Digital Commons Network^™

Application Of Randomness In Finance, Jose Sanchez, Daanial Ahmad, Satyanand Singh

Publications and Research

Brownian Motion which is also considered to be a Wiener process and can be thought of as a random walk. In our project we had briefly discussed the fluctuations of financial indices and related it to Brownian Motion and the modeling of Stock prices.

Chemical Exposure From Manufactured Gas Plants: Demographic & Governmental Research, Aneeza Hussain

Publications and Research

There are thousands of brownfields in New York on former Manufactured Gas Plants (MGP) similar to the Public Place site in Gowanus, Brooklyn. Public Place is an active brownfield abutting an EPA Superfund site currently undergoing remediation. After consulting recent literature finding that populations living on and near superfund sites have lower life expectancy that also correlate with “sociodemographic factors” like income and race, we used American Community Survey data to conduct a demographic analysis of census districts within the rezone area. Assessment of current demographic data shows that Gowanus residents living within census districts overlapping with the rezone area …

Oral Manifestations Of Covid-19, Ibeth Erazo

Publications and Research

Some oral manifestations have been observed in patients with coronavirus disease 2019 (COVID-19). However, there is still a question about whether these lesions are due to coronavirus infection or secondary manifestations resulting from patient's stress, medications, and/or other related immunosuppressive factors and systemic conditions or by the actions of opportunistic infections brought by other viruses, bacteria, and fungi in the oral cavity. There is growing evidence that angiotensin-converting enzyme 2 (ACE2), the main host cell receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is highly expressed on the cells of the oral mucosal epithelia and of the salivary glands, …

The Effects Of Late Spring Frost On Forest And Landscape Health And Recovery Of The Black Rock Forest, New York, Caroline Eco, Oliver Imhans, Aaron Davitt, Andrew B. Reinmann

Publications and Research

Projected changes in climate are expected to increase the frequency of late spring frost events in the Northeast US. Such events can be harmful to trees because freezing temperatures that occur after leaf-out can damage or kill young leaves. The resultant defoliation typically forces a second flush of leaves, but delays canopy development, which in turn delays the onset of canopy carbon uptake and alters canopy thermal properties. In this study, we analyzed a recent freeze event that occurred on 8-9 May 2020 (DOY 129-130) at Black Rock Forest (BRF), which is in the Hudson Highlands of southeastern New York …

Control Of Pre-Replicative Complex During The Division Cycle In Chlamydomonas Reinhardtii, Amy E. Ikui, Noriko Ueki, Kresti Pecani, Frederick R. Cross

Publications and Research

DNA replication is fundamental to all living organisms. In yeast and animals, it is triggered by an assembly of pre-replicative complex including ORC, CDC6 and MCMs. Cyclin Dependent Kinase (CDK) regulates both assembly and firing of the pre-replicative complex. We tested temperature-sensitive mutants blocking Chlamydomonas DNA replication. The mutants were partially or completely defective in DNA replication and did not produce mitotic spindles. After a long G1, wild type Chlamydomonas cells enter a division phase when it undergoes multiple rapid synchronous divisions (‘multiple fission’). Using tagged transgenic strains, we found that MCM4 and MCM6 were localized to the nucleus throughout …

Nmr Solution Structures Of Runella Slithyformis Rna 2'-Phosphotransferase Tpt1 Provide Insights Into Nad+ Binding And Specificity, Sébastien Alphonse, Ankan Banerjee, Swathi Dantuluri, Stewart Shuman, Ranajeet Ghose

Publications and Research

Tpt1, an essential component of the fungal and plant tRNA splicing machinery, catalyzes transfer of an internal RNA 2′-PO₄ to NAD⁺ yielding RNA 2′-OH and ADP-ribose-1′,2′-cyclic phosphate products. Here, we report NMR structures of the Tpt1 ortholog from the bacterium Runella slithyformis (RslTpt1), as apoenzyme and bound to NAD⁺. RslTpt1 consists of N- and C-terminal lobes with substantial inter-lobe dynamics in the free and NAD⁺-bound states. ITC measurements of RslTpt1 binding to NAD⁺ (K_D ∼31 μM), ADP-ribose (∼96 μM) and ADP (∼123 μM) indicate that substrate affinity is determined primarily by …

Gifts From The Dark: Learning From The Incarceration Experience [Chapter 12], Joni Schwartz, John R. Chaney

