Digital Commons Network^™

Droid: Dose-Ranging Approach To Optimizing Dose In Oncology Drug Development, Beibei Guo, Ying Yuan

Faculty Publications

In the era of targeted therapy, there has been increasing concern about the development of oncology drugs based on the “more is better” paradigm, developed decades ago for chemotherapy. Recently, the US Food and Drug Administration (FDA) initiated Project Optimus to reform the dose optimization and dose selection paradigm in oncology drug development. To accommodate this paradigm shifting, we propose a dose-ranging approach to optimizing dose (DROID) for oncology trials with targeted drugs. DROID leverages the well-established dose-ranging study framework, which has been routinely used to develop non-oncology drugs for decades, and bridges it with established oncology dose-finding designs to …

Taxonomic Profiling Of Nasutitermes Takasagoensis Microbiota To Investigate The Role Of Termites As Vectors Of Bacteria Linked To Ironwood Tree Decline In Guam, Garima Setia, Junyan Chen, Robert Schlub, Claudia Husseneder

Faculty Publications

The ironwood tree (Casuarina equisetifolia, family Casuarinaceae), an indigenous agroforestry species in Guam, has been threatened by ironwood tree decline (IWTD) since 2002. Formation of bacterial ooze by the wilt pathogen from the Ralstonia solanacearum species complex and wetwood bacteria (primarily Klebsiella species) has been linked to IWTD. In addition, termite infestation of trees was statistically associated with IWTD. Termites are known carriers of a diverse microbiome. Therefore, we hypothesized that termites could be vectors of bacteria linked to IWTD. To investigate the potential role of termites as pathogen vectors, we employed next-generation 16S rRNA gene sequencing to describe the …

Modeling Of Cryopreservation Pathway Operation At An Aquatic Biomedical Stock Center For Zebrafish, Sarah Bodenstein, Fidan Abdullayeva, Joy M. Murphy, Zoltan M. Varga, Terrence R. Tiersch

Faculty Publications

Aquatic biomedical model organisms play a substantial role in advancing our understanding of human health, however, comparably little work has been directed towards developing dependable, high-throughput storage programs for valuable genetic resources. The Zebrafish International Resource Center (ZIRC) has developed a standardized cryopreservation pathway and stored thousands of genetic lines in their repository for use by the biomedical research community. This has yet to be replicated in other facilities, and an overall repository-level pathway has never been analyzed for aquatic species. To encourage repository development for other biomedical models and to improve the ZIRC storage process and system, this study …

Increased Lipogenesis Is Important For Hexavalent Chromium-Transformed Lung Cells And Xenograft Tumor Growth, James T.F. Wise, Kazuya Kondo

Faculty Publications

Hexavalent chromium, Cr(VI), is a known carcinogen and environmental health concern. It has been established that reactive oxygen species, genomic instability, and DNA damage repair deficiency are important contributors to the Cr(VI)-induced carcinogenesis mechanism. However, some hallmarks of cancer remain under-researched regarding the mechanism behind Cr(VI)-induced carcinogenesis. Increased lipogenesis is important to carcinogenesis and tumorigenesis in multiple types of cancers, yet the role increased lipogenesis has in Cr(VI) carcinogenesis is unclear. We report here that Cr(VI)-induced transformation of three human lung cell lines (BEAS-2B, BEP2D, and WTHBF-6) resulted in increased lipogenesis (palmitic acid levels), and Cr(VI)-transformed cells had an increased …

Deep Learning For Enhanced Free-Space Optical Communications, M. P. Bart, N. J. Savino, P. Regmi, L. Cohen, H. Safavi, H. C. Shaw, S. Lohani, T. A. Searles, B. T. Kirby, H. Lee, R. T. Glasser

