Colleges and Department Research

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[2018 Part 1] Research Publishing Strategies: Asking the Right Questions in the Right Order
(2018-02-01) Anderson, Rick
Rick Anderson, Associate Dean for Collections and Scholarly Communication at the University of Utah, is a regular contributor to the 'Scholarly Kitchen Blog' and past president of the Society for Scholarly Publishing. He is a popular speaker on subjects related to the future of scholarly communication and research libraries. Mr. Anderson will provide an interdisciplinary presentation on research publication strategies including traditional publishing avenues, open access options, author/publication charges, and how to watch out for predatory publishers.
[2018 Part 2] Understanding Discipline Norms in Terms of Publishing, Peer Review, Open Access, Data, Metrics
(2018-02-01) Anderson, Rick; Thorne, Debbie; Gabor, Caitlin R.; Jennings, Wes; Rohde, Rodney E.; Shields, Patricia M.
In-depth discussion with Rick Anderson and a panel of Texas State University academic administrators and faculty on discipline-specific publishing issues and trends including: (1) Texas State University's view on scholarship and peer review, (2) Open access publishing, (3) Identifying quality journals by discipline, (4) Handling solicitations by publishers (possible predatory publishers), and (5) Tried and true strategies for increasing the impact of ones research.
21st Century Expeditionary Mindset and Core Values: A Review of the Literature
(2009-10-31) Shields, Patricia M.
This paper reviews literature on the expeditionary mindset and core values taking into account the 21st century security and technology environments. The paper begins by developing the historical context and providing definitions. Next, the paper explores the connection between the expeditionary mindset and military transformation. Key tenets of the 21st century expeditionary mindset are identified and examined. Soldiers with an expeditionary mindset should first, be mentally prepared to deploy on short notice anywhere in the world; second, have the critical-thinking skills necessary to adapt quickly to a changing operational environment; third, work cooperatively with members of a Joint team; fourth, posses knowledge of the culture in the area of the local populace, and; fifth, the expeditionary force will be using 21st century network centric technology. The paper concludes with a discussion of military core values within the context of an expeditionary mindset.
3D Nanomolding and Fluid Mixing in Micromixers with Micro-patterned Microchannel Walls
(Springer, 2017) Farshchian, Bahador; Amirsadeghi, Alborz; Choi, Junseo; Park, Daniel S.; Kim, Namwon; Park, Sunggook
Microfluidic devices where the microchannel walls were decorated with micro and nanostructures were fabricated using 3D nanomolding. Using 3D molded microfluidic devices with microchannel walls decorated with microscale gratings, the fluid mixing behavior was investigated through experiments and numerical simulation. The use of microscale gratings in the micromixer was predicated by the fact that large obstacles in a microchannel enhances the mixing performance. Slanted ratchet gratings on the channel walls resulted in a helical flow along the microchannel, thus increasing the interfacial area between fluids and cutting down the diffusion length. Increasing the number of walls decorated with continuous ratchet gratings intensified the strength of the helical flow, enhancing mixing further. When ratchet gratings on the surface of the top cover plate were aligned in a direction to break the continuity of gratings from the other three walls, a stack of two helical flows was formed one above each other. This work concludes that the 3D nanomolding process can be a cost-effective tool for scaling-up the fabrication of microfluidic mixers with improved mixing efficiencies.Graphical abstractIn this paper we show that a micromixer with patterned walls can be fabricated using 3D nanomolding and solvent-assisted bonding to manipulate the flow patterns to improve mixing.
A Collective Impact Model Towards Increasing STEM Major Student Retention
(Texas State University, The Education Institute, 2020-02) Martinez Ortiz, Araceli; Novoa, Clara; Sriraman, Vedaraman
This article presents the research findings of a multidisciplinary team's collective research effort at one university over a five-year period as funded by the National Science Foundation's Improving Undergraduate STEM Education (IUSE) program. A collaborative learning and retention action research effort at a large Hispanic Serving Institution is analyzed using mixed methods to document the power of collective impact as the foundation for a learning support model for students historically underrepresented majoring in science, technology, engineering and mathematics (STEM) academic programs. The actions of the team of researchers are presented to describe the Rising Stars Collective Impact model and the impacts achieved. This is a model that aligns objectives, intervention efforts, and reports collective results. The long-term goals of the Rising Stars Collective Impact multiple programs managed by the funded program team included the following: (a) to improve the campus sense of community for students historically under-represented in STEM, (b) to establish innovative and robust STEM education research-based practices to support critical skill attainment for students, and (c) to support faculty understanding of the funds of knowledge of diverse students. The positive student retention and success impacts of this research effort are measured through quantitative statistical analysis of the changes in second-year STEM undergraduate student retention rates and representation rates of women, Hispanics, and African American STEM majors.
