Physical Sciences and Mathematics Commons^™

The Effects Of Thermal Stress On Fluorescent Protein Expression In An Indo-Pacific Scleractinian Coral Species, Acropora Tenuis, Anna Knochel

Independent Study Project (ISP) Collection

The scleractinian coral species that so heavily define tropical coral reefs are increasingly threatened by anthropogenic global warming. Rising sea surface temperatures in combination with light stress causes the photosynthetic breakdown of the coral’s algal symbiont, Symbiodinium. Corals have developed a number of physiological responses to handle acute stressors, such as the production of ultraviolet-protecting amino acids, heat shock proteins, the ability to shift symbionts, and the production of fluorescent proteins. The latter has been thought to play a photoprotective role in the coral holobiont, and studies have shown evidence that corals orient these pigments to divert harmful light away …

A Study Of The Hydrophobic Interactions Between Twenty-Three Cb1 Selective Jwh Compounds And An Active-State Cb1 Receptor Model To Discover Key Structural Features Of The Jwh Compounds And Key Protein Residues Of The Cb1 Receptor, Lyncyn Louise Reliquias

Honors Theses

Synthetic cannabinoids, commonly found in Spice, have recently become a popular substitute for marijuana as they have similar effects to THC, the most powerful constituent of marijuana. Additionally, they are increasingly becoming a source of drug abuse as they cannot be detected with normal drug test screenings. This study specifically analyzed a total of twenty-three CB1 selective JWH compounds and their hydrophobic interactions with an active-state CB1 receptor model. The ligands were categorized per their structural similarities, and this study was aimed to find patterns within each structural moiety that would lead to the discovery of key structural features and/or …

Silence, Please!: Interrupting In-Car Phone Conversations, Soledad López Gambino, Casey Kennington, David Schlangen

Computer Science Faculty Publications and Presentations

Holding phone conversations while driving is dangerous not only because it occupies the hands, but also because it requires attention. Where driver and passenger can adapt their conversational behavior to the demands of the situation, and e.g. interrupt themselves when more attention is needed, an interlocutor on the phone cannot adjust as easily. We present a dialogue assistant which acts as 'bystander' in phone conversations between a driver and an interlocutor, interrupting them and temporarily cutting the line during potentially dangerous situations. The assistant also informs both conversation partners when the line has been cut, as well as when it …

Kidrec: Children & Recommender Systems: Workshop Co-Located With Acm Conference On Recommender Systems (Recsys 2017), Jerry Alan Fails, Maria Soledad Pera, Franca Garzotto, Mirko Gelsomini

Computer Science Faculty Publications and Presentations

The 1^st Workshop on Children and Recommender Systems (KidRec) is taking place in Como, Italy August 27^th, 2017 in conjunction with the ACM RecSys 2017 conference. The goals of the workshop are threefold: (1) discuss and identify issues related to recommender systems used by children including specific challenges and limitations, (2) discuss possible solutions to the identified challenges and plan for future research, and (3) build a community to directly work on these important issues.

Edos: Edge Assisted Offloading System For Mobile Devices, Hank H. Harvey, Ying Mao, Yantian Hou, Bo Sheng

Computer Science Faculty Publications and Presentations

Offloading resource-intensive jobs to the cloud and nearby users is a promising approach to enhance mobile devices. This paper investigates a hybrid offloading system that takes both infrastructure-based networks and Ad-hoc networks into the scope. Specifically, we propose EDOS, an edge assisted offloading system that consists of two major components, an Edge Assistant (EA) and Offload Agent (OA). EA runs on the routers/towers to manage registered remote cloud servers and local service providers and OA operates on the users’ devices to discover the services in proximity. We present the system with a suite of protocols to collect the potential service …

Panel: Influencing Culture And Curriculum Via Revolution, Amit Jain

Computer Science Faculty Publications and Presentations

The goal of this panel session is to introduce audience members to the challenges and successes of significant cultural and curricular change as enacted by awardees in the NSF program Revolutionizing Engineering and Computer Science Departments (RED). This panel will explore how organizations go about the process of cultural investigation and how they embark on culture change, using RED awardees of 2016 as the featured panelists (the second cohort). These teams are engaged in high-risk, high-trust-required activities focused on both the organizational and operational structure of their departments, and on re-envisioning engineering and computer science curricula to create professionals able …

