Physical Sciences and Mathematics Commons^™

College Of Natural Sciences Newsletter, February 2022, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 3, Issue 2

Page 1 Dean's Message
Page 2 Awards & Recognition
Page 3-4 Media Coverage of CNS
Page 5- 6 Local Boy Scouts Earn Their Chemistry Merit Badges
Page 7-8 Mount Vernon Teacher Wins 2022 South Dakota Outstanding Physical Science Teacher Award
Page 9 Middle Schoolers Visit SDSU
Page 10 Microbiology Club Tours POET
Page 11 53rd Geography Convention
Page 12 Open PRAIRIE Data

A Bayesian Phase I/Ii Biomarker-Based Design For Identifying Subgroup-Specific Optimal Dose For Immunotherapy, Beibei Guo, Yong Zang

Faculty Publications

Immunotherapy is an innovative treatment that enlists the patient's immune system to battle tumors. The optimal dose for treating patients with an immunotherapeutic agent may differ according to their biomarker status. In this article, we propose a biomarker-based phase I/II dose-finding design for identifying subgroup-specific optimal dose for immunotherapy (BSOI) that jointly models the immune response, toxicity, and efficacy outcomes. We propose parsimonious yet flexible models to borrow information across different types of outcomes and subgroups. We quantify the desirability of the dose using a utility function and adopt a two-stage dose-finding algorithm to find the optimal dose for each …

Singing Strategies Are Linked To Perch Use On Foraging Territories In Heart-Nosed Bats, Grace C. Smarsh, Ashley M. Long, Michael Smotherman

Faculty Publications

Acoustic communication allows animals to coordinate and optimize resource utilization in space. Cardioderma cor, the heart-nosed bat, is one of the few species of bats known to sing during nighttime foraging. Previous research found that heart-nosed bats react aggressively to song playback, supporting the territorial defense hypothesis of singing in this species. We further investigated the territorial defense hypothesis from an ecological standpoint, which predicts that singing should be associated with exclusive areas containing a resource, by tracking 14 individuals nightly during the dry seasons in Tanzania. We quantified the singing behavior of individuals at all perches used throughout the …

Strict Lyapunov Functions And Feedback Controls For Sir Models With Quarantine And Vaccination, Hiroshi Ito, Michael Malisoff, Frederic Mazenc

Faculty Publications

We provide a new global strict Lyapunov function construction for a susceptible, infected, and recovered (or SIR) disease dynamics that includes quarantine of infected individuals and mass vaccination. We use the Lyapunov function to design feedback controls to asymptotically stabilize a desired endemic equilibrium, and to prove input-to-state stability for the dynamics with a suitable restriction on the disturbances. Our simulations illustrate the potential of our feedback controls to reduce peak levels of infected individuals.

Docking And Molecular Dynamic Of Microalgae Compounds As Potential Inhibitors Of Beta-Lactamase, Roberto Pestana-Nobles, Yani Aranguren-Diaz, Elwi Machado-Sierra, Juvenal Yosa, Nataly J. Galan-Freyle,, Laura X. Sepulveda-Montano, Daniel G. Kuroda, Leonardo C. Pacheco-Londono

Faculty Publications

Bacterial resistance is responsible for a wide variety of health problems, both in children and adults. The persistence of symptoms and infections are mainly treated with beta-lactam antibiotics. The increasing resistance to those antibiotics by bacterial pathogens generated the emergence of extended-spectrum beta-lactamases (ESBLs), an actual public health problem. This is due to rapid mutations of bacteria when exposed to antibiotics. In this case, beta-lactamases are enzymes used by bacteria to hydrolyze the beta-lactam rings present in the antibiotics. Therefore, it was necessary to explore novel molecules as potential beta-lactamases inhibitors to find antibacterial compounds against infection caused by ESBLs. …

Whole-Genome Sequencing And Rna-Seq Reveal Differences In Genetic Mechanism For Flowering Response Between Weedy Rice And Cultivated Rice, Richard S. Garcia, Sapphire Coronejo, Jonathan Concepcion, Prasanta K. Subudhi

Faculty Publications

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified …

Time-Efficient Algorithm For The Order-Statistic Operations In Lattice Data Structure, Joseph Mendis