A Combined Gene Expression and Functional Study Reveals the Crosstalk Between N-Myc and Differentiation-inducing MicroRNAs in Neuroblastoma Cells
(Impact Journals, 2016-10) Zhao, Zhenze; Ma, Xiuye; Shelton, Spencer D.; Sung, Derek C.; Li, Monica; Hernandez, Daniel; Zhang, Maggie; Losiewicz, Michael D.; Chen, Yidong; Pertsemlidis, Alexander; Yu, Xiaojie; Liu, Yuanhang; Du, Liqin
MYCN amplification is the most common genetic alteration in neuroblastoma and plays a critical role in neuroblastoma tumorigenesis. MYCN regulates neuroblastoma cell differentiation, which is one of the mechanisms underlying its oncogenic function. We recently identified a group of differentiation-inducing microRNAs. Given the demonstrated inter-regulation between MYCN and microRNAs, we speculated that MYCN and the differentiation-inducing microRNAs might form an interaction network to control the differentiation of neuroblastoma cells. In this study, we found that eight of the thirteen differentiation-inducing microRNAs, miR-506-3p, miR-124-3p, miR-449a, miR-34a-5p, miR-449b-5p, miR-103a-3p, miR-2110 and miR-34b-5p, inhibit N-Myc expression by either directly targeting the MYCN 3'UTR or through indirect regulations. Further investigation showed that both MYCN-dependent and MYCN-independent pathways play roles in mediating the differentiation-inducing function of miR-506-3p and miR-449a, two microRNAs that dramatically down-regulate MYCN expression. On the other hand, we found that N-Myc inhibits the expression of multiple differentiation-inducing microRNAs, suggesting that these miRNAs play a role in mediating the function of MYCN. In examining the published dataset collected from clinical neuroblastoma specimens, we found that expressions of two miRNAs, miR-137 and miR-2110, were significantly anti-correlated with MYCN mRNA levels, suggesting their interactions with MYCN play a clinically-relevant role in maintaining the MYCN and miRNA expression levels in neuroblastoma. Our findings altogether suggest that MYCN and differentiation-inducing miRNAs form an interaction network that play an important role in neuroblastoma tumorigenesis through regulating cell differentiation.
A Cross-Level Exploratory Analysis of “Neighborhood Effects” on Urban Behavior: An Evolutionary Perspective
(Multidisciplinary Digital Publishing Institute, 2015-11) Weaver, Russell
It is now generally accepted that spatially-based neighborhood or contextual attributes influence individual behaviors. However, studies of contextual effects often operationalize “neighborhoods” as static, single-level administrative units that are chosen for data availability rather than theoretical reasons. This practice has led to new calls for sound conceptual models that guide data collection efforts and statistical analyses related to these phenomena. While many such models are in use or being proposed in the social sciences, this article argues that research in the field of evolutionary studies offers alternative and interesting ways of investigating neighborhood effects. Accordingly, the article pursues two objectives. First, it makes connections between neighborhood effects research in the social sciences and relevant literature in evolutionary game theory and evolutionary urban geography. Second, these interdisciplinary interactions guide the development of a cross-level conceptual model of neighborhood effects on urban social behavior. The conceptual model is then translated into an empirical model that tests whether and how property maintenance behavior in a selected U.S. study area changes as a function of neighborhood context. The findings reveal that neighborhood effects operate at multiple, interacting spatial levels in the study area, which suggests that conventional single-level administrative boundaries are not equipped to capture these effects. While they are proffered as exploratory, the results nonetheless imply that insights from evolutionary research can add depth and theoretical grounding to contextual effects studies in the social sciences.
A Crystalline Oxide Passivation on In0.53Ga0.47As (100)
(American Institute of Physics Publishing, 2017-03-29) Qin, Xiaoye; Wang, Wei-E; Droopad, Ravi; Rodder, Mark S.; Wallace, Robert M.