Publications and Research

While in no way supporting the systemic injustices and disparities of mass incarceration, Gifts from the Dark: Learning from the Incarceration Experience argues that we have much to learn from those who have been and are in prison. Schwartz and Chaney profile the contributions of literary giants, social activists, entrepreneurs, and other talented individuals who, despite the disorienting dilemma of incarceration, are models of adult transformative learning that positively impact the world. The authors interweave narratives with both qualitative and quantitative research references to analyze the role of solitude, writing, non-verbal communication; race and gender; physical exercise; education; technology; family …

Sexuality And Borders In Right Wing Times: A Conversation, Alyosxa Tudor, Miriam Ticktin

Publications and Research

We respond to prompts about the relationships between race, migration, and sexuality, as these intersecting differences have been forced into the same frame by the violent practices of right-wing regimes, and brought into relief by Covid19. Even as we have long known that sexual politics are a way to govern bodies, and to distribute uneven states of vulnerability, we are seeing new incarnations of government. What we aim to point out is how people who are seen as “different” are being attacked, maimed, dispossessed and murdered. But perhaps more importantly, we insist on the specific nature of right-wing times because …

Exhibitions Of Impact: Introducing The Special Issue, David H. Lee

Publications and Research

The Exhibitions of Impact (EOI) special issue of American Behavioral Scientist consists of six articles from authors in communication studies and rhetoric, public health, medicine and bioethics, memory studies, and art therapy. Each article profiles some exhibition or memorial related to a pressing social issue, including gun violence, racist terrorism, domestic violence, religious fundamentalism, corporations selling harmful products, and how society treats those regarded as cognitively and behaviorally different. First, examples from today’s headlines show a global outcry over racist monuments and artifacts, and a global pandemic, which casts doubt on the future of exhibitions. Historical examples and explanatory concepts …

The Insular Herpetofauna Of Mexico: Composition, Conservation, And Biogeographic Patterns, Juan Valentín Pliego‐Sánchez, Christopher Blair, Aníbal H. Díaz De La Vega‐Pérez, Víctor H. Jiménez‐Arcos

Publications and Research

We compile a Mexican insular herpetofaunal checklist to estimate endemism, conservation status, island threats, net taxonomic turnover among six biogeographic provinces belonging to the Nearctic and Neotropical regions, and the relationships between island area and mainland distance versus species richness. We compile a checklist of insular herpetofaunal through performing a literature and collection review. We define the conservation status according to conservation Mexican law, the Red List of International Union for Conservation of Nature, and Environmental Vulnerability Scores. We determine threat percentages on islands according to the 11 major classes of threats to biodiversity. We estimate the net taxonomic turnover …

Nanoanalytical Analysis Of Bisphosphonate-Driven Alterations Of Microcalcifications Using A 3d Hydrogel System And In Vivo Mouse Model, Jessica L. Ruiz, Joshua D. Hutcheson, Luis Cardoso, Amirala Bakhshian Nik, Alexandra Condado De Abreu, Tan Pham, Fabrizio Buffolo, Sara Busatto, Stefania Frederici, Andrea Ridolfi, Masanori Aikawa, Sergio Bertazzo, Paolo Bergese, Sheldon Weinbaum, Elena Aikawa

Publications and Research

Vascular calcification predicts atherosclerotic plaque rupture and cardiovascular events. Retrospective studies of women taking bisphosphonates (BiPs), a proposed therapy for vascular calcification, showed that BiPs paradoxically increased morbidity in patients with prior acute cardiovascular events but decreased mortality in event-free patients. Calcifying extracellular vesicles (EVs), released by cells within atherosclerotic plaques, aggregate and nucleate calcification. We hypothesized that BiPs block EV aggregation and modify existing mineral growth, potentially altering microcalcification morphology and the risk of plaque rupture. Three-dimensional (3D) collagen hydrogels incubated with calcifying EVs were used to mimic fibrous cap calcification in vitro, while an ApoE−/− mouse was used …

Allogeneic Bone Marrow–Derived Mesenchymal Stem Cell Safety In Idiopathic Parkinson’S Disease, Timothy M. Ellmore

Publications and Research

Background Neuroinflammation plays a key role in PD pathogenesis, and allogeneic bone marrow–derived mesenchymal stem cells can be used as an immunomodulatory therapy. Objective The objective of this study was to prove the safety and tolerability of intravenous allogeneic bone marrow–derived mesenchymal stem cells in PD patients. Methods This was a 12‐month single‐center open‐label dose‐escalation phase 1 study of 20 subjects with mild/moderate PD assigned to a single intravenous infusion of 1 of 4 doses: 1, 3, 6, or 10 × 106 allogeneic bone marrow–derived mesenchymal stem cells/kg, evaluated 3, 12, 24, and 52 weeks postinfusion. Primary outcome safety measures …