Does Timing Of Herbicide Use Influence Rates Of Germination Or Seedling Biomass Of Native Plants Used For Restoration?, Christine Mcmanamen

Graduate Student Theses, Dissertations, & Professional Papers

Invasive plants can negatively impact native grasslands by changing their species composition, productivity, and function. Managers commonly use herbicides as a control method; however, this practice can lead to secondary invasion by other non-native invasive plants, unless measures are taken to promote natives. Because of this, managers often seed native plants after spraying herbicides. There is evidence, however, that chemical control of invasive plants may reduce the effectiveness of subsequent seed-addition treatments, but there is currently little quantitative information on optimal timing between spraying and seeding or on variation in herbicide sensitivity among native plants commonly used in seed mixes. …

The Balancing Act: Ecological Interventions And Decision Tradeoffs To Preserve Wilderness Character, Lucy A. Lieberman

Graduate Student Theses, Dissertations, & Professional Papers

Global climate change, land use intensification and increasing development are impacting federal wildernesses in new and unprecedented ways. Ecological restoration is one tool that that wilderness managers are using to combat degradation, though the decision to intervene in wilderness is complicated by the Wilderness Act’s legal mandate to preserve wilderness character and demonstrate managerial restraint. The purpose of this study is to document a baseline of ecological interventions that have occurred in the NWPS over the last five years, and to understand how wilderness managers make decisions related to ecological interventions. I sent a quantitative survey to over five hundred …

The Influence Of Tree Height On Lidar’S Ability To Accurately Characterize Forest Structure And Spatial Pattern Across Reference Landscapes, Haley L. Wiggins

Graduate Student Theses, Dissertations, & Professional Papers

Successful restoration of degraded forest landscapes requires reference models that adequately capture structural heterogeneity at multiple spatial scales. Field-based methods for assessing variation in forest structure are costly and inherently suffer from limited replication and spatial coverage. LiDAR is a more cost-effective approach for generating landscape-scale data, but it has a limited ability to detect understory trees. Increased understanding of appropriate height cut-offs for trees to be reliably included in LiDAR-based analysis could improve applications of LiDAR to assessments of landscape-scale forest structure. Toward that end, I investigated the effect of varying tree-height criterion (minimum height cutoffs of 6, 9, …

Xic Clustering By Baseyian Network, Kyle J. Handy

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Estimating The Effects Of Overstory Retention, Vegetative Competition, And Site Quality On The Height Growth Of Small Ponderosa Pine Trees Using Regression Quantiles, Colin P. Kirkmire

Graduate Student Theses, Dissertations, & Professional Papers

Ponderosa pine (Pinus ponderosa C. Lawson) forests in the Inland Northwestern region of the US are increasingly managed under multi-aged silvicultural systems that provide stand structure for wildlife habitat, timber production, enhanced aesthetic, or restoration of presettlement conditions (O'Hara 2005). Partial retention harvest, where an element of the previous stand's overstory structure is retained, is commonly used to achieve a multi-aged stand structure. However, little is known about how ponderosa pine trees in the understory respond to overstory and understory competitive factors following partial retention harvest. The height growth of small trees was hypothesized to be influenced by site …

Ponderosa Pine Responses To Biochar, Fertilizer, Or Mastication On The Bitterroot National Forest, Usa, Haley C. Anderson

Graduate Student Theses, Dissertations, & Professional Papers

Management and restoration practices in even-age ponderosa pine (Pinus ponderosa Lawson & C. Lawson) stands in the Intermountain West can be improved by developing a more thorough understanding of the effects of soil amendment treatments on tree growth and soil properties. Biochar is a charcoal- soil amendment that is created by burning woody biomass in an environment with limited oxygen through a process known as pyrolysis. Biochar has been recommended as a soil amendment for a number of reasons; including increased water and nutrient retention, and building soil aggregates. However, the effects of biochar on temperate forest soils and …