The passivation of In0.53Ga0.47As surfaces is highly desired for transistor performance. In this study, the feasibility of a crystalline oxide passivation on In0.53Ga0.47As (100) is demonstrated experimentally. The (3 x 1) and (3 x 2) crystalline oxide reconstructions are formed on the de-capped In0.53Ga0.47As (100) surfaces through the control of the surface oxidation states. By monitoring the evolution of chemical states and associated structures of the In0.53Ga0.47As (100) surfaces upon O2 and subsequent atomic hydrogen exposure, we find that the control of the Ga oxide states is critical to the formation of the crystalline oxide reconstructions. The stability of the crystalline oxide layers upon the atomic layer deposition of HfO2 is investigated as well. Furthermore, the capacitance voltage behavior of metal oxide semiconductor capacitors with an HfO2 dielectric layer reveals that the crystalline oxide reconstructions result in a decrease in the density of interface traps (D it) from ~1 x 10 13 cm-2 eV-1 to ~1 x 10 12 cm-2 eV-1 compared with the de-capped surface. The crystalline oxide passivation offers a platform to develop In0.53Ga0.47As devices with a low density of interface states.
A Dataset for the Flood Vulnerability Assessment of the Upper Cross River Basin Using Morphometric Analysis
(Elsevier, 2020-02) Ogarekpe, Nkpa; Obio, Ekpe; Tenebe, Imokhai; Emenike, PraiseGod; Nnaji, Chidozie
The on-site collection of data is not only time consuming, but expensive and perhaps near impossible in restive communities within the upper Cross River basin (UCRB). Therefore, the importance of this data cannot be overemphasized. This article presents a Digital Elevation Model (DEM), land use and land cover (LULC) map, soil map, geology map and climatic datasets which enhance the understanding of the physical characteristics of the upper Cross River basin using morphometric analysis. The use of the LULC map, soil map and the DEM in conjunction with the climatic data enhance the creation of the Hydrologic Response Units (HRUs) and the water balance modelling. The simulation of the water balance at the HRU level enables the routing of the runoff to the reaches of the sub-basins and then to the channels. The geology map provides confirmatory information to the morphometric analysis. The compound factor computed from all the derived morphometric parameters enhance the determination of the overall flood potential of the congruent sub-basins.
A General Hypothesis of Species Diversity
(The American Society of Naturalists, 1979-01) Huston, Michael A.
Many explanations for diversity patterns have been proposed, and there have been several recent reviews of the subject (Pianka 1966, 1974; Ricklefs 1973; Pielou 1975). High diversity has been attributed both to intense competition which forces niche restriction (Dobzhansky 1950; MacArthur and Wilson 1967)and reduced competition resulting from predation (Paine 1966; Harper 1969; Janzen 1970; Connell 1975). Diversity has been positively correlated with productivity (Connell and Orias 1964; Pianka 1966; MacArthur 1969) and negatively correlated with productivity (Yount 1956; Margalef 1969). The question is far from settled. This paper develops an approach to the problem of species diversity based on the nonequilibrium interactions of competing populations. Under nonequilibrium conditions, differences in diversity are strongly influenced by variations in the rates of competitive displacement between communities, and such factors as relative competitive abilities, niche partitioning, etc., may not be particularly important. This approach deals primarily with the maintenance of diversity, as opposed to the generation of diversity. While most of the current diversity hypotheses have some relation to the evolutionary origin of diversity, this will not be emphasized here.
A Geographically Weighted Regression Analysis of the Underlying Factors Related to the Surface Urban Heat Island Phenomenon
(Multidisciplinary Digital Publishing Institute, 2018-09) Zhao, Chunhong; Jensen, Jennifer L. R.; Weng, Qihao; Weaver, Russell
This study investigated how underlying biophysical attributes affect the characterization of the Surface Urban Heat Island (SUHI) phenomenon using (and comparing) two statistical techniques: global regression and geographically weighted regression (GWR). Land surface temperature (LST) was calculated from Landsat 8 imagery for 20 July 2015 for the metropolitan areas of Austin and San Antonio, Texas. We sought to examine SUHI by relating LST to Lidar-derived terrain factors, land cover composition, and landscape pattern metrics developed using the National Land Cover Database (NLCD) 2011. The results indicate that (1) land cover composition is closely related to the SUHI effect for both metropolitan areas, as indicated by the global regression coefficients of building fraction and NDVI, with values of 0.29 and −0.74 for Austin, and 0.19 and −0.38 for San Antonio, respectively. The terrain morphology was also an indicator of the SUHI phenomenon, implied by the elevation (0.20 for Austin and 0.09 for San Antonio) and northness (0.20 for Austin and 0.09 for San Antonio); (2) the SUHI phenomenon of Austin on 20 July 2015 was affected by the spatial pattern of the land use and land cover (LULC), which was not detected for San Antonio; and (3) with a local determination coefficient higher than 0.8, GWR had higher explanatory power of the underlying factors compared to global regression. By accommodating spatial non-stationarity and allowing the model parameters to vary in space, GWR illustrated the spatial heterogeneity of the relationships between different land surface properties and the LST. The GWR analysis of SUHI phenomenon can provide unique information for site-specific land planning and policy implementation for SUHI mitigation.
A Harmine-derived Beta-carboline Displays Anti-cancer Effects in vitro by Targeting Protein Synthesis
(Elsevier, 2017-06) De Carvalho, Annelise; Chu, Jennifer; Meinguet, Celine; Kiss, Robert; Vandenbussche, Guy; Masereel, Bernard; Wouters, Johan; Kornienko, Alexander; Pelletier, Jerry; Mathieu, Veronique
Growing evidence indicates that protein synthesis is deregulated in cancer onset and progression and targeting this process might be a selective way to combat cancers. While harmine is known to inhibit DYRK1A and intercalate into the DNA, tri-substitution was shown previously to modify its activity profile in favor of protein synthesis inhibition. In this study, we thus evaluated the optimized derivative CM16 in vitro anti-cancer effects unfolding its protein synthesis inhibition activity. Indeed, the growth inhibitory profile of CM16 in the NCI 60-cancer-cell-line-panel correlated with those of other compounds described as protein synthesis inhibitors. Accordingly, CM16 decreased in a time- and concentration-dependent manner the translation of neosynthesized proteins in vitro while it did not affect mRNA transcription. CM16 rapidly penetrated into the cell in the perinuclear region of the endoplasmic reticulum where it appears to target translation initiation as highlighted by ribosomal disorganization. More precisely, we found that the mRNA expression levels of the initiation factors EIF1AX, EIF3E and EIF3H differ when comparing resistant or sensitive cell models to CM16. Additionally, CM16 induced eIF2α phosphorylation. Those effects could explain, at least partly, the CM16 cytostatic anti-cancer effects observed in vitro while neither cell cycle arrest nor DNA intercalation could be demonstrated. Therefore, targeting protein synthesis initiation with CM16 could represent a new promising alternative to current cancer therapies due to the specific alterations of the translation machinery in cancer cells as recently evidenced with respect to EIF1AX and eIF3 complex, the potential targets identified in this present study.
A Heuristic Storage Location Assignment Based on Frequent Itemset Classes to Improve Order Picking Operations
(Multidisciplinary Digital Publishing Institute, 2021-02-19) Li, Yue; Mendez-Mediavilla, Francis A.; Temponi, Cecilia; Kim, Junwoo; Jimenez, Jesus
Most large distribution centers’ order picking processes are highly labor-intensive. Increasing the efficiency of order picking allows these facilities to move higher volumes of products. The application of data mining in distribution centers has the capability of generating efficiency improvements, mainly if these techniques are used to analyze the large amount of data generated by orders received by distribution centers and determine correlations in ordering patterns. This paper proposes a heuristic method to optimize the order picking distance based on frequent itemset grouping and nonuniform product weights. The proposed heuristic uses association rule mining (ARM) to create families of products based on the similarities between the stock keeping units (SKUs). SKUs with higher similarities are located near the rest of the members of the family. This heuristic is applied to a numerical case using data obtained from a real distribution center in the food retail industry. The experiment results show that data mining-driven developed layouts can reduce the traveling distance required to pick orders.
A Hierarchical Bayesian Approach to Ecological Count Data: A Flexible Tool for Ecologists
(Public Library of Science, 2011-11-21) Fordyce, James; Gompert, Zachariah; Forister, Matthew L.; Nice, Chris C.
Many ecological studies use the analysis of count data to arrive at biologically meaningful inferences. Here, we introduce a hierarchical Bayesian approach to count data. This approach has the advantage over traditional approaches in that it directly estimates the parameters of interest at both the individual-level and population-level, appropriately models uncertainty, and allows for comparisons among models, including those that exceed the complexity of many traditional approaches, such as ANOVA or non-parametric analogs. As an example, we apply this method to oviposition preference data for butterflies in the genus Lycaeides. Using this method, we estimate the parameters that describe preference for each population, compare the preference hierarchies among populations, and explore various models that group populations that share the same preference hierarchy.
A Meta-Model to Predict the Drag Coefficient of a Particle Translating in Viscoelastic Fluids: A Machine Learning Approach
(Multidisciplinary Digital Publishing Institute, 2022-01-21) Faroughi, Salah; Roriz, Ana; Fernandes, Celio
This study presents a framework based on Machine Learning (ML) models to predict the drag coefficient of a spherical particle translating in viscoelastic fluids. For the purpose of training and testing the ML models, two datasets were generated using direct numerical simulations (DNSs) for the viscoelastic unbounded flow of Oldroyd-B (OB-set containing 12,120 data points) and Giesekus (GI-set containing 4950 data points) fluids past a spherical particle. The kinematic input features were selected to be Reynolds number, 0
A Method for the Detection of Poorly-Formed or Misclassified Saccades: A case study using the GazeCom Dataset
(2022-02) Friedman, Lee; Djanian, Shagen; Komogortsev, Oleg
There are many automatic methods for the detection of eye movement types like fixation and saccades. Evaluating the accuracy of these methods can be a difficult and time-consuming process. We present a method to detect misclassified or poorly formed saccades\footnote{Throughout the manuscript, when we use the word ``misclassified'', we will be referring to both misclassified or poorly formed. saccades.}, regardless of how they were classified. We developed and tested our method on saccades from the very large and publicly available GazeCom dataset. We started out by creating a total of 9 metrics (velocity shape, velocity shape amplitude, position shape, position shape amplitude, flatness, entropy, kurtosis, skewness, and the Dip Test statistic of multimodality) which will be explained below. We applied these metrics to horizontal saccades of 20, 40 and 60 ms duration. For each duration, we performed a data reduction step with factor analysis to see how these 9 metrics were naturally grouped. For every duration, there were 2 factors, one which was dominated by our velocity shape metric and one which was dominated by our entropy metric. We determined that the entropy metric was the single most valuable metric for detecting misclassified saccades. We illustrate the types of saccades that our entropy metric indicates are misclassified. Link to Python Code https://github.com/sdjanian/sacanalysis
A New Crown for an Old Friend
(1995-01) Vaverek, Margaret
Much has changed at SWT since its charter in 1899 and its opening in 1903. Yet, two things remain in the memories of all those who have passed through this school - the San Marcos River and Old Main. The river flows gently through the campus, bringing life and beauty to its citizens. Old Main sits majestically atop Chautauqua Hill, casting a protective shadow over the campus community. She, like the river, is always changing but somehow ever the same. Recent renovation of the roof has once again restored her color and brought her new life.
A Non-Invasive Stress Assay Shows That Tadpole Populations Infected with Batrachochytrium dendrobatidis Have Elevated Corticosterone Levels
(Public Library of Science, 2013-02-13) Gabor, Caitlin R.; Fisher, Matthew C.; Bosch, Jaime
Batrachochytrium dendrobatidis (Bd) is a fungus that causes the disease chytridiomycosis and is associated with widespread amphibian declines. Populations vary in their susceptibility to Bd infections, and the virulence of the infecting lineage can also vary. Both of these factors may manifest as a differential physiological stress response. In addition, variation in disease susceptibility across amphibian populations may be influenced by immunosuppression caused by chronic stress imposed by environmental factors. Here, we use a non-invasive water-borne hormone technique to assess stress levels (corticosterone) of free-living tadpole populations that are infected by Bd. We found that corticosterone release rates were higher in infected populations of two species of tadpoles (Alytes obstetricans and A. muletensis) than in an uninfected population for both species. The relationship between corticosterone and the intensity of infection differed between species, with only the infected A. obstetricans population showing a significant positive correlation. The higher corticosterone release rates found in A. obstetricans may be an outcome of infection by a highly virulent lineage of Bd (BdGPL), whereas A. muletensis is infected with a less virulent lineage (BdCAPE). These results suggest that different lineages of Bd impose different levels of stress on the infected animals, and that this may influence survival. The next step is to determine whether higher corticosterone levels make individuals more susceptible to Bd or if Bd infections drive the higher corticosterone levels.