Faculty Publications

Atmospheric effects, such as turbulence and background thermal noise, inhibit the propagation of light used in ON-OFF keying (OOK) free-space optical (FSO) communication. Here we present and experimentally validate a convolutional neural network (CNN) to reduce the bit error rate of FSO communication in post-processing that is significantly simpler and cheaper than existing solutions based on advanced optics. Our approach consists of two neural networks, the first determining the presence of bit sequences in thermal noise and turbulence and the second demodulating the bit sequences. All data used for training and testing our network is obtained experimentally by generating OOK …

Author Correction: Multiphoton Quantum Van Cittert-Zernike Theorem (Npj Quantum Information, (2023), 9, 1, (50), 10.1038/S41534-023-00720-W), Chenglong You, Ashe Miller, Roberto De J. León-Montiel, Omar S. Magaña-Loaiza

Faculty Publications

Correction to: npj Quantum Information, published online 26 May 2023 In the abstract for this article, the sentence “This fundamental theorem demonstrates that the quantum statistical fluctuations, which define the nature of diverse light sources, can be modified upon propagation in the absence of light-matter interactions” was inadvertently truncated after the text ‘quantum statistical fluctuations; the following text was missing ‘which define the nature of diverse light sources’. The original article has been corrected.

Multiphoton Quantum Van Cittert-Zernike Theorem, Chenglong You, Ashe Miller, Roberto De J. León-Montiel, Omar S. Magaña-Loaiza

Faculty Publications

Recent progress on quantum state engineering has enabled the preparation of quantum photonic systems comprising multiple interacting particles. Interestingly, multiphoton quantum systems can host many complex forms of interference and scattering processes that are essential to perform operations that are intractable on classical systems. Unfortunately, the quantum coherence properties of multiphoton systems degrade upon propagation leading to undesired quantum-to-classical transitions. Furthermore, the manipulation of multiphoton quantum systems requires nonlinear interactions at the few-photon level. Here, we introduce the quantum van Cittert-Zernike theorem to describe the scattering and interference effects of propagating multiphoton systems. This fundamental theorem demonstrates that the quantum …

Thermally Initiated Cationic Frontal Polymerization Of Epoxies And Vinyl Ethers Through A Lone Onium Salt, Brecklyn R. Groce, Madison M. Ferguson, John A. Pojman

Faculty Publications

Frontal polymerization (FP) of epoxy monomers is typically achieved with a radical-induced cationic frontal polymerization (RICFP) process that combines a thermal radical initiator with an onium salt superacid generator. In this paper, we show that both thermal and UV-initiated cationic frontal polymerizations are possible for common epoxy and vinyl ether monomers with only an iodonium superacid generator in the absence of a standalone thermal radical initiator. Increasing superacid generator concentration resulted in an increase in front velocity, as did the addition of vinyl ether to epoxies. The front velocity is reduced by the addition of 4-methoxyphenol (MeHQ), indicating free-radicals play …

Mid-Miocene Sea Level Altitude Of The Qaidam Basin, Northern Tibetan Plateau, Yuanyuan Sun, Yu Liang, Hu Liu, Jun Liu, Junliang Ji, Xue Ke, Xiaobo Liu, Yuxin He, Huanye Wang, Bin Zhang, Yongsu Zhang, Guangsheng Zhuang, Junling Pei, Yongxiang Li, Cheng Quan, Jianxing Li, Jonathan C. Aitchison, Weiguo Liu, Zhonghui Liu

Faculty Publications

A detailed uplift history of the Tibetan Plateau is essential for disentangling the proposed geodynamical models and assessing its impacts on climate and biodiversity. However, when and how the plateau formed remains highly controversial. Here, we present unusual geochemical indicators of marine signatures in the Cenozoic terrestrial strata of the Qaidam Basin, northern Tibetan Plateau, with strong implications for the basin altitude. Our investigations across the basin reveal typical marine alkenones and anomalously high carbonate carbon isotopic values during the mid-Miocene, but not at earlier stages, which are accompanied by a divergent trend in the paired carbonate oxygen and leaf …