Lighting The Way: Recent Insights Into The Structure And Regulation Of Phototropin Blue Light Receptors, Jaynee E. Hart, Kevin H. Gardner

Publications and Research

The phototropins (phots) are light-activated kinases that are critical for plant physiology and the many diverse optogenetic tools that they have inspired. Phototropins combine two bluelight- sensing Light–Oxygen–Voltage (LOV) domains (LOV1 and LOV2) and a C-terminal serine/threonine kinase domain, using the LOV domains to control the catalytic activity of the kinase. While much is known about the structure and photochemistry of the light-perceiving LOV domains, particularly in how activation of the LOV2 domain triggers the unfolding of alpha helices that communicate the light signal to the kinase domain, many questions about phot structure and mechanism remain. Recent studies have made …

Survey On Quantum Circuit Compilation For Noisy Intermediate-Scale Quantum Computers: Artificial Intelligence To Heuristics, Janusz Kusyk, Samah Mohamed Saeed, Muharrem Umit Uyar

Publications and Research

Computationally expensive applications, including machine learning, chemical simulations, and financial modeling, are promising candidates for noisy intermediate scale quantum (NISQ) computers. In these problems, one important challenge is mapping a quantum circuit onto NISQ hardware while satisfying physical constraints of an underlying quantum architecture. Quantum circuit compilation (QCC) aims to generate feasible mappings such that a quantum circuit can be executed in a given hardware platform with acceptable confidence in outcomes. Physical constraints of a NISQ computer change frequently, requiring QCC process to be repeated often. When a circuit cannot directly be executed on a quantum hardware due to its …

Alternative View Of Oxygen Reduction On Porous Carbon Electrocatalysts: The Substance Of Complex Oxygen-Surface Interactions, Giacomo De Falco, Marc Florent, Jacek Jagiello, Yongqiang Cheng, Luke L. Daemen, Anibal J. Ramirez-Cuesta, Teresa J. Bandosz

Publications and Research

Electrochemical oxygen reduction reaction (ORR) is an important energy-related process requiring alternative catalysts to expensive platinum-based ones. Although recently some advancements in carbon catalysts have been reported, there is still a lack of understanding which surface features might enhance their efficiency for ORR. Through a detailed study of oxygen adsorption on carbon molecular sieves and using inelastic neutron scattering, we demonstrated here that the extent of oxygen adsorption/interactions with surface is an important parameter affecting ORR. It was found that both the strength of O2 physical adsorption in small pores and its specific interactions with surface ether functionalities in the …

Open-Source Computational Framework For Studying Drosophila Behavioral Phase, Boyan Kostadinov, Hannah Lee Pettibone, Evardra Valerie Bell, Xiaona Zhou, Ausra Pranevicius, Orie Thomas Shafer, Maria Paz Fernandez

Publications and Research

This protocol describes a standardized method for analyzing Drosophila behavioral rhythmicity under light dark cycles, temperature ramps, and free running conditions. The protocol constitutes a step-by-step guide from generation of appropriate Drosophila genetic crosses to behavioral experiments. We also provide an opensource computational framework using R for the analysis of the phase of behavior using circular statistics. An extended method for complete use is also provided. For complete details on the use and execution of this protocol, please refer to Fernandez et al. (2020).

Gap Junction-Mediated Glycinergic Inhibition Ensures Precise Temporal Patterning In Vocal Behavior, Boris P. Chagnaud, Jonathan T. Perelmuter, Paul M. Forlano, Andrew H. Bass

Publications and Research

Precise neuronal firing is especially important for behaviors highly dependent on the correct sequencing and timing of muscle activity patterns, such as acoustic signaling. Acoustic signaling is an important communication modality for vertebrates, including many teleost fishes. Toadfishes are well known to exhibit high temporal fidelity in synchronous motoneuron firing within a hindbrain network directly determining the temporal structure of natural calls. Here, we investigated how these motoneurons maintain synchronous activation. We show that pronounced temporal precision in population-level motoneuronal firing depends on gap junction-mediated, glycinergic inhibition that generates a period of reduced probability of motoneuron activation. Super-resolution microscopy confirms …

A Deep Learning Approach To Diagnostic Classification Of Prostate Cancer Using Pathology–Radiology Fusion, Pegah Khosravi, Maria Lysandrou, Mahmoud Eljalby, Qianzi Li, Ehsan Kazemi, Pantelis Zisimopoulos, Alexandros Sigaras, Matthew Brendel, Josue Barnes, Camir Ricketts, Dmitry Meleshko, Andy Yat, Timothy D. Mcclure, Brian D. Robinson, Andrea Sboner, Olivier Elemento, Bilal Chughtai, Iman Hajirasouliha

Publications and Research

Background

A definitive diagnosis of prostate cancer requires a biopsy to obtain tissue for pathologic analysis, but this is an invasive procedure and is associated with complications.