Undergraduate University Honors Capstones

Data structures are an essential part of almost all software programs. The primary operations of most data structures are searching, insertion, deletion, and finding the Kth smallest element. To be of practical use, operations on data structures should be fast and should not use much memory space; in other words, the time and space complexities should not be enormous. This research project provides an algorithm, called FindKth, for the order-statistic operations of finding the ATth smallest element in Lattice Data Structures. In the average case, our algorithm is of time complexity O(n3/2), and it is of time complexity O(n) for …

Volumetric Lattice Boltzmann Method For Wall Stresses Of Image-Based Pulsatile Flows, Xiaoyu Zhang, Joan Gomez-Paz, Xi Chen, James M. Mcdonough, Md Mahfuzul Islam, Yiannis Andreopoulos, Luoding Zhu, Huidan Yu

Mechanical Engineering Faculty Publications

Image-based computational fluid dynamics (CFD) has become a new capability for determining wall stresses of pulsatile flows. However, a computational platform that directly connects image information to pulsatile wall stresses is lacking. Prevailing methods rely on manual crafting of a hodgepodge of multidisciplinary software packages, which is usually laborious and error-prone. We present a new computational platform, to compute wall stresses in image-based pulsatile flows using the volumetric lattice Boltzmann method (VLBM). The novelty includes: (1) a unique image processing to extract flow domain and local wall normality, (2) a seamless connection between image extraction and VLBM, (3) an en-route …

Mir-4521 Plays A Tumor Repressive Role In Growth And Metastasis Of Hepatocarcinoma Cells By Suppressing Phosphorylation Of Fak/Akt Pathway Via Targeting Fam129a, Munawar Ayesha, Abbasi Majid, Dongting Zhao, Frederick T. Greenaway, Naimeng Yan, Qinlong Liu, Shuqing Liu, Ming Zhong Sun

Chemistry

Introduction: Globally, hepatocellular carcinoma (HCC) is the sixth most common malignancy and it has the fourth highest mortality. MicroRNAs play a significant part in biological processes in cell formation and advancement by targeting genes in many cancers including HCC. Objective: In the present study we examine the involvement of miR-4521 and FAM129A correlations in HCC occurrence and progression. Methods: Expression levels of miR-4521 and FAM129A in HCC tissues and cells were detected. Immunohistochemistry was carried out to detect expression of FAM129A, MMP9 and TIMP-1 in HCC tissues. Western blot assays were used to examine expression levels of different genes involve …

Performance Analysis Of Lightweight Internet Of Things Devices On Blockchainnetworks, Cem Kösemen, Gökhan Dalkiliç, Şafak Öksüzer

Turkish Journal of Electrical Engineering and Computer Sciences

Potential integration or cooperation of the Internet of things (IoT) systems and the blockchain technology is nowadays attracting remarkable interest from the researchers. These inter-operating systems often have to rely on lowcost, low-power, and robust IoT devices that can communicate with the blockchain network through smart contracts. In this work, we designed and ran a benchmark study for ESP32-based lightweight IoT devices interacting within the Quorum blockchain. A software library was built for ESP32 devices to enable elliptic-curve digital signing, Keccak-256 hashing, decoding, encoding, and secure private key generation capabilities, which all are the basic functional requirements for running a …

Tri-Op Redactable Blockchains With Block Modification, Removal, And Insertion, Mohammad Sadeq Dousti, Alpteki̇n Küpçü

Turkish Journal of Electrical Engineering and Computer Sciences

In distributed computations and cryptography, it is desirable to record events on a public ledger, such that later alterations are computationally infeasible. An implementation of this idea is called blockchain, which is a distributed protocol that allows the creation of an immutable ledger. While such an idea is very appealing, the ledger may be contaminated with incorrect, illegal, or even dangerous data, and everyone running the blockchain protocol has no option but to store and propagate the unwanted data. The ledger is bloated over time, and it is not possible to remove redundant information. Finally, missing data cannot be inserted …

Blocksim-Net: A Network-Based Blockchain Simulator, Prashanthi Ramachandran, Nandini Agrawal, Osman Bi̇çer, Alpteki̇n Küpçü

Turkish Journal of Electrical Engineering and Computer Sciences

Since its proposal by Eyal and Sirer (CACM '13), selfish mining attacks on proof-of-work blockchains have been studied extensively. The main body of this research aims at both studying the extent of its impact and defending against it. Yet, before any practical defense is deployed in a real world blockchain system, it needs to be tested for security and dependability. However, real blockchain systems are too complex to conduct any test on or benchmark the developed protocols. Instead, some simulation environments have been proposed recently, such as BlockSim (Maher et al., SIGMETRICS Perform. Eval. Rev. '19), which is a modular …