African Bovid Tribe Classification Using Transfer Learning And Computer Vision, Manuel Domínguez-Rodrigo, Juliet Brophy, Gregory J. Mathews, Marcos Pizarro-Monzo, Enrique Baquedano

Faculty Publications

Objective analytical identification methods are still a minority in the praxis of paleobiological sciences. Subjective interpretation of fossils and their modifications remains a nonreplicable expert endeavor. Identification of African bovids is a crucial element in the reconstruction of paleo-landscapes, ungulate paleoecology, and, eventually, hominin adaptation and ecosystemic reconstruction. Recent analytical efforts drawing on Fourier functional analysis and discrimination methods applied to occlusal surfaces of teeth have provided a highly accurate framework to correctly classify African bovid tribes and taxa. Artificial intelligence tools, like computer vision, have also shown their potential to be objectively more accurate in the identification of taphonomic …

Morphodynamic Modeling Of Fourleague Bay In Mississippi River Delta: Sediment Fluxes Across River-Estuary-Wetland Boundaries, Nan Wang, Qin Chen, Kelin Hu, Kehui Xu, Samuel J. Bentley, Jiaze Wang

Faculty Publications

To mitigate land losses in the Mississippi River Delta, sediment diversions are being employed to enable the flow of river water and sediments into wetlands experiencing degradation. A two-dimensional coupled flow-wave Delft3D model was used in this study to explore the hydrodynamics and sediment transport in Fourleague Bay (FLB), Louisiana, USA, which has been considered an analog site for studying the efficiency of sediment diversion projects. In-situ measurements of sediment accretion and hydrodynamic characteristics from 2015 to 2016 were utilized to calibrate and validate the morphodynamic model. The validated model was then applied to quantify sediment transport in FLB and …

Single-Cell Analysis In Hypersaline Brines Predicts A Water-Activity Limit Of Microbial Anabolic Activity, Emily R. Paris, Nestor Arandia-Gorostidi, Benjamin Klempay, Jeff S. Bowman, Alexandra Pontefract, Claire E. Elbon, Jennifer B. Glass, Ellery D. Ingall, Peter T. Doran, Sanjoy M. Som, Britney E. Schmidt, Anne E. Dekas

Faculty Publications

Hypersaline brines provide excellent opportunities to study extreme microbial life. Here, we investigated anabolic activity in nearly 6000 individual cells from solar saltern sites with water activities (aw) ranging from 0.982 to 0.409 (seawater to extreme brine). Average anabolic activity decreased exponentially with aw, with nuanced trends evident at the single-cell level: The proportion of active cells remained high (>50%) even after NaCl saturation, and subsets of cells spiked in activity as aw decreased. Intracommunity heterogeneity in activity increased as seawater transitioned to brine, suggesting increased phenotypic heterogeneity with increased physiological stress. No microbial activity was detected in the …

Breaking Boundaries In Wind Engineering: Lsu Wise Open-Jet Facility Revolutionizes Solar Panel And Building Design, Aly Mousaad Aly

Faculty Publications

Featured Application: The Louisiana State University (LSU) Windstorm Impact, Science, and Engineering (WISE) Open-Jet Testing facility is instrumental in enhancing structural resilience under windstorms. The facility represents a Mid-Scale Research Infrastructure to address grand challenges and the need for experimental capabilities in the mid-scale range. Its unique capabilities enable the comprehensive testing and evaluation of critical infrastructure components, encompassing low- and high-rise buildings, photovoltaic (PV) solar panels, wind turbines, bridges, vegetation (nature-based solutions), power transmission lines, and more. Through controlled wind conditions, researchers can gain invaluable insights into the behaviour and performance of these critical infrastructures. The facility is pivotal …

What The Book Of First Enoch And The Aramaic Dead Sea Scrolls Reveal About The History Of The Qumran Community, Kenneth Atkinson

