Systems Biology Commons^™

City As Cemetery, Siqiao Zhao

Masters Theses

The traditional funeral service industry has enormous environmental and financial costs. In contrast, green burial, and Natural Organic Reduction (NOR), accelerate the human body’s degradation and reduce toxic substances in the land, assuming responsibility for our burden on the earth. They provide a gateway between us and the processes of nature and ask us to set aside self-consciousness to accept our oneness with the universe. By gifting our bodies back to the earth, where decomposition enriches soils and nurtures the growth of other life forms, we honor those who have transitioned to another state by continuing the cycle of renewal. …

Phylogenetics And Integrative Taxonomy Of African Water Snakes (Squamata: Colubridae: Grayia), Teslin Chaney

Open Access Theses & Dissertations

Grayia is a genus of relatively large (1.5 - 2.5 m) aquatic Afrotropical snakes. Recent molecular phylogenies recovered Grayia in its own distinct subfamily (Grayiinae), which was strongly supported as the sister group to Colubrinae. Because tropical African snakes are generally understudied, the relationships within Grayia are poorly known. Due to high degrees of intra- and interspecies variation, identification is often difficult and previous studies involving Grayia included misidentified specimens in other genera. The goal of this study is to create a phylogenetic tree that can be used to understand the relationships and taxonomy of Grayia via an integrative taxonomic …

The Bellarmine Bee Bed: Organizing A Native Plant Garden Using Feedback From The Local Community, Kate Moran

Undergraduate Theses

Animal pollinators are the cornerstone of healthy ecosystems. Their survival is essential for the persistence of entire food chains: from the flowers they cross-pollinate directly, to the animals who depend on those plants for nutrition. The establishment of pollinator gardens—particularly ones that consist of native plants—is an effective way to enhance their biodiversity, abundance, and well-being.

The main goal of this thesis is to construct a pollinator garden that maximizes the benefits for animal pollinators using feedback from local gardeners. A survey was used to gather information about the popularity and preferences of 40 flowering plants, and after analyzing the …

Analysis Of Germany’S Experience On Development Of Biosphere Reserves And Suggestions To China, Yijie Xian, Ning Liu, Na Qiao, Qiang Fang, Qunli Han, Ding Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Germany has integrated biosphere reserves into the national strategy of sustainable development, and has built an outstanding biosphere reserve system nationwide, which has played a key role in maintaining the stability of ecosystem, exploring sustainable use of natural resources, innovating social development models, prospering local economies and providing an important platform to carry out comprehensive research on human and nature relationship. The experience of Germany includes:long and solid accumulation in the development of protected areas; deep understanding from authorities and the folk of the concept of Man and the Biosphere Programme (MAB) and the value of biosphere reserves, and more …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Effects Of Foliar Application Of Zno Nanoparticles On Lentil Production, Stress Level And Nutritional Seed Quality Under Field Conditions, Marek Kolenčík, Dávid Ernst, Matej Komár, Martin Urík, Martin Šebesta, Ľuba Ďurišová, Marek Bujdoš, Ivan Černý, Juraj Chlpík, Martin Juriga, Ramakanth Illa, Yu Qian, Huan Feng, Gabriela Kratošová, Karla Čech Barabaszová, Ladislav Ducsay, Elena Aydın

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Nanotechnology offers new opportunities for the development of novel materials and strategies that improve technology and industry. This applies especially to agriculture, and our previous field studies have indicated that zinc oxide nanoparticles provide promising nano-fertilizer dispersion in sustainable agriculture. However, little is known about the precise ZnO-NP effects on legumes. Herein, 1 mg·L⁻¹ ZnO-NP spray was dispersed on lentil plants to establish the direct NP effects on lentil production, seed nutritional quality, and stress response under field conditions. Although ZnO-NP exposure positively affected yield, thousand-seed weight and the number of pods per plant, there was no statistically significant …

Of Biodiversity, Boundaries, And Distribution: The Myxomycetes Of The Philippines And Beyond, Sittie Aisha Bustamante Macabago