Block Size Optimization For Pow Consensus Algorithm Based Blockchainapplications By Using Whale Optimization Algorithm, Betül Aygün, Hi̇lal Arslan

Turkish Journal of Electrical Engineering and Computer Sciences

Blockchain-based applications come up with cryptocurrencies, especially Bitcoin, introducing a distributed ledger technologies for peer-to-peer networks and essentially records the transactions in blocks containing hash value of the previous blocks. Block generation constitutes the basis of this technology, and the optimization of such systems is among the most crucial concerns. Determining either the block size or the number of transactions in the block brings out a remarkable problem that has been solved by the miners in recent years. First, higher block size results in higher transaction time, on the other hand, smaller block size has many disadvantages such as security, …

Estonian Internet Voting With Anonymous Credentials, İsa Sertkaya, Peter Roenne, Peter Y. A. Ryan

Turkish Journal of Electrical Engineering and Computer Sciences

The Estonian Internet voting (EIV) scheme is a unique example of a long-term nation-wide, legally binding electronic voting deployment. The EIV scheme is used in parallel with standard paper-based election day voting, of course invalidating an already cast i-vote. This necessarily requires careful authentication of the eligible voters and makes the Estonian identity card solution a crucial part of the scheme, however, note that Parsovs has recently drawn attention to the security flaws found in Estonian ID-cards. In this study, we propose an e-voting scheme EIV-AC that integrates the EIV scheme with anonymous credentials based on self-sovereign identity. In addition …

Forming A Decentralized Research Network: Ds4h, Eni̇s Karaarslan, Meli̇h Bi̇ri̇m, Hüseyi̇n Emre Ari

Turkish Journal of Electrical Engineering and Computer Sciences

There is a trend toward decentralized systems, but these systems are developed without conducting enough software tests. Also, the performance, scalability, and sustainability of the decentralized systems are not taken into account. One of the reasons is the time-consuming testing process. The other is the hardware requirements and the complexity of the software installations of the testing environment. Developer communities need stable and secure research networks to test and develop prototypes before releasing the working versions. Cloud-based blockchain test networks are available, but it allows using a specific framework. Also, users are required to learn how to use each framework. …

Data Immutability And Event Management Via Blockchain In The Internet Of Things, Hakan Altaş, Gökhan Dalkiliç, Umut Can Çabuk

Turkish Journal of Electrical Engineering and Computer Sciences

The Internet of things (IoT) is the key enabler of the smart systems used in many areas, from agriculture to aviation, industrial automation to autonomous vehicles. Most IoT deployments employ cost-efficient lightweight devices with limited resources (e.g., bandwidth, energy, storage). Although an IoT network must be built in its simplest form, engineers include more sophisticated devices like gateways and servers to provide web-based services and benefit from cloud systems. So, although the nodes can be widely distributed geographically or topologically, the system becomes centralized, which causes bottlenecks and single-points-of-failure. Furthermore, providing data integrity, nonrepudiation, and event management becomes tricky. In …

Knowledge Graph Embedding By Normalizing Flows, Changyi Xiao, Xiangnan He, Yixin Cao

Research Collection School Of Computing and Information Systems

A key to knowledge graph embedding (KGE) is to choose a proper representation space, e.g., point-wise Euclidean space and complex vector space. In this paper, we propose a unified perspective of embedding and introduce uncertainty into KGE from the view of group theory. Our model can incorporate existing models (i.e., generality), ensure the computation is tractable (i.e., efficiency) and enjoy the expressive power of complex random variables (i.e., expressiveness). The core idea is that we embed entities/relations as elements of a symmetric group, i.e., permutations of a set. Permutations of different sets can reflect different properties of embedding. And the …

What Really Matters?: Characterising And Predicting User Engagement Of News Postings Using Multiple Platforms, Sentiments And Topics, Kholoud K. Aldous, Jisun An, Bernard J. Jansen

Research Collection School Of Computing and Information Systems

This research characterises user engagement of approximately 3,000,000 news postings of 53 news outlets and 50,000,000 associated user comments during 8 months on 5 social media platforms (i.e. Facebook, Instagram, Twitter, YouTube, and Reddit). We investigate the effect of sentiments and topics on user engagement across four levels of user engagement expressions (i.e. views, likes, comments, cross-platform posting). We find that sentiments and topics differ by both news outlets and social media platforms, and both sentiments and topics by the four levels of user engagement expression. Finally, we predict a volume of four user engagement levels for given news content, …

Choices Are Not Independent: Stackelberg Security Games With Nested Quantal Response Models, Tien Mai, Arunesh Sinha

Research Collection School Of Computing and Information Systems

The quantal response (QR) model is widely used in Stackelberg security games (SSG) to model a bounded rational adversary. The QR model is a model of human response from among a large variety of prominent models known as discrete choice models. QR is the simplest type of discrete choice models and does not capture commonly observed phenomenon such as correlation among choices. We introduce the nested QR adversary model (based on nested logit model in discrete choice theory) in SSG which addresses shortcoming of the QR model. We present tractable approximation of the resulting equilibrium problem with nested QR adversary. …

Understanding In-App Advertising Issues Based On Large Scale App Review Analysis, Cuiyun Gao, Jichuan Zeng, David Lo, Xin Xia, Irwin King, Michael R. Lyu

Research Collection School Of Computing and Information Systems

Context: In-app advertising closely relates to app revenue. Reckless ad integration could adversely impact app quality and user experience, leading to loss of income. It is very challenging to balance the ad revenue and user experience for app developers. Objective: Towards tackling the challenge, we conduct a study on analyzing user concerns about in-app advertisement. Method: Specifically, we present a large-scale analysis on ad-related user feedback. The large user feedback data from App Store and Google Play allow us to summarize ad-related app issues comprehensively and thus provide practical ad integration strategies for developers. We first define common ad issues …

Simultaneous Material Identification And Target Imaging With Commodity Rfid Devices, Ju Wang, Jie Xiong, Xiaojiang Chen, Hongbo Jiang, Rajesh Krishna Balan, Dingyi Fang

Research Collection School Of Computing and Information Systems

Material identification and target imaging play an important role in many applications. This paper introduces TagScan, a system that can identify the material type and image the horizontal cut of a target simultaneously with cheap commodity Radio-Frequency IDentification (RFID) devices. The key intuition is that different materials and/or target sizes cause different amounts of phase and RSS (Received Signal Strength) changes, when radio frequency (RF) signal penetrates through the target. Multiple challenges need to be addressed before we can turn the idea into a functional system, including (i) indoor environments exhibit rich multipath which breaks the linear relationship between the …

New-Media Advertising And Retail Platform Openness, Jianqing Chen, Zhiling Guo

Research Collection School Of Computing and Information Systems

We recently have witnessed two important trends in online retailing: the advent of new media (e.g., social media and search engines) makes advertising affordable for small sellers, and large online retailers (e.g., Amazon and JD.com) opening their platforms to allow even direct competitors to sell on their platforms. We examine how new-media advertising affects retail platform openness. We develop a game-theoretic model in which a leading retailer, who has both valuation and awareness advantages, and a third-party seller, who sells an identical product, engage in price competition. We find that the availability of relatively low-cost advertising through new media plays …

Modeling Functional Similarity In Source Code With Graph-Based Siamese Networks, Nikita Mehrotra, Navdha Agarwal, Piyush Gupta, Saket Anand, David Lo, Rahul Purandare

Research Collection School Of Computing and Information Systems

Code clones are duplicate code fragments that share (nearly) similar syntax or semantics. Code clone detection plays an important role in software maintenance, code refactoring, and reuse. A substantial amount of research has been conducted in the past to detect clones. A majority of these approaches use lexical and syntactic information to detect clones. However, only a few of them target semantic clones. Recently, motivated by the success of deep learning models in other fields, including natural language processing and computer vision, researchers have attempted to adopt deep learning techniques to detect code clones. These approaches use lexical information (tokens) …

Butte Area Npl Site Butte Priority Soils Operable Unit (Bpsou), Trec Inc., A Woodard And Curran Company

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

The Stellar-Age Dependence Of X-Ray Emission From Normal Star-Forming Galaxies In The Goods Fields, Woodrow Gilbertson, Bret D. Lehmer, Keith Doore, Rafael Eufrasio, Antara Basu-Zych, William N. Brandt, Tassos Fragos, Kristen Garofali, Konstantinos Kovlakas, Bin Luo, Paolo Tozzi, Fabio Vito, Benjamin F. Williams, Yongquan Xue

Space and Planetary Science Faculty Publications and Presentations

The Chandra Deep Field-South and North surveys (CDFs) provide unique windows into the cosmic history of X-ray emission from normal (nonactive) galaxies. Scaling relations of normal-galaxy X-ray luminosity (LX) with star formation rate (SFR) and stellar mass (M⋆) have been used to show that the formation rates of low-mass and high-mass X-ray binaries (LMXBs and HMXBs, respectively) evolve with redshift across z ≈ 0–2 following LHMXB/SFR ∝ (1 + z) and LLMXB/M⋆ ∝ (1 + z)2−3. However, these measurements alone do not directly reveal the physical mechanisms behind the redshift …

The Impact Of Neutron Transfer Reactions On The Heating And Cooling Of Accreted Neutron Star Crusts, H. Schatz, Z. Meisel, E. F. Brown, S. S. Gupta, G. W. Hitt, W. R. Hix, R. Jain, R. Lau, P. Möller, W. J. Ong, P. S. Shternin, Y. Xu, M. Wiescher

Physics and Engineering Science

Nuclear reactions heat and cool the crust of accreting neutron stars and need to be understood to interpret observations of X-ray bursts and long-term cooling in transiently accreting systems. It was recently suggested that previously ignored neutron transfer reactions may play a significant role in the nuclear processes. We present results from full nuclear network calculations that now include these reactions and determine their impact on crust composition, crust impurity, heating, and cooling. We find that a large number of neutron transfer reactions indeed occur and impact crust models. In particular, we identify a new type of reaction cycle that …

Perioperative Registries In Resource-Limited Settings: The Way Forward For Pakistan, Usama Waqar, Shaheer Ahmed, Ayesha Nasir Hameed, Namrah Aziz, Hina Inam

Medical College Documents

Capable of improving surgical quality, perioperative registries can allow performance benchmarking, reliable reporting and the development of risk-prediction models. Well established in high-income countries, perioperative registries remain limited in lower- and middle-income countries due to several challenges. First, ensuring comprehensive data entry forums to power the registries is difficult because of limited electronic medical records requiring sustained efforts to develop and integrate these into practice. Second, lack of adequate expertise and resources to develop and maintain registry software necessitates the involvement of software developers and information technology personnel. Third, case ascertainment and item completion are challenging secondary to poor-quality medical …

Mental Health In The Uk Biobank: A Roadmap To Self-Report Measures And Neuroimaging Correlates, Rosie K. Dutt, Kayla Hannon, Ty O. Easley, Joseph C. Griffis, Wei Zhang, Janine D. Bijsterbosch

Statistical and Data Sciences: Faculty Publications

The UK Biobank (UKB) is a highly promising dataset for brain biomarker research into population mental health due to its unprecedented sample size and extensive phenotypic, imaging, and biological measurements. In this study, we aimed to provide a shared foundation for UKB neuroimaging research into mental health with a focus on anxiety and depression. We compared UKB self-report measures and revealed important timing effects between scan acquisition and separate online acquisition of some mental health measures. To overcome these timing effects, we introduced and validated the Recent Depressive Symptoms (RDS-4) score which we recommend for state-dependent and longitudinal research in …

Propagation Of Inflowing Urban Stormwater Pulses Through Reservoir Embayments, Megan Fork, Ryan A. Mcmanamay, James B. Heffernan

Biology Faculty Publications

Flashy hydrology and high solute loads in stormflow are well-studied effects of the built environment on urban streams. The physical and chemical interactions between inflowing stormwater of urban streams and their termination in large impoundments, however, is poorly understood. Determining the spatial distribution of urban stormwater in reservoirs is an important step in understanding the effects of the heat and contaminant loads in these systems, which provide multiple services for adjacent cities. Here, we show that signals of stormwater from a small urban stream can propagate more than 800 m from the stream mouth. Stormflow can also break down the …

Chandra Revisits Wr 48a: Testing Colliding Wind Models In Massive Binaries, Svetozar A. Zhekov, Marc Gagné, Stephen L. Skinner

Earth & Space Sciences Faculty Publications

We present results of new Chandra High-Energy Transmission Grating (HETG) observations (2019 November-December) of the massive Wolf-Rayet binary WR 48a. Analysis of these high-quality data showed that the spectral lines in this massive binary are broadened (full width at half-maximum, FWHM = 1400 km s(-1)) and marginally blueshifted (similar to-100 km s(-1)). A direct modelling of these high-resolution spectra in the framework of the standard colliding stellar wind (CSW) picture provided a very good correspondence between the shape of the theoretical and observed spectra. Also, the theoretical line profiles are in most cases an acceptable representation of the observed ones. …