Faculty Publications

The Aramaic book commonly known as First Enoch is among the most important of all the compositions found in the Dead Sea Scrolls. The fragments of this pseudepigraphal work and related documents provide new information about the use and growth of the Enochic traditions, as well as how their contents influenced the community that collected and placed the Dead Sea Scrolls in the caves in the vicinity of Khirbet Qumran. Research on the Enochic literature in this corpus of documents is important for Jewish studies and for understanding the history of Christianity since the New Testament cites from and alludes …

Remote Testing Of Adult Neurogenic Tests: Implications And Recommendations For Speech-Language Pathologists, Angela Burda, Carrie Axt, Samantha Balk, Zoe Bleile, Madilyn Fahey, Paul Kort Freeman, Heather Hogelucht, Paeten Schultz, Kamryn Shaffer, Kara Wright

Faculty Publications

Purpose: One purpose of this preliminary case report was to document the challenges that can arise when giving adult neurogenic tests via telepractice. Another purpose was to develop recommendations on adaptations that can be made when speech-language pathologists give the tests employed in this report. Though one test was adapted by its authors to be given remotely, the other two tests have little or no published adaptations regarding remote administration. Methods: A 33 year old female and a 51 year old male, both of whom have acquired neurogenic communicative disorders, were given the Apraxia Battery for Adults-2nd edition, the Ross …

Sentencing In An Era Of Plea Bargains, Jeffrey Bellin, Jenia I. Turner

Faculty Publications

The literature offers inconsistent answers to a question that is foundational to criminal law: Who imposes sentences? Traditional narratives place sentencing responsibility in the hands of the judge. Yet, in a country where 95% of criminal convictions come from guilty pleas (not trials), modern American scholars center prosecutors—who control plea terms—as the deciders of punishment. This Article highlights and seeks to resolve the tension between these conflicting narratives by charting the pathways by which sentences are determined in a system dominated by plea bargains.

After reviewing the empirical literature on sentence variation, examining state and federal plea-bargaining rules and doctrines, …

Help! One Of My Church Members Is Doubting The Trinity!, S. Jsoeph Kidder, Timothy Baze

Faculty Publications

No abstract provided.

Do Contributing Files Provide Information About Oss Newcomers' Onboarding Barriers?, Felipe Fronchetti, David C. Shepherd, Igor Wiese, Christoph Treude, Marco Aurélio Gerosa, Igor Steinmacher

Faculty Publications

Effectively onboarding newcomers is essential for the success of open source projects. These projects often provide onboarding guidelines in their 'CONTRIBUTING' files (e.g., CONTRIBUTING.md on GitHub). These files explain, for example, how to find open tasks, implement solutions, and submit code for review. However, these files often do not follow a standard structure, can be too large, and miss barriers commonly found by newcomers. In this paper, we propose an automated approach to parse these CONTRIBUTING files and assess how they address onboarding barriers. We manually classified a sample of files according to a model of onboarding barriers from the …

Light-Driven And Nutrient-Driven Displacements Of Subsurface Chlorophyll Maximum Depth In Subtropical Gyres, Xiaogang Xing, Peng Xiu, Edward A. Laws, Guo Yang, Xin Liu, Fei Chai

Faculty Publications

The mechanism that determines the dynamics of subsurface chlorophyll maximum depth (zSCM) has long been debated. Although a coupling between zSCM and the top of nitracline (znit) has been widely observed in the open ocean, a co-location of zSCM and an isolume depth (ziso) has often been reported in oligotrophic waters. In this study, based on continuous observations of ten BGC-Argo floats, we found that the seasonal displacement of zSCM in all subtropical gyres was driven mainly by light, but zSCM displayed a nutrient-driven pattern occasionally when znit became shallower than ziso. We therefore proposed a “two-group competition framework”: zSCM …

Search For Evidence Of Baryogenesis And Dark Matter In B+→Ψd+P Decays At Babar, J. P. Lees, V. Poireau, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu. G. Kolomensky, M. Fritsch, H. Koch, R. Cheaib, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, V. P. Druzhinin, E. A. Kravchenko, Milind Purohit, Et. Al.

