Digital Commons Network^™

Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Publications and Research

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …

Public Land Revisited: Municipalization And Privatization In Newark And New York City, Samuel Stein, Oksana Mironova

Publications and Research

Public land plays a central role in contemporary urban planning struggles. Using a comparative case study approach focused on the north-eastern US cities of Newark and New York City, we uncover patterns of land acquisition and dispossession that fit five broad and often overlapping periods in planning history: City Beautiful, metropolitan reorganization, deindustrialization, and devaluation, followed by hyper-commodification in New York City and redevelopment amidst disinvestment in Newark. Through this periodization, we find that accumulation and alienation of urban public land has largely taken place through two modes of municipalization (targeted and reactive) and two modes of privatization (community-led and …

The International Conference On Intelligent Biology And Medicine (Icibm) 2018: Bioinformatics Towards Translational Applications, Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhuan Ruan, Degui Zhi

Publications and Research

The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks, which covered a wild range of aspects of bioinformatics, medical informatics, systems biology and intelligent computing. Here, we summarize nine research articles selected for publishing in BMC Bioinformatics.

A New Insight Into Underlying Disease Mechanism Through Semi-Parametric Latent Differential Network Model, Yong He, Jiadong Ji, Lei Xie, Xinsheng Zhang, Fuzhong Xue

Publications and Research

Background

In genomic studies, to investigate how the structure of a genetic network differs between two experiment conditions is a very interesting but challenging problem, especially in high-dimensional setting. Existing literatures mostly focus on differential network modelling for continuous data. However, in real application, we may encounter discrete data or mixed data, which urges us to propose a unified differential network modelling for various data types.

Results

We propose a unified latent Gaussian copula differential network model which provides deeper understanding of the unknown mechanism than that among the observed variables. Adaptive rank-based estimation approaches are proposed with the assumption …

Using Physical Contact Heterogeneity And Frequency To Characterize Dynamics Of Human Exposure To Nonhuman Primate Bodily Fluids In Central Africa, Victor Narat, Mamdou Kampo, Thibut Heyer, Stephanie Rupp, Philippe Ambata, Richard Njouom, Tamara Giles-Vernick

Publications and Research

Emerging infectious diseases of zoonotic origin constitute a recurrent threat to global health. Nonhuman primates (NHPs) occupy an important place in zoonotic spillovers (pathogenic transmissions from animals to humans), serving as reservoirs or amplifiers of multiple neglected tropical diseases, including viral hemorrhagic fevers and arboviruses, parasites and bacteria, as well as retroviruses (simian foamy virus, PTLV) that are pathogenic in human beings. Hunting and butchering studies in Africa characterize at-risk human social groups, but overlook critical factors of contact heterogeneity and frequency, NHP species differences, and meat processing practices. In southeastern Cameroon, a region with a history of zoonotic emergence …

Understanding Urbanization: A Study Of Census And Satellite-Derived Urban Classes In The United States, 1990-2010, Deborah Balk, Stefan Leyk, Bryan Jones, Mark R. Montgomery, Anastasia Clark

Publications and Research

Most of future population growth will take place in the world’s cities and towns. Yet, there is no well-established, consistent way to measure either urban land or people. Even censusbased urban concepts and measures undergo frequent revision, impeding rigorous comparisons over time and place. This study presents a new spatial approach to derive consistent urban proxies for the US. It compares census-designated urban blocks with proxies for landbased classifications of built-up areas derived from time-series of the Global Human Settlement Layer (GHSL) for 1990–2010. This comparison provides a new way to understand urban structure and its changes: Most land that …

Non-Pharmacological Solutions To Sleep And Circadian Rhythm Disruption: Voiced Bedside Experiences Of Hospice And End-Oflife Staff Caregivers, Rana Sagha Zadeh, Elizabeth Capezuti, Paul Eshelman, Nicole Woody, Jennifer Tiffany, Ana C. Krieger

Publications and Research

Background: Sleep disturbance is a significant issue, particularly for patients with advanced terminal illness. Currently, there are no practice-based recommended approaches for managing sleep and circadian disruptions in this population. To address this gap, a cross-sectional focus group study was performed engaging 32 staff members at four hospices/end-of-life programs in three demographically diverse counties in New York State.

Methods: Participants responded to structured open-ended questions. Responses were transcribed and subjected to qualitative content analysis. The themes and recommendations for improved practice that emerged were tabulated using Atlas TI qualitative software.