Graduate Theses and Dissertations

This dissertation contains a compilation of independently performed studies primarily focusing on the myxomycetes (plasmodial slime molds) from the Philippines and integrating local and worldwide data to demonstrate regional and global trends. The major themes include the following: (I) a review of the diverse group of spore-producing amoeboid protists, including the myxomycetes; (II-IV) diversity assessments in three different groups of islands in the Philippine archipelago; (V) mapping the myxomycetes found in the Philippines for databasing and analyzing the geocoded data; (VI) a study on regional boundaries, including the Philippines, using myxomycete species composition; and, (VII) creating a global species distribution …

Knowing What We Know: Leveraging Community Knowledge Through Automated Text-Mining, Justin Gardner, Jonathan Tory Toole, Hemant Kalia, Garry Spink Jr., Gordon Broderick

Advances in Clinical Medical Research and Healthcare Delivery

No abstract provided.

Corticospinal Excitability During A Perspective Taking Task As Measured By Tms-Induced Motor Evoked Potentials, Elizabeth Murray, Janet Brenya, Katherine Chavarria, Karen J. Kelly, Anjel Fierst, Nathira Ahmad, Caroline Anton, Layla Shaffer, Kairavi Kapila, Logan Driever, Kayla Weaver, Caroline Dial, Maya Crawford, Iso Hartman, Tommy Infantino, Fiona Butler, Abigail Straus, Shakeera L. Walker, Brianna Balugas, Matthew Pardillo, Briana Goncalves, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

Only by understanding the ability to take a third-person perspective can we begin to elucidate the neural processes responsible for one’s inimitable conscious experience. The current study examined differences in hemispheric laterality during a first-person perspective (1PP) and third-person perspective (3PP) taking task, using transcranial magnetic stimulation (TMS). Participants were asked to take either the 1PP or 3PP when identifying the number of spheres in a virtual scene. During this task, single-pulse TMS was delivered to the motor cortex of both the left and right hemispheres of 10 healthy volunteers. Measures of TMS-induced motor-evoked potentials (MEPs) of the contralateral abductor …

The Feasibility Of Renewable Natural Gas In New Jersey, Anneliese Dyer, Amelia Christine Miller, Brianna Chandra, Juan Galindo Maza, Carley Tran, Justin Bates, Vicky Olivier, Amy Tuininga

Publications

With traditional natural gas being one of the top options for heating in the United States and the present threat of climate change, there is a demand for an alternative clean fuel source. A Renewable Natural Gas Implementation Decision-Making Conceptual Model was created to provide a framework for considering the feasibility of renewable natural gas (RNG) projects and applied to New Jersey, specifically investigating landfills and wastewater treatment plants (WWTPs). Data from the US EPA’s Landfill Methane Outreach Program and New Jersey’s Department of Environmental Protection Sewage Sludge databases were used to identify seven landfills and 22 WWTPs as possible …

Homicide And Drug Trafficking In Impoverished Communities In Brazil, Elenice De Souza De Souza Oliveira, Braulio Figueiredo Alves Da Silva, Flavio Luiz Sapori, Gabriela Gomes Cardoso

Department of Justice Studies Faculty Scholarship and Creative Works

Many studies demonstrate that homicides are heavily concentrated in impoverished neighborhoods, but not all socially disadvantaged neighborhoods are hotbeds of violence. Conducted in Belo Horizonte, Brazil, this study hypothesizes that the association between high rates of homicide and impoverished areas is influenced by the emergence of a specific type of street drug-dealing common to favelas (slums). The study applies econometric techniques to police data on homicides and drug arrests from 2008 to 2011, as well as 2010 Census data, to test its hypothesis. The findings provide insight into the development of crime prevention policies in areas of high social vulnerability.

Preliminary Evidence Of The Role Of Medial Prefrontal Cortex In Self-Enhancement: A Transcranial Magnetic Stimulation Study, Birgitta Taylor-Lillquist, Vivek Kanpa, Maya Crawford, Mehdi El Filali, Julia Oakes, Alex Jonasz, Amanda Disney, Julian Keenan

Department of Biology Faculty Scholarship and Creative Works

Humans employ a number of strategies to improve their position in their given social hierarchy. Overclaiming involves presenting oneself as having more knowledge than one actually possesses, and it is typically invoked to increase one’s social standing. If increased expectations to possess knowledge is a perceived social pressure, such expectations should increase bouts of overclaiming. As the medial prefrontal cortex (MPFC) is sensitive to social pressure and disruption of the MPFC leads to decreases in overclaiming, we predicted that transcranial magnetic stimulation (TMS) applied to the MPFC would reduce overclaiming and the effects would be enhanced in the presence of …

The Bioethical Significance Of “The Origin Of Man’S Ethical Behavior” (October 1941, Unpublished) By Ernest Everett Just And Hedwig Anna Schnetzler Just, Theodore Walker Jr.

Journal of the South Carolina Academy of Science

Abstract –

E. E. Just (1883-1941) is an acknowledged “pioneer” in cell biology, and he is perhaps the pioneer in study of egg cell fertilization. Here we discover that Just also made pioneering contributions to general biology and evolutionary bioethics.

Within Just’s published contributions to observational cell biology, there are substantial fragments of his theory of ethical behavior, a theory with roots in cell biology. In addition to such previously available fragments, Just’s fully developed theory is now available. This recently discovered unpublished book-length manuscript argues for the biological origins of ethical behavior (evolving from cells to humans, within a …

Do Corporate Owned Adaptive Learning Platforms Perpetuate Banking Style Learning? Integrating Technology For Activism Into Transformational Sustainability Education, Tina M. Garner

Leadership for Sustainability Education Comprehensive Papers

We live in a world that tends to be controlled by corporations. The public school system should be wary of the problems that corporate control has on education. Even though public schools should not have corporate influence, the fact remains that they do, and this perpetuates Freire's banking style learning. Through time, the corporate influence in education was through educational materials such as book sales. Since the decline of the use of books and the growth of the use of technologies, corporations have followed suit through the sales of Adaptive Learning Platforms. Through leveraging the technology which students enjoy using, …

Examining Patterns In Nest Predation Using Artificial Nests, Victoria L. Simonsen

School of Natural Resources: Dissertations, Theses, and Student Research

The use of artificial nests to study the predation of avian nests has faced disregard by ecologists due to inconsistencies found between the survival rates of real and artificial nests across studies and reviews. The negative perception of artificial nests providing an inconsistent assessment of survival has thus fostered the perception that artificial nests are a secondary option to be used to overcome logistical hurdles associated with achieving sufficient sample sizes in systems where study species are rare or elusive, or as merely a preliminary method to study predation across gradients. We argue that the greatest mistake ecologists have made …

Radical Social Ecology As Deep Pragmatism: A Call To The Abolition Of Systemic Dissonance And The Minimization Of Entropic Chaos, Arielle Brender

Student Theses 2015-Present

This paper aims to shed light on the dissonance caused by the superimposition of Dominant Human Systems on Natural Systems. I highlight the synthetic nature of Dominant Human Systems as egoic and linguistic phenomenon manufactured by a mere portion of the human population, which renders them inherently oppressive unto peoples and landscapes whose wisdom were barred from the design process. In pursuing a radical pragmatic approach to mending the simultaneous oppression and destruction of the human being and the earth, I highlight the necessity of minimizing entropic chaos caused by excess energy expenditure, an essential feature of systems that aim …

Hydrology And Macroinvertebrates As Biological Indicators- An Integrated Study Of The Río Zamora Watershed, Loja, Ecuador, Isabel Ryde

Independent Study Project (ISP) Collection

Water quality and access is under grave threat in Ecuador, yet remains poorly studied. Macroinvertebrates were used as biological indicators to study water quality around Reserva Natural Madrigal del Podocarpus, Loja Province, Ecuador. Data on macroinvertebrates was combined with hydrologic measurements of stream functions. Macroinvertebrate sampling was conducted from 6 sites within the Upper Río Zamora watershed. Geologic outcrops were observed along several roadcuts and stream banks. Hydrologic data was collected by measuring discharge, elevation change, and finding the highest permanent spring. The EPT index (number of EPT individuals and percentage of EPT individuals) and the BMWP/Colombia Index for macroinvertebrates …

Bioethics In The Work Of Ernest Everett Just: + Missing - Some 400 Pages, Theodore Walker

Perkins Faculty Research and Special Events

Biology + ethics = bioethics. Here we see that Howard University biologist Ernest Everett Just (born 1883, died 1941) connected biology to ethics.

According to Just, various forms of specific biology (including especially cell biology) plus “general biology” are necessary for explaining adequately the origin of ethical behaviors. Social ethical behaviors, especially mutual aid and cooperative interactions with others and the environment, are essential to evolutionary advances among living creatures, ranging from humans to cells. Accordingly, theory of ethics (moral theory) should have roots in biology.

Also, Just wrote an unpublished book-length manuscript—“some 400 typed pages” (Just 1940)—on seeking the …

Harpy Eagle (Harpia Harpyja) Conservation: Juvenile Behavior And Diet At A Nest Near Pijibasal, Darien, Hannah Rodgers

Independent Study Project (ISP) Collection

The Harpy Eagle (Harpia harpyja), the largest and most powerful bird of prey in the Americas, is declining throughout its range in Neotropical forests. Hunting and deforestation threaten populations in the most important remaining eagle habitat in Central America, the Darien province of Panama. These eagles may have the longest postfledging juvenile dependency of any raptor, though juvenile behavior during this period is poorly studied. This study monitored an 11-month-old juvenile for 7 days at a nest near the indigenous community of Pijibasal in order to study behavior and diet. Researchers recorded the juvenile’s location and behavior, studied prey remains …

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

The Greenhouse Effect: Decomposition Rates In Human Remains Wrapped In Plastic, Barbara R. Forman

Masters Theses

Determining an accurate estimation of the postmortem interval (PMI) of human remains is important for several reasons. First, it is used to determine whether the individual is recently deceased, and therefore of medicolegal concern. If so, the estimated PMI is used in narrowing the possible identities of the deceased. PMI can also be used in excluding, or convicting, a murder suspect.

Though deviations may occur, it has been found that PMI can be calculated from the decomposition stages with reasonable accuracy (Galloway 1989, Megyesi 2001, Megyesi et al. 2005, Schiel 2008, Simmons et al. 2010). Some factors, such as low …

Linking Old Librarianship To New: Aligning 5-Steps Of The Innovator's Dna In Creating Thematic Discovery Systems For The Everglades, L. Bryan Cooper, Margarita Perez Martinez

Works of the FIU Libraries

This poster presentation from the May 2015 Florida Library Association Conference, along with the Everglades Explorer discovery portal at http://ee.fiu.edu, demonstrates how traditional bibliographic and curatorial principles can be applied to: 1) selection, cross-walking and aggregation of metadata linking end-users to wide-spread digital resources from multiple silos; 2) harvesting of select PDFs, HTML and media for web archiving and access; 3) selection of CMS domains, sub-domains and folders for targeted searching using an API.

Choosing content for this discovery portal is comparable to past scholarly practice of creating and publishing subject bibliographies, except metadata and data are housed in …

Pathological Effects Of Repeated Concussive Tbi In Mouse Models: Periventricular Damage And Ventriculomegaly, Richard H. Wolferz Jr.

Honors Scholar Theses

Repeated concussive traumatic brain injury (rcTBI) is the most prominent form of head injury affecting the brain, with an estimated 1.7 million Americans affected each year (Kuhn 2012). Neurologists have been concerned about the danger of repeated head impacts since the 1920’s, but researchers have only begun to understand the long-term effects of rcTBI (McKee 2009). Although symptoms can be as mild as dizziness, current research suggests that multiple concussions can lead to a progressive degenerative brain disease known as chronic traumatic encephalopathy (CTE) (Luo 2008, McKee 2009, Kane 2013). Research on the brain is just beginning to scratch the …

Fish Use Of Largely Unexplored Sub-Tidal Habitats In The Hinchinbrook Channel Estuary, Queensland, Alexandra Parisien

Independent Study Project (ISP) Collection

This study examines the use of sub-tidal open-bottom, rocky, and seagreass habitats by the Siganus genus (herbivores), Gerres genus (benthivores), and planktivores in the Hinchinbrook Channel Estuary in Queensland, Australia. The Hinchinbrook Channel Estuary, a tropical estuary cutting between Hinchinbrook Island and the Australian mainland, is surrounded primarily by mangroves. Its sub-tidal habitats are largely unexplored due to factors such as low visibility and the presence of estuarine crocodiles. In this study, I reviewed 699 underwater videos collected by James Cook University PhD candidate Michael Bradley in order to analyze feeding and movement behavior of pre-identified fish.

The results of …

Fauna Census Of Intertidal Cliffs, Mangapwani, Zanzibar, Emily Jankowski

Independent Study Project (ISP) Collection

Due to their extreme variations in condition over the course of a day, intertidal zones are challenging environments. Organisms that live there must be prepared to cope with both exposure and submersion, not to mention the temperature variations that accompany these conditions. The differing tolerances and adaptations of various organisms to these conditions generally cause patterns of vertical zonation to occur in the intertidal zone, especially when the shore is steep and rocky. Understanding the ecology of shore environments is important to future conservation and management efforts. This study was conducted on a beach in Mangapwani, Zanzibar at at 6˚ …

'In' Or 'As' Space?: A Model Of Complexity, With Philosophical, Simulatory, And Empirical Ramifications, Charles H. Smith

DLPS Faculty Publications

A General Systems model based on ideas originating with the writings of Benedict de Spinoza is described, starting with its philosophical underpinnings, and proceeding on to its relation to modern systems concepts, including attempts to simulate the relationships posed, and measure real world structures. Central to the idea is the notion that spatial extension may not have a prior existence, but emerges only through an entropy maximization process in which information and energy exchange is balanced among some limited number of subsystems that in sum comprise any given functioning complex system. Related published empiricism concerning geographical/geological systems – the hypsometry …

Monteverde: Ecology And Conservation Of A Tropical Cloud Forest - 2014 Updated Chapters, Nalini M. Nadkarni, Nathaniel T. Wheelwright

Bowdoin Scholars' Bookshelf

The Monteverde Cloud Forest Reserve has captured the worldwide attention of biologists, conservationists, and ecologists and has been the setting for extensive investigation over the past 40 years. Roughly 40,000 ecotourists visit the Cloud Forest each year, and it is often considered the archetypal high-altitude rain forest. “Monteverde: Ecology and Conservation of a Tropical Cloud Forest”, edited by Nalini Nadkarni and Nathaniel T. Wheelwright (Oxford University Press, 2000 and Bowdoin’s Scholar’s Bookshelf. Book 1 ), features synthetic chapters and specific accounts written by more than 100 biologist and local residents, presenting in a single volume everything known in 2000 about …

The Envenoming Pandemic And The Misguided Views Of Snakes: Developing Sustainable Relationships Between Native Poisonous Snakes Of India And The Citizens Of Maharashtra Through The Use Of The Irula Model., Destiny Villanueva

Animal Science

Due to its vast population and general negative consensus regarding snakes, India is notorious for having more snakebite incidents than any other country. Snakes are simultaneously revered and feared in Indian religion and culture. This stigma is perpetuated through propaganda, family beliefs, and innate fears of snakes.These stigmas are more pronounced within rural areas, such as the region of Mahad within the state of Maharshtra. Envenoming is endemic in these areas, and others like them. The World Health Organization identified envenoming as one of the most neglected tropical diseases of the 21st century (Nature India, 2013). Additionally, both nonvenomous and …

A Pedagogical Simulation Of The Spatial Distribution Of Carbon Flux Dynamics In Peat Soils, Alan Gilmer

Conference Papers

No abstract provided.

Site Assessment For Environmental Restoration, David A. Bainbridge

David A Bainbridge

Restoring degraded desert ecosystems is challenging but it can be done. The first key step is understanding the site history and understanding the disturbance and current site conditions. With this information the appropriate steps can be taken to improve the site ecosystem function and structure.