Faculty Publications

A new dark sector antibaryon, denoted ψD, could be produced in decays of B mesons. This Letter presents a search for B⁺→ψ_D+p (and the charge conjugate) decays in e⁺e⁻ annihilations at 10.58 GeV, using data collected in the BABAR experiment. Data corresponding to an integrated luminosity of 398 fb⁻¹ are analyzed. No evidence for a signal is observed. Branching fraction upper limits in the range from 10⁻⁷–10⁻⁵ are obtained at 90% confidence level for masses of 1.0<mψ_D< 4.3 GeV/c². The result is also reinterpreted to provide …

Detailed Characterization Of A Khz-Rate Laser-Driven Fusion At A Thin Liquid Sheet With A Neutron Detection Suite, Benjamin M. Knight, Connor M. Gautam, Colton R. Stoner, Bryan V. Egner, Joseph R. Smith, Christopher M. Orban, Juan J. Manfredi, Kyle Frische, Michael L. Dexter, Enam A. Chowdury, Anil K. Patnaik

Faculty Publications

We present detailed characterization of laser driven fusion and neutron production (∼10⁵/second) employing 8 mJ, 40fs laser pulses on a thin (< 1 µm) D₂O liquid sheet employing a measurement suite. At relativistic intensity (∼5×10¹⁸W/cm²) and high repetition-rate (1 kHz), the system produces consistent D-D fusion, allowing for consistent neutron generation. Evidence of D-D fusion neutron production is verified b y a measurement suite with three independent detection systems: an EJ-309 organic scintillator with pulse-shape discrimination, a ³He proportional counter, and a set of 36 bubble detectors. Time-of-flight analysis of the scintillator data shows …

Measurement Of Additional Radiation In The Initial-State-Radiation Processes E+E- →Μ+Μ- Y And E+E- → ℼ+ℼ- Y At Babar, J. P. Lees, V. Poireau, V. Tisserand, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu. G. Kolomensky, M. Fritsch, H. Koch, R. Cheaib, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, V. P. Druzhinin, E. A. Kozyrev, Milind Purohit, Et. Al.

Faculty Publications

A dedicated measurement of additional radiation in e⁺e⁻ → µ⁺µ⁻γ and e⁺e⁻ → π⁺π⁻γ initial-state-radiation events is presented using the full BABAR data sample. For the first time results are presented at next-to- and next-to-next-to-leading order, with one and two additional photons, respectively, for radiation from the initial and final states. Comparison with predictions from PHOKHARA and AFKQED Monte Carlo generators is performed, revealing discrepancies in the one-photon rates and angular distributions for the former. This disagreement has a negligible effect on the BABAR measurement of …

Feasibility Of An Abstract Verb Naming Treatment For Aphasia, Dallin J. Bailey, Lisa Bunker, Julie L. Wambaugh

Faculty Publications

Purpose

Verb production impairments in aphasia have important implications for sentence production and communication in general. Verbs with low concreteness may be especially important for certain functional uses, and yet limited data regarding their response to treatment are available. This study was designed to examine a novel behavioral treatment approach to improve low concreteness verb naming in persons with aphasia.

Method

Three persons with nonfluent aphasia participated in a single-subject experimental design research study examining the feasibility of the novel treatment. The treatment was based on approaches that target the verb as the central node of meaning during sentence construction. …

Evaluating Hpx And Kokkos On Risc-V Using An Astrophysics Application Octo-Tiger, Patrick Diehl, Gregor Daiss, Steven Brandt, Alireza Kheirkhahan, Hartmut Kaiser, Christopher Taylor, John Leidel

Faculty Publications

In recent years, computers based on the RISC-V architecture have raised broad interest in the high-performance computing (HPC) community. As the RISC-V community develops the core instruction set architecture (ISA) along with ISA extensions, the HPC community has been actively ensuring HPC applications and environments [10, 29] are supported. In this context, assessing the performance of asynchronous many-task runtime systems (AMT) is essential. In this paper, we describe our experience with porting of a full 3D adaptive mesh-refinement, multi-scale, multi-model, and multi-physics application, Octo-Tiger, that is based on the HPX AMT, and we explore its performance characteristics on different RISC-V …