Purpose

To develop an artificial intelligence (AI)-based model (named AI-biopsy) for the early diagnosis of prostate cancer using magnetic resonance (MR) images labeled with histopathology information.

Study Type

Retrospective.

Population

Magnetic resonance imaging (MRI) data sets from 400 patients with suspected prostate cancer and with histological data (228 acquired in-house and 172 from external publicly available databases).

Field Strength/Sequence

1.5 to 3.0 Tesla, T2-weighted image pulse sequences.

Assessment

MR images reviewed and selected …

Supply Chain Viability: Conceptualization, Measurement, And Nomological Validation, Salomée Ruel, Jamal El Baz, Dmitry Ivanov, Ajay Das

Publications and Research

Supply chain viability (SCV) is an emerging concept of growing importance in operations management. This paper aims to conceptualize, develop, and validate a measurement scale for SCV. SCV is first defined and operationalized as a construct, followed by content validation and item measure development. Data have been collected through three independent samplings comprising a total of 558 respondents. Both exploratory and confirmatory factor analyses are used in a step-wise manner for scale development. Reliability and validity are evaluated. A nomological model is theorized and tested to evaluate nomological validity. For the first time, our study frames SCV as a novel …

How New England Island Residents View The Influence Of The Natural Environment In Their Lives, Nicole Kras, Jennifer Keenan

Publications and Research

While the multiple benefits of natural environments on individual’s lives have been well noted, one population that is scarcely studied in current literature are adults who live on islands in the Northeast region of the United States. This is an important population to study because these adults live in a geographical location highly immersed in natural landscapes and they are likely to have a high exposure to natural environments. This exploratory study uses participant questionnaire responses (N=51) to gain insight into how they believe the natural environment influences their lives and offers guidance for future research. Residents identified benefits and …

Seeing Through The Aesthetic Worldview, Andrew Lambert

Publications and Research

Examines the various ways in which the Chinese intellectual tradition has been characterized as an 'aesthetic tradition'. In particular, this paper explores Roger Ames’ and David Hall’s claim that the classical Confucian tradition is an aesthetic tradition, comprising an aesthetic order.

Hba1c Performance In African Descent Populations In The United States With Normal Glucose Tolerance, Prediabetes, Or Diabetes: A Scoping Review, Lakshay Khosla, Sonali Bhat, Lee Ann Fullington, Margrethe F. Horlyck-Romanovsky

Publications and Research

IntroductionAfrican descent populations in the United States have high rates of type 2 diabetes and are incorrectly represented as a single group. Current glycated hemoglobin A1c (HbA1c) cutoffs (5.7% to

Methods A PubMed, Scopus, and Cumulative Index to Nursing and Allied Health Literature (CINAHL) search (January 2020) yielded 3,238 articles published from January 2000 through January 2020. After review of titles, abstracts, and full texts, 12 met our criteria. HbA1c results were compared with other ethnic groups or validated against the oral glucose tolerance test (OGTT), fasting plasma glucose (FPG), or previous diagnosis. We classified study results by the …

Detection Of Mutations Associated With Variants Of Concern Via High Throughput 2 Sequencing Of Sars-Cov-2 Isolated From Nyc Wastewater, Davida S. Smyth, Monica Trujillo, Kristen Cheung, Anna Gao, Irene Hoxie, Sherin Kannoly, Nanami Kubota, Michelle Markman, Kaung Myat San, Geena Sompanya, John J. Dennehy

Publications and Research

Monitoring SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To date, most data on SARS-CoV-2 genetic diversity has come from the sequencing of clinical samples, but such studies may suffer limitations due to costs and throughput. Wastewater-based epidemiology may provide an alternative and complementary approach for monitoring communities for novel variants. Given that SARS-CoV-2 can infect the cells of the human gut and is found in high concentrations in feces, wastewater may be a valuable source of SARS-CoV-2 RNA, which can be deep sequenced …

Pirnas As Modulators Of Disease Pathogenesis, Kayla J. Rayford, Ayorinde Cooley, Jelonia T. Rumph, Ashutosh Arun, Girish Rachakonda, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Smita Misra, Pius N. Nde

Publications and Research

Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and …

Effects Of Structural Isomers Of Spermine On The Higher-Order Structure Of Dna And Gene Expression, Tomoki Kitagawa, Takashi Nishio, Yuko Yoshikawa, Naoki Umezawa, Tsunehiko Higuchi, Chwen-Yang Shew, Takahiro Kenmotsu, Kenichi Yoshikawa

Publications and Research

Polyamines are involved in various biological functions, including cell proliferation, differentiation, gene regulation, etc. Recently, it was found that polyamines exhibit biphasic effects on gene expression: promotion and inhibition at low and high concentrations, respectively. Here, we compared the effects of three naturally occurring tetravalent polyamines, spermine (SPM), thermospermine (TSPM), and N4-aminopropylspermidine (BSPD). Based on the single DNA observation with fluorescence microscopy together with measurements by atomic force microscopy revealed that these polyamines induce shrinkage and then compaction of DNA molecules, at low and high concentrations, respectively. We also performed the observation to evaluate the effects of these polyamine isomers …

Earliest Palaeocene Purgatoriids And The Initial Radiation Of Stem Primates, Gregory P. Wilson Mantilla, Stephen B. Chester, William A. Clemens, Jason R. Moore, Courtney J. Sprain, Brody T. Hovatter, William S. Mitchell, Wade W. Mans, Roland Mundil, Paul R. Renne

Publications and Research

Plesiadapiform mammals, as stem primates, are key to understanding the evolutionary and ecological origins of Pan-Primates and Euarchonta. The Purgatoriidae, as the geologically oldest and most primitive known plesiadapiforms and one of the oldest known placental groups, are also central to the evolutionary radiation of placentals and the Cretaceous-Palaeogene biotic recovery on land. Here, we report new dental fossils of Purgatorius from early Palaeocene (early Puercan) age deposits in northeastern Montana that represent the earliest dated occurrences of plesiadapiforms. We constrain the age of these earliest purgatoriids to magnetochron C29R and most likely to within 105–139 thousand years post- K/Pg …

Neuronal Actions Of Transspinal Stimulation On Locomotor Networks And Reflex Excitability During Walking In Humans With And Without Spinal Cord Injury, Md. Anamul Islam, Timothy S. Pulverenti, Maria Knikou

Publications and Research

This study investigated the neuromodulatory effects of transspinal stimulation on soleus H-reflex excitability and electromyographic (EMG) activity during stepping in humans with and without spinal cord injury (SCI). Thirteen able-bodied adults and 5 individuals with SCI participated in the study. EMG activity from both legs was determined for steps without, during, and after a single-pulse or pulse train transspinal stimulation delivered during stepping randomly at different phases of the step cycle. The soleus H-reflex was recorded in both subject groups under control conditions and following single-pulse transspinal stimulation at an individualized exactly similar positive and negative conditioning-test interval. The EMG …

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …

A Bisphosphonate With A Low Hydroxyapatite Binding Affinity Prevents Bone Loss In Mice After Ovariectomy And Reverses Rapidly With Treatment Cessation, Abigail A. Coffman, Jelena Basta-Pljakic, Rosa M. Guerra, Frank H. Ebetino, Mark W. Lundy, Robert J. Majeska, Mitchell B. Schaffler

Publications and Research

Bisphosphonates (BPs) are a mainstay of osteoporosis treatment; however, concerns about bone health based on oversuppression of remodeling remain. Long-term bone remodeling suppression adversely affects bone material properties with microdamage accumulation and reduced fracture toughness in animals and increases in matrix mineralization and atypical femur fractures in patients. Although a “drug holiday” from BPs to restore remodeling and improve bone quality seems reasonable, clinical BPs have long functional half-lives because of their high hydroxyapatite (HAP) binding affinities. This places a practical limit on the reversibility and effectiveness of a drug holiday. BPs with low HAP affinity and strong osteoclast inhibition …

Beauty That Moves: Dance For Parkinson’S Effects On Affect, Self-Efficacy, Gait Symmetry, And Dual Task Performance, Cecilia Fontanesi, Joseph F. X. Desouza

Publications and Research

Background: Previous studies have investigated the effects of dance interventions on Parkinson’s motor and non-motor symptoms in an effort to develop an integrated view of dance as a therapeutic intervention. This within-subject study questions whether dance can be simply considered a form of exercise by comparing a Dance for Parkinson’s class with a matched-intensity exercise session lacking dance elements like music, metaphorical language, and social reality of art-partaking.

Methods: In this repeated-measure design, 7 adults with Parkinson’s were tested four times; (i) before and (ii) after a Dance for Parkinson’s class, as well as (iii) before and (iv) after a …