A Novel Evaluation of Two Related, and Two Independent Algorithms for Eye Movement Classification during Reading
(2018) Friedman, Lee; Rigas, Ioannis; Abdulin, Evgeny; Komogortsev, Oleg
This repository contains classified eye-movement data from the submitted paper, "Novel Evaluation of Two Related, and Two Independent Algorithms for Eye Movement Classification during Reading" Lee Friedman, Ioannis Rigas, Evgeny Abdulin and Oleg V. Komogortsev The Department of Computer Science, Texas State University, San Marcos, Texas. As of 2/19/2018, the third revision is under review at Behavior Research Methods. There are 4 directories included, each with exactly 20 files. These are the 20 files that were evaluated with 4 scoring methods. ONH – These data were scored by the method described in [1]. MNH – These data were scored by the method presented in the manuscript. IRF – These data were scored by the method presented in [2]. EDF – These data were scored by the EyeLink Parser. File naming convention: Take, for example, this name: “S_1051_S1_TEX_Class_EyeLink.csv”. This is data from Subject number 1051, recording session 1, the TEX (poetry reading) task and it contains classification data scored by the EyeLink Parser. “S_1066_S2_TEX_Class_IRF.csv” is data from Subject number 1066, recording session 2, the TEX (poetry reading) task and it contains classification data scored by [2]. “S_1334_S2_TEX_Class_ONH.csv” is data from Subject number 1334, recording session 2, the TEX (poetry reading) task and it contains classification data scored by [1]. Files like “S_1282_S2_TEX_Class_MNH.csv” were scored by the method described in the manuscript. The first column of every dataset is a msec timestamp. Only the first 26,000 msec of each file were processed for the manuscript. The second column of every dataset is the horizontal (X) eye position signal in degrees of visual angle. In the case of the ONH and the MNH methods, these position signals were smoothed. See manuscript for details. The third column of every dataset is the vertical (Y) eye position signal in degrees of visual angle. In the case of the ONH and the MNH methods, these position signals were smoothed. See manuscript for details. The fourth column of every dataset is the radial velocity of the eye movement signals. Please see manuscript for details of this calculation for every dataset. The fifth column of each dataset is a classification code, where 1 = fixation, 2 = saccade, 3 = post-saccadic oscillation, 4 = noise or artifact, and 5 is unclassified. Note that the IRF coded data did not use an “unclassified” category. References: [1] M. Nystrom and K. Holmqvist, "An adaptive algorithm for fixation, saccade, and glissade detection in eyetracking data," Behav Res Methods, vol. 42, no. 1, pp. 188-204, Feb 2010. [2] R. Zemblys, D. C. Niehorster, O. Komogortsev, and K. Holmqvist, "Using machine learning to detect events in eye-tracking data," Behav Res Methods, Feb 23 2017.
A Review of Game Theory Applications for Seaport Cooperation and Competition
(Multidisciplinary Digital Publishing Institute, 2020-02) Pujats, Karlis; Golias, Mihalis; Konur, Dincer
In the ever-changing maritime shipping industry, ports, and more specifically, container terminals, are always on the search for better policy and operational plan developments. As the maritime shipping sector changes, new areas of research emerge. In this paper, we present a review of recent game theory applications for seaport cooperation and competition, accompanied by summary review tables stating the study, the modeling technique used, the methodology and objective, and summary of the results of each study. In total, we have reviewed 33 studies that used game theory models that investigated seaport and container terminal competition and cooperation involving various stakeholders with dating publication years from 2008 to 2019. The paper concludes with a discussion and proposed future research directions. The purpose of the paper is to serve as a reference guide to recent game theory applications on seaport cooperation and competition that would allow a quick understanding of work done in the field.

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