A Computational Approach For Mapping Electrochemical Activity Of Multi-Principal Element Alloys, Jodie A. Yuwono, Xinyu Li, Tyler D. Dolezal, Adib J. Samin, Javen Qinfeng Shi, Zhipeng Li, Nick Birbilis

Faculty Publications

Multi principal element alloys (MPEAs) comprise an atypical class of metal alloys. MPEAs have been demonstrated to possess several exceptional properties, including, as most relevant to the present study a high corrosion resistance. In the context of MPEA design, the vast number of potential alloying elements and the staggering number of elemental combinations favours a computational alloy design approach. In order to computationally assess the prospective corrosion performance of MPEA, an approach was developed in this study. A density functional theory (DFT) – based Monte Carlo method was used for the development of MPEA ‘structure’; with the AlCrTiV alloy used …

A Novel Application Of Spinning Disk Technology To Collect Plasma From Whole Blood Prior To Quantifying Plasma Rna, Naomi Rapier-Sharman, Mae-Lynn L. Hutchinson, Carlos M. Moreno, Abraham Quaye, Brian D. Poole, K. Scott Weber, William G. Pitt, Brett E. Pickett

Faculty Publications

The spinning disk technology has previously been utilized to isolate bacterial components from blood in hours instead of days. We hypothesized that this platform could be applied as an alternative approach to isolating plasma RNA from a whole blood sample. We consequently tested the efficacy of the spinning disk technology to extract plasma from whole blood upstream of RNA isolation and analysis. To do so, we collected plasma using either the spinning disk or the typical two-spin centrifuge method. We found that the spinning disk method results in significantly more hemolysis during collection than the conventional two-spin centrifuge method. However, …

Shifting Taxonomic And Functional Community Composition Of Rivers Under Land Use Change, Kai Chen, Stephen R. Midway, Brandon K. Peoples, Beixin Wang, Julian D. Olden

Faculty Publications

Land use intensification has led to conspicuous changes in plant and animal communities across the world. Shifts in trait-based functional composition have recently been hypothesized to manifest at lower levels of environmental change when compared to species-based taxonomic composition; however, little is known about the commonalities in these responses across taxonomic groups and geographic regions. We investigated this hypothesis by testing for taxonomic and geographic similarities in the composition of riverine fish and insect communities across gradients of land use in major hydrological regions of the conterminous United States. We analyzed an extensive data set representing 556 species and 33 …

Weight And Protozoa Number But Not Bacteria Diversity Are Associated With Successful Pair Formation Of Dealates In The Formosan Subterranean Termite, Coptotermes Formosanus, Junyan Chen, Garima Setia, Li Hsiang Lin, Qian Sun, Claudia Husseneder

Faculty Publications

New colonies of Formosan subterranean termites are founded by monogamous pairs. During swarming season, alates (winged reproductives) leave their parental colony. After swarming, they drop to the ground, shed their wings, and male and female dealates find suitable nesting sites where they mate and become kings and queens of new colonies. The first generation of offspring is entirely dependent on the nutritional resources of the founder pair consisting of the fat and protein reserves of the dealates and their microbiota, which include the cellulose-digesting protozoa and diverse bacteria. Since termite kings and queens can live for decades, mate for life …

Labeling Effects Of Initial Juvenile Justice System Processing Decision On Youth Interpersonal Ties*, Zachary R. Rowan, Adam Fine, Laurence Steinberg, Paul J. Frick, Elizabeth Cauffman

Faculty Publications

The juvenile justice system can process youth in myriad ways. Youth who are formally processed, relative to being informally processed, may experience more public and harsh sanctions that label youth more negatively as “deviant.” Drawing on labeling theory, the current study evaