhancement In Plymouth Sound, Guy Hooper, Matthew Ashley, Tom Mullier, Martin Attrill, Amelia Sturgeon, Zoe Sydenham, Mark Parry, Katey Valentine, Sian Rees

School of Biological and Marine Sciences

Seagrass is an important marine habitat that provides benefits to society in the form of ecosystem services. Services include the provision of food via fisheries, the regulation of water quality and the ability to sequester and store carbon. In the UK, seagrass beds are in decline, increasing the risk of ecosystem service loss. Current efforts to protect, restore and create seagrass habitat, beyond spatial management measures, rely on grant funding and donations. Emerging carbon, biodiversity and wider ecosystem service markets offering potential revenue sources could facilitate the enhancement of seagrass habitat at scale. Participation in ecosystem service markets, requires that …

Targeting Trem2 Signaling Shows Limited Impact On Cerebrovascular Calcification, Sucheta Sridhar, Yingyue Zhou, Adiljan Ibrahim, Sergio Bertazzo, Tania Wyss, Amanda Swain, Upasana Maheshwari, Sheng-Fu Huang, Marco Colonna, Annika Keller

2020-Current year OA Pubs

Brain calcification, the ectopic mineral deposits of calcium phosphate, is a frequent radiological finding and a diagnostic criterion for primary familial brain calcification. We previously showed that microglia curtail the growth of small vessel calcification via the triggering receptor expressed in myeloid 2 (TREM2) in the

Exploring The Interconnectivity Between Soilless Substrate Hydraulic Properties And Plant Root Morphology, Kristopher S. Criscione

LSU Doctoral Dissertations

Horticultural container production heavily relies upon porous soilless substrates to mass produce specialty crops. Soilless substrates are responsible for continuously maintaining optimal water, mineral nutrients, and air balances to promote healthy root growth and support productive shoot yield (foliage or fruit). Increasing evidence of substrate research continues to highlight the strong relationships associated with root development and substrate physiochemical properties. Despite the importance of the root system for overall plant health, most horticultural research to-date has focused on shoot development. Research tends to report total root biomass as the primary root-growth metric; however, this results in several developmental features becoming …

Modern Lakeshore Processes And Historic Lake And Glacial Changes In Taylor Valley, Antarctica, Michael Stanley Stone

LSU Doctoral Dissertations

Taylor Valley, which opens to the Ross Sea, is one of several ice-free valleys comprising the McMurdo Dry Valleys, Antarctica. The valley is home to several close-basin, perennially ice-covered lakes, whose lake levels largely reflect a balance between meltwater inputs and lake ice ablation; both being driven by climate. A dynamic environment exists where the lake ice covers meet the lakeshore, with the ice grounding to the substrate throughout the cold and dark of winter, and melting to form a perimeter of thin-to-no ice around the lake during the summer. These marginal freeze-thaw regions are known as moats. Here, physical, …

Engineered Cas9 Variants Bypass Keap1-Mediated Degradation In Human Cells And Enhance Epigenome Editing Efficiency, Jianfeng Chen, Siyuan Su, Adrian Pickar-Oliver, Anna M Chiarella, Quentin Hahn, Dennis Goldfarb, Erica W Cloer, George W Small, Smaran Sivashankar, Dale A Ramsden, Michael B Major, Nathaniel A Hathaway, Charles A Gersbach, Pengda Liu

2020-Current year OA Pubs

As a potent and convenient genome-editing tool, Cas9 has been widely used in biomedical research and evaluated in treating human diseases. Numerous engineered variants of Cas9, dCas9 and other related prokaryotic endonucleases have been identified. However, as these bacterial enzymes are not naturally present in mammalian cells, whether and how bacterial Cas9 proteins are recognized and regulated by mammalian hosts remain poorly understood. Here, we identify Keap1 as a mammalian endogenous E3 ligase that targets Cas9/dCas9/Fanzor for ubiquitination and degradation in an 'ETGE'-like degron-dependent manner. Cas9-'ETGE'-like degron mutants evading Keap1 recognition display enhanced gene editing ability in cells. dCas9-'ETGE'-like degron …

The Rider (2024-10-28), Natalie Lapsley

The Rider Archives

Vol.10 No.10

Adapting To Drought And Floods In The Semi-Arid Landscape Of Santa Cruz County, Arizona, Cynthia L. Sorrensen

The Geographical Bulletin

This paper analyzes the actions of key interest groups and major institutional regulatory agreements that influence land use change and water demand in Santa Cruz County, Arizona, in order to better understand the capacity of residents in the county to adapt to hydroclimatic hazards (drought and flooding). We found that there are strong special interest groups working in the region to ensure their own livelihoods and interests. At times, the actions of these groups enhance the adaptive capacity of the county, but their actions can also conflict with each other, producing a less-clear outcome for adaptation. We also note that …

A Genome-Wide Association Study Identifies Genetic Determinants Of Hemoglobin Glycation Index With Implications Across Sex And Ethnicity, John S. House, Joseph H. Breeyear, Farida S. Akhtari, Violet Evans, John B. Buse, James Hempe, Alessandro Doria, Josyf C. Mychaleckyi, Vivian Fonseca, Mengyao Shi, Changwei Li, Shuqian Liu, Tanika N. Kelly, Daniel Rotroff, Alison A. Motsinger-Reif

School of Medicine Faculty Publications

Introduction: We investigated the genetic determinants of variation in the hemoglobin glycation index (HGI), an emerging biomarker for the risk of diabetes complications. Methods: We conducted a genome-wide association study (GWAS) for HGI in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial (N = 7,913) using linear regression and additive genotype encoding on variants with minor allele frequency greater than 3%. We conducted replication analyses of top findings in the Atherosclerosis Risk in Communities (ARIC) study with inverse variance-weighted meta-analysis. We followed up with stratified GWAS analyses by sex and self-reported race. Results: In ACCORD, we identified single …

(Un)Know Thy “Self”: Interconnected Consciousness And Different Ways Of Knowing, Laurel Waterman, Karyn Cooper

The Qualitative Report

This paper draws on preliminary data from a qualitative study in curriculum and pedagogy, “Stories of Teaching about Consciousness: An Inquiry into Worldviews and Wellbeing.” An emerging theme is the concept of the self and how it entwines with perspectives on consciousness. Analyzing consciousness and the self through The Five Contexts framework reveals assumptions at the heart of research and education that often go unquestioned. We wonder, what might alternative perspectives on consciousness and the self offer to researchers and educators? The study aims to inform a larger project of “consciousness education,” defined as education about perspectives on the source …

The Contribution Of Neutrophil Extracellular Traps To Coagulopathy In Patients With Covid-19-Related Thrombosis, Carolyn Enochs, Gabriela Delevati Colpo, Lucy Couture, Lynae Baskin, Ana E Cahuiche, Eunyoung Angela Lee, Shahid Nimjee, Louise D Mccullough

Faculty, Staff and Student Publications

COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is associated with hypercoagulability and increased incidence of thrombotic events. In this study, we investigated the levels of neutrophil extracellular trap biomarkers and von Willebrand factor to assess if these could predict the occurrence of a thrombotic event in COVID-19 patients. We enrolled 202 patients hospitalized with symptomatic COVID-19 infection. Of those, 104 patients did not experience any type of thrombotic events before or during their hospitalization. These patients were compared to the other cohort of 98, who experienced thrombotic events before or during their hospitalization. In total, …

Right Heart Failure After Tricvalve Implantation For Symptomatic Torrential Tricuspid Regurgitation: A Case Report, King Sum Luk, Chun Kit Wong

Journal of the Hong Kong College of Cardiology

Patients with symptomatic torrential tricuspid regurgitation (TR) presenting with right heart failure are associated with significant morbidity and mortality. While medical therapy is often ineffective, the perioperitive risks of surgical correction are high. Transcatheter TricValve implantation is one of the evolving therapeutic options for this condition with many unanswered questions. We reported a case of life-threatening right heart failure after transcatheter TricValve implantation despite initial improvement. Important considerations of TricValve implantation are discussed. In particular, careful patient selection and evaluation with perioperative echocardiogram are of paramount importance.

Radiomics-Based Machine Learning With Natural Gradient Boosting For Continuous Survival Prediction In Glioblastoma, Mert Karabacak, Shiv Patil, Zachary C. Gersey, Ricardo J. Komotar, Konstantinos Margetis

SKMC Student Presentations and Publications

(1) Background: Glioblastoma (GBM) is the most common primary malignant brain tumor in adults, with an aggressive disease course that requires accurate prognosis for individualized treatment planning. This study aims to develop and evaluate a radiomics-based machine learning (ML) model to estimate overall survival (OS) for patients with GBM using pre-treatment multi-parametric magnetic resonance imaging (MRI). (2) Methods: The MRI data of 865 patients with GBM were assessed, comprising 499 patients from the UPENN-GBM dataset and 366 patients from the UCSF-PDGM dataset. A total of 14,598 radiomic features were extracted from T1, T1 with contrast, T2, and FLAIR MRI sequences …

Pengaruh Larangan Ekspor Karang Hias Terhadap Kondisi Terumbu Karang Di Indonesia, Fitrian Dwi Cahyo, Muhammad Halley Yudhistira

Jurnal Kebijakan Ekonomi

Indonesia has the largest coral population in the world, contributed as the world’s second largest ornamental corals exporter after Japan. Coral trade sparked the issues of habitat destruction, illegal trade, and coral health problems has prompted the government to banning of ornamental coral export. This study aims to find an empirical evidence does the policies mentioned above affect the condition of coral reefs in Indonesia. The author uses the Fixed-Effect Model on the Difference in Difference regression equation whose result show that export banning of ornamental corals does not significantly affect the condition of coral reefs in Indonesia.

Specialized Contact Sites Regulate The Fusion Of Chlamydial Inclusion Membranes, Christine Linton, Jordan Wesolowski, Anna Lobley, Toshiyuki Yamaji, Kentaro Hanada, Fabienne Paumet

Department of Microbiology and Immunology Faculty Papers

The intracellular bacterial pathogen Chlamydia trachomatis replicates within a membrane-bound compartment called the inclusion. Upon infection with several chlamydiae, each bacterium creates its own inclusion, resulting in multiple inclusions within each host cell. Ultimately, these inclusions fuse together in a process that requires the chlamydial protein IncA. Here, we show that inclusions form unique contact sites (inclusion contact sites, ICSs) prior to fusion, that serve as fusogenic platforms in which specific lipids and chlamydial proteins concentrate. Fusion depends on IncA clustering within ICSs and is regulated by PI(3,4)P₂ and sphingolipids. As IncA concentrates within ICSs, its C-terminus likely interacts …

Ten Challenges And Opportunities In Computational Immuno-Oncology, Riyue Bao, Alan Hutson, Anant Madabhushi, Vanessa D Jonsson, Spencer R Rosario, Jill S Barnholtz-Sloan, Elana J Fertig, Himangi Marathe, Lyndsay Harris, Jennifer Altreuter, Qingrong Chen, James Dignam, Andrew J Gentles, Edgar Gonzalez-Kozlova, Sacha Gnjatic, Erika Kim, Mark Long, Martin Morgan, Eytan Ruppin, David Van Valen, Hong Zhang, Natalie Vokes, Daoud Meerzaman, Song Liu, Eliezer M Van Allen, Yi Xing

Faculty, Staff and Student Publications

Immuno-oncology has transformed the treatment of cancer, with several immunotherapies becoming the standard treatment across histologies. Despite these advancements, the majority of patients do not experience durable clinical benefits, highlighting the imperative for ongoing advancement in immuno-oncology. Computational immuno-oncology emerges as a forefront discipline that draws on biomedical data science and intersects with oncology, immunology, and clinical research, with the overarching goal to accelerate the development of effective and safe immuno-oncology treatments from the laboratory to the clinic. In this review, we outline 10 critical challenges and opportunities in computational immuno-oncology, emphasizing the importance of robust computational strategies and interdisciplinary …