Mirage: A Novel Multiple Protein Sequence Alignment Tool, Alex Nord

Graduate Student Theses, Dissertations, & Professional Papers

A fundamental problem in computational biology is the organization of many related sequences into a multiple sequence alignment (MSA) [2]. MSAs have a range of research applications, such as inferring phylogeny [22] and identifying regions of conserved sequence that indicate functional similarity [18]. In the case of protein isoforms, MSAs are valuable tools for transitively annotating post-translational modifications (PTMs) by enabling information transfer between known PTM sites and the sites that they align to [11].

For protein MSA tools, one challenging biological phenomenon is alternative splicing, wherein identical genomic sequence will differentially select from a subset of available coding regions …

Fire Management Provisions In Federal Wilderness Law, Erik D. Alnes

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Assessing Riparian Ecosystem Condition And Monitoring Recovery From Natural And Anthropogenic Disturbance, Rachel Powers

Graduate Student Theses, Dissertations, & Professional Papers

Riparian ecosystems are the transition zones between river systems and uplands. They provide many valuable ecological functions including creating habitat for wildlife, stabilizing banks from erosion and providing a buffer that prevents excess nutrients from entering streams. Fires and other disturbances alter the function of these ecosystems. Currently, there is a lack of broadly used standardized assessments and monitoring methods in riparian areas within our current water policy framework. This study aims to examine this gap in riparian ecosystem protection by reviewing the assessment methods currently in use, selecting one method for field testing, and analyzing the effort involved in …

The Status Of Virginia's Public Oyster Resource 2016, Melissa Southworth, Roger L. Mann

Reports

This report summarizes data collected during 2016 in the Virginia portion of the Chesapeake Bay. The report is composed of two parts, part one, oyster recruitment (shell string) in Virginia and part two, dredge survey of selected oyster bars in Virginia.

City Of Fredericksburg, Virginia - Shoreline Inventory Report: Methods And Guidelines, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl Hershner

Reports

The 2017 Inventory for the City of Fredericksburg was generated using on-screen, digitizing techniques in ArcGIS® -ArcMap v10.4.1 while viewing conditions observed in Binghigh resolution oblique imagery, Google Earth, and 2013 imagery from the Virginia Base Mapping Program (VBMP).FourGIS shapefiles are developed.The first describes land use and bank conditions (Fredericksburg_lubc_2017). The second portrays the presence of beaches (Fredericksburg_beaches_2017). The third reports shoreline structures that are described as arcs or lines(e.g. riprap)(Fredericksburg _sstru_2017). The final shapefile includes all structures that are represented as points(e.g. piers)(Fredericksburg _astru_2017).The metadata file accompanies the shapefiles and defines attribute accuracy, data development, and any use restrictions …

Summary Tables: Surry County, Virginia Shoreline Inventory Report, Marcia Berman, Karinna Nunez, Sharon Killeen, Tamia Rudnicky, Julie Bradshaw, Karen A. Duhring, Kallie Brown, Jessica Hendricks, David Stanhope, David Weiss, Carl H. Herschner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Summary Tables: King George County, Virginia Shoreline Inventory Report, Marcia Berman, Karinna Nunez, Sharon A. Killeen, Tamia Rudnicky, Julie G. Bradshaw, Kory Angstadt, Karen Duhring, Kallie Brown, Jessica Hendricks, David Weiss, Carl H. Herschner

Reports

The Shoreline Inventory Summary Tables quantify observed conditions based on river systems, such as the combined length of linear features (e.g. shoreline miles surveyed, miles of bulkhead and revetment), the total number of point features (e.g. docks, boathouses, boat ramps) & total acres of polygon features (tidal marshes).