Results: This report details the experiences of hospice and end-of-life …

Nano-Based Systems And Biomacromolecules As Carriers For Metallodrugs In Anticancer Therapy, Mina Poursharifi, Marek T. Wlodarczyk, Aneta J. Mieszawska

Publications and Research

Since the discovery of cisplatin and its potency in anticancer therapy, the development of metallodrugs has been an active area of research. The large choice of transition metals, oxidation states, coordinating ligands, and different geometries, allows for the design of metal-based agents with unique mechanisms of action. Many metallodrugs, such as titanium, ruthenium, gallium, tin, gold, and copper-based complexes have been found to have anticancer activities. However, biological application of these agents necessitates aqueous solubility and low systemic toxicity. This minireview highlights the emerging strategies to facilitate the in vivo application of metallodrugs, aimed at enhancing their solubility and bioavailability, …

But Are They Actually Healthier? Challenging The Health/Wellness Divide Through The Ethnography Of Embodied Ecological Heritage, Kristina Baines

Publications and Research

A holistic definition of ‘health’ remains difficult to operationalize, despite decades of attempts by medical anthropologists and the World Health Organization to do so. Anthropologists routinely reject dichotomous notions – belief vs. knowledge, wellness vs. health, mental vs. physical, environment vs. self – yet demands for physiological evidence of ‘health’ persist. In this article, I ask what evidence would sufficiently demonstrate health, and explore the possibility of measures that move beyond the physiological. Using ethnographic data collected in indigenous Maya communities in Belize and in immigrant communities in New York City, I argue that ecological heritage practices can provide a …

Interference And Control Of The Nosocomial Transmission Of Methicillin-Resistant Staphylococcus Aureus, Sen Pei, Flaviano Morone, Fredrik Liljeros, Hernan Makse, Jeffrey L. Shaman

Publications and Research

Methicillin-resistant Staphylococcus aureus (MRSA) is a continued threat to human health in both community and healthcare settings. In hospitals, control efforts would benefit from accurate estimation of asymptomatic colonization and infection importation rates from the community. However, developing such estimates remains challenging due to limited observation of colonization and complicated transmission dynamics within hospitals and the community. Here, we develop an inference framework that can estimate these key quantities by combining statistical filtering techniques, an agent-based model, and real-world patient-to-patient contact networks, and use this framework to infer nosocomial transmission and infection importation over an outbreak spanning 6 years in …

Nurse Practitioner Knowledge, Attitudes, And Beliefs When Caring For Transgender People, Catherine Paradiso, Robin M. Lally

Publications and Research

Purpose: The aim of this study was to explore Nurse Practitioner (NP) knowledge, attitudes, and beliefs when working with transgender people and to inform about Practitioner education needs.

Methods: A qualitative descriptive design was used to explore (NP) experiences. Focused semistructured interviews were conducted in 2016 with 11 (N = 11) NPs in the northeastern United States who represent various years of experience and encounters with transgender patients. The interviews explored NP knowledge attitudes and beliefs when caring for transgender patients and described their overall experiences in rendering care in the clinical setting. The interviews were professionally transcribed and analyzed …

Effects Of Urbanization On The Foraging Ecology And Microbiota Of The Generalist Seabird Larus Argentatus, Matthew Fuirst, Richard R. Veit, Megan Hahn, Nolwenn Dheilly, Lesley H. Thorne

Publications and Research

Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. …

A Classroom Activity For Teaching Kohlberg’S Theory Of Moral Development, Cheryl L. Carmichael, Anna M. Schwartz, Maureen Coyle, Matthew H. Goldberg

Publications and Research

In two studies, we demonstrate an engaging classroom activity that facilitates student learning about Kohlberg’s theory of moral development by using digital resources to foster active, experiential learning. In addition to hearing a standard lecture about moral development, students watched a video of a morally provocative incident, then worked in small groups to classify user comments posted in response to the video according to Kohlberg’s six stages. Students in both studies found the activity enjoyable and useful. Moreover, students’ scores on a moral development quiz improved after completing the activity (Study 1), and students who completed the activity in addition …

Prefronto-Cerebellar Neuromodulation Affects Appetite In Obesity, Elena M. Marron, Raquel Viejo-Sobera, Guillem Cuatrecasas, Diego Redolar-Ripoll, Pilar García Lorda, Abhishek Datta, Marom Bikson, Greta Magerowksi, Miguel Alonso-Alonso

Publications and Research

Human neuroimaging studies have consistently reported changes in cerebellar function and integrity in association with obesity. To date, however, the nature of this link has not been studied directly. Emerging evidence suggests a role for the cerebellum in higher cognitive functions through reciprocal connections with the prefrontal cortex. The purpose of this exploratory study was to examine appetite changes associated with noninvasive prefronto-cerebellar neuromodulation in obesity. 12 subjects with class I obesity (mean BMI 32.9 kg/m2) underwent a randomized, single-blinded, sham-controlled, crossover study, during which they received transcranial direct current stimulation (tDCS; active/sham) aimed at simultaneously enhancing the activity of …

Gofish: A Versatile Nested Pcr Strategy For Environmental Dna Assays For Marine Vertebrates, Mark Y. Stoeckle, Mithun Das Mishu, Zachary Charlop-Powers

Publications and Research

Here we describe GoFish, a strategy for single-species environmental DNA (eDNA) presence/absence assays using nested PCR. The assays amplify a mitochondrial 12S rDNA segment with vertebrate metabarcoding primers, followed by nested PCR with M13-tailed, species-specific primers. Sanger sequencing confirms positives detected by gel electrophoresis. We first obtained 12S sequences from 77 fish specimens for 36 northwestern Atlantic taxa not well documented in GenBank. Using these and existing 12S records, we designed GoFish assays for 11 bony fish species common in the lower Hudson River estuary and tested seasonal abundance and habitat preference at two sites. Additional assays detected nine cartilaginous …

Forever? Or Ursula K. Le Guin Makes America Great Again By Repositioning Trump As The Dispossessed, Marleen S. Barr

Publications and Research

This is a poem about Ursula K. Le Guin and Trump.

Open Source Foundations For Spatial Decision Support Systems, Jochen Albrecht

Publications and Research

Spatial Decision Support Systems (SDSS) were a hot topic in the 1990s, when researchers tried to imbue GIS with additional decision support features. Successful practical developments such as HAZUS or CommunityViz have since been built, based on commercial desktop software and without much heed for theory other than what underlies their process models. Others, like UrbanSim, have been completely overhauled twice but without much external scrutiny. Both the practical and the theoretical foundations of decision support systems have developed considerably over the past 20 years. This article presents an overview of these developments and then looks at what corresponding tools …

Embracing Intersectionality To Create A Collective Living Theory Of Practice, Sara B. Woolf, Nathalis Wamba

Publications and Research

In this paper, we describe pivotal experiences that have shaped our respective professional journeys when teaching action research. We situate these experiences in relation to how they have contributed to our collective living theory of practice. This discussion unfolded as we explored ways to improve our own practices and the practices of our students. We conclude that this and similar questions can only be authentically answered when we as practitioners and faculty in higher education settings are willing to interrogate the contexts within which we interact and the complex intersections between our own intentional practices and selves and our students’ …

Age-Tastic! An Evaluation Of An Evidence-Based Intervention For Older Adults, Manoj Pardasani, Jackie Berman, Mebane Powell

Publications and Research

Background: Raising awareness of holistic health and safety among older adults is critical to enhancing their wellbeing in many cases, improving health outcomes and motivating positive behavioral changes. Age-Tastic! is a comprehensive health and safety promotion intervention that uses the concept of a competitive board game to entice older adults to participate and stay engaged.

Objective: The purpose of this study was to evaluate the impact of Age-Tastic! on the level of awareness, health literacy, self-efficacy and positive behavioral change among the participants.

Methods: A randomized control trial was conducted with 98 older adults assigned to an experimental and control …

Milch Sees A Great Future For Art Administrators, Aldemaro Romero Jr.

Publications and Research

“I didn’t choose art, art chose me.” That’s how Professor David Milch explains his personal and professional fascination with the arts. “I came from a family where there was always music or always something artistic happening. It was where I felt at home; it was where I found people I could relate to, found ideas, and found the outlets to share the creations we would make with a wider group of people,” says he.

The Investigation Of The French Curve, Cheriyah Wilmot

Publications and Research

The creation of irregular curves has evolved from employing splines to computer aided design (CAD); with French Curves being an integral part of this evolution. Such curvilinear irregularity can be seen in the curve of the auditorium at the new academic building. This project investigates the origins of the French Curve, in terms of its history, usage, and mathematical components. For centuries, French curves were used to accurately create portions of ellipticals and other curves in schematic drawings. The commonly used Burmester set contains an amalgamation of mathematical equations where the point of inflection is not symmetrical. These are derived …

Analysis And Simulation Of Convolution Reverb Using City Tech’S New Auditorium, Tian Leng

Publications and Research

In digital signal processing, convolution reverb can simulate the reverberation of a real acoustic space. The acoustics of different seating areas in an auditorium can vary from each other. To determine the reverberant characteristics of City Tech new building’s auditorium, impulse response (IR) signals are recorded in five key locations of the auditorium.

Directly recorded balloon burst is chosen as the source of impulse source. An omnidirectional and a cardioid microphone with flat frequency response curves are used to record IR signals to 24-bit monophonic wav files. Each IR signal, along with a vocal, is convoluted in MATLAB through both …

Law And Modern Technology: Lack Of Tech Knowledge In Legal Profession May Cause Injustice, Md Wahidur Rahman, Marissa Moran

Publications and Research

There is no such field where technology hasn’t reached. It will be a dream to think something without technology. In today’s world every field requires tech knowledge. The courtroom and law offices have changed with the evolution of technology. Most courts don’t accept paper files anymore. Law offices use virtual file to store client information. However, due to old age or other reason a significant number of attorneys and judges are not competent in technology.

This paper will examine the use of technology in our legal system and what problem arises due to lack of proper tech knowledge. Increasing use …

Forensic Science: Complex Admissibility Standard For Scientific Evidence And Expert Witness's Testimony, Md Wahidur Rahman, Marissa J. Moran

Publications and Research

Modern science forces the world to accept new theories and invention. Science has invented several tools, which are used in the legal system to dispute criminal cases. Scientific evidence and expert witness testimony have weight in the courtroom because those are scientifically proved to be true. Even though there are few case laws and Federal rule of evidence 1975, still the admissibility standard is complex which may lead injustice.

This article examines the Federal rule of evidence, case laws and scholars’ opinion to address the complexity of the admissibility standard of scientific evidence and expert testimony. The first legal question …

Computational Techniques For Scattering Amplitudes, Juliano A. Everett

Publications and Research

Scattering amplitudes in quantum field theory can be described as the probability of a scattering process to happen within a high energy particle interaction, as well as a bridge between experimental measurements and the prediction of the theory.

In this research project, we explore the Standard Model of Particle Theory, it’s representation in terms of Feynman diagrams and the algebraic formulas associated with each combination.

Using the FeynArts program as a tool for generating Feynman diagrams, we evaluate the expressions of a set of physical processes, and explain why these techniques become necessary to achieve this goal.

Smart Iot Sprinkler System, Galib F. Rahman

Publications and Research

The average family spends more than $1000 in water costs per year. One-way water is commonly wasted in many households is via inefficient sprinkler systems for lawns. Current technology has enabled the development of automatic sprinkler systems, which can be preconfigured to operate at desired times of day and intervals. Although these systems may reduce the amount of water utilized overall, they are not weather forecast aware. In situations when rainfall is upcoming the systems still water the lawn. In this project, we plan to implement a smart sprinkler system that has full awareness of upcoming weather and take account …

Instances Of Influenza In The United States Visualized, Parth Patel

Publications and Research

The Tycho Project collects large data sets related to healthcare and in particular, instances and geographical information of diseases. We look at the instance counts and locations of Influenza from 1919-1951 across the United States. We hope to find seasonal and geographical insight to the spread of the disease.

Historical Effects Of Electronic Interfaces, G James Mitchell

Publications and Research

Electronic interfaces are a primary tool for most professional and personal communication currently happening. Electronics, like the human mind, are limited by the understanding of executing will, or commands. This can be characterized as “interface limitations” of digital technology. Identifying this bottleneck in technological development has been critical in historical changes to both hardware and software technology. Recent medical research examines a novel user interface to reduce task load. I hypothesize, interface developments that take cues from nonverbal human communication enhance and sustain the significance of those technologies in society. By examining pivotal moments of historical technology we can identify …

Fractals And The Geometry Of Matrix Operators, Xiaona Zhou

Publications and Research

In this project, we are interested in how certain fractals can be generated by using introductory linear algebra techniques. A fractal is an object or a structure that is self-similar in all length scales. Sierpinski Carpet and Sierpinski Triangle are two classic examples of fractals. Fractals have many applications in real life, for instance, in imaging, art and biological sciences. In this project, we apply classes of linear transformation to describe and generate fractals in the Euclidean plane, and we generate different examples of fractal using MATLAB.

Peer-Leaders’ Perceptions Of Learning After A Semester Of Peer Facilitation, Yasmine A. Soofi, Nadia Kennedy

Publications and Research

The study examines the perceptions of a group of new peer-leaders of their learning during a semester of peer-leading training and experience working with a group of students. Data was collected through individual interviews in the beginning of the semester and through administering a survey at the end of the semester. The data was organized, analyzed and presented at the poster session.