Viewed By Too Many Or Viewed Too Little: Using Information Dissemination For Audience Segmentation, Bernard J. Jansen, Soon-Gyu Jung, Joni Salminen, Jisun An, Haewoon Kwak

Research Collection School Of Computing and Information Systems

The identification of meaningful audience segments, such as groups of users, consumers, readers, audience, etc., has important applicability in a variety of domains, including for content publishing. In this research, we seek to develop a technique for determining both information dissemination and information discrimination of online content in order to isolate audience segments. The benefits of the technique include identification of the most impactful content for analysis. With 4,320 online videos from a major news organization, a set of audience attributes, and more than 58 million interactions from hundreds of thousands of users, we isolate the key pieces of content …

A Two-Sided Collaborative Transparent Display Supporting Workspace Awareness, Jiannan Li, Saul Greenberg, Ehud Sharlin

Research Collection School Of Computing and Information Systems

Transparent displays naturally support workspace awareness during face-to-face interactions. Viewers see another person’s actions through the display: gestures, gaze, body movements, and what one is manipulating on the display. Yet we can design even better collaborative transparent displays. First, collaborators on either side should be able to directly interact with workspace objects. Second, and more controversially, both sides should be capable of presenting different content. This affords: reversal of images/text in place (so that people on both sides see objects correctly); personal and private territories aligned atop each other; and GUI objects that provide different visuals for feedthrough vs. feedback. …

Rfid Ownership Transfer With Positive Secrecy Capacity Channels, Jorge Munilla, Mike Burmester, Alberto Peinado, Guomin Yang, Willy Susilo

Research Collection School Of Computing and Information Systems

RFID ownership transfer protocols (OTPs) transfer tag ownership rights. Recently, there has been considerable interest in such protocols; however, guaranteeing privacy for symmetric-key settings without trusted third parties (TTPs) is a challenge still unresolved. In this paper, we address this issue and show that it can be solved by using channels with positive secrecy capacity. We implement these channels with noisy tags and provide practical values, thus proving that perfect secrecy is theoretically possible. We then define a communication model that captures spatiotemporal events and describe a first example of symmetric-key based OTP that: (i) is formally secure in the …

On The Effectiveness Of Code-Reuse-Based Android Application Obfuscation, Xiaoxiao Tang, Yu Liang, Xinjie Ma, Yan Lin, Debin Gao

Research Collection School Of Computing and Information Systems

Attackers use reverse engineering techniques to gain detailed understanding of executable for malicious purposes, such as re-packaging an Android app to inject malicious code or advertising components. To make reverse engineering more difficult, researchers have proposed various code obfuscation techniques to conceal purposes or logic of code segments. One interesting idea of code obfuscation is to apply codereuse techniques (e.g., Return-Oriented Programming) to (re-)distribute essential code segments before they are reconstructed at runtime. Such techniques are well understood on x86 platform, but relatively less explored on Android. In this paper, we present an evaluation on the extent to which code-reuse-based …

Exploring Representativeness And Informativeness For Active Learning, Bo Du, Zengmao Wang, Lefei Zhang, Liangpei Zhang, Wei Liu, Jialie Shen, Dacheng Tao

Research Collection School Of Computing and Information Systems

How can we find a general way to choose the most suitable samples for training a classifier? Even with very limited prior information? Active learning, which can be regarded as an iterative optimization procedure, plays a key role to construct a refined training set to improve the classification performance in a variety of applications, such as text analysis, image recognition, social network modeling, etc. Although combining representativeness and informativeness of samples has been proven promising for active sampling, state-of-the-art methods perform well under certain data structures. Then can we find a way to fuse the two active sampling criteria without …

Research Strategies For Biomedical And Health Informatics: Some Thought-Provoking And Critical Proposals To Encourage Scientific Debate On The Nature Of Good Research In Medical Informatics, Reinhold Haux, Et Al.

Research Collection School Of Computing and Information Systems

Medical informatics, or biomedical and health informatics (BMHI), has become an established scientific discipline. In all such disciplines there is a certain inertia to persist in focusing on well-established research areas and to hold on to well-known research methodologies rather than adopting new ones, which may be more appropriate. To search for answers to the following questions: What are research fields in informatics, which are not being currently adequately addressed, and which methodological approaches might be insufficiently used? Do we know about reasons? What could be consequences of change for research and for education? Outstanding informatics scientists were invited to …

H-Binder: A Hardened Binder Framework On Android Systems, Dong Shen, Zhangkai Zhang, Xuhua Ding, Zhoujun Li, Robert H. Deng

Research Collection School Of Computing and Information Systems

The Binder framework is at the core of Android systems due to its fundamental role for interprocess communications. Applications use the Binder to perform high level tasks such as accessing location information. The importance of the Binder makes it an attractive target for attackers. Rootkits on Android platforms can arbitrarily access any Binder transaction data and therefore have system-wide security impact. In this paper, we propose H-Binder to secure the Binder IPC channel between two applications. It runs transparently with Android and COTS applications without making changes on their binaries. In this work, we design a bare-metal ARM hypervisor with …

Avoiding Zombies In Archival Replay Using Serviceworker, Sawood Alam, Mat Kelly, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

[First paragraph] A Composite Memento is an archived representation of a web page with all the page requisites such as images and stylesheets. All embedded resources have their own URIs, hence, they are archived independently. For a meaningful archival replay, it is important to load all the page requisites from the archive within the temporal neighborhood of the base HTML page. To achieve this goal, archival replay systems try to rewrite all the resource references to appropriate archived versions before serving HTML, CSS, or JS. However, an effective server-side URL rewriting is difficult when URLs are generated dynamically using JavaScript. …

Gender Difference And Employees' Cybersecurity Behaviors, Mohd Anwar, Wu He, Ivan Ash, Xiaohong Yuan, Ling Li, Li Xu

Information Technology & Decision Sciences Faculty Publications

Security breaches are prevalent in organizations and many of the breaches are attributed to human errors. As a result, the organizations need to increase their employees' security awareness and their capabilities to engage in safe cybersecurity behaviors. Many different psychological and social factors affect employees' cybersecurity behaviors. An important research question to explore is to what extent gender plays a role in mediating the factors that affect cybersecurity beliefs and behaviors of employees. In this vein, we conducted a cross-sectional survey study among employees of diverse organizations. We used structural equation modelling to assess the effect of gender as a …

Elevated Trace Metal Content Of Prokaryotic Communities Associated With Marine Oxygen Deficient Zones, Daniel C. Ohnemus, Sara Rauschenberg, Gregory A. Cutter, Jessica N. Fitzsimmons, Robert M. Sherrell, Benjamin S. Twining

OES Faculty Publications

Little is known about the trace metal content of marine prokaryotes, in part due to their co-occurrence with more abundant particulate phases in the upper ocean, such as phytoplankton and biogenic detritus, lithogenic minerals, and authigenic Mn and Fe oxyhydroxides. We attempt to isolate these biomass signals in particulate data from the US GEOTRACES Eastern Pacific Zonal Transect (cruise GP16) in the Eastern Tropical South Pacific (ETSP), which exhibited consistent maxima in P and other bioactive trace metals, and minima in particulate Mn, in the oxygen deficient zones (ODZs) of 13 stations. Nitrite maxima and nitrate deficits indicated the presence …

Community Production Modulates Coral Reef Ph And The Sensitivity Of Ecosystem Calcification To Ocean Acidification, Thomas M. Decarlo, Anne L. Cohen, George T. F. Wong, Fuh-Kwo Shiah, Steven J. Lentz, Kristen A. Davis, Kathryn E. F. Shamberger, Pat Lohmann

OES Faculty Publications

Coral reefs are built of calcium carbonate (CaCO₃) produced biogenically by a diversity of calcifying plants, animals, and microbes. As the ocean warms and acidifies, there is mounting concern that declining calcification rates could shift coral reef CaCO3 budgets from net accretion to net dissolution. We quantified net ecosystem calcification (NEC) and production (NEP) on Dongsha Atoll, northern South China Sea, over a 2 week period that included a transient bleaching event. Peak daytime pH on the wide, shallow reef flat during the nonbleaching period was ~8.5, significantly elevated above that of the surrounding open ocean (~8.0-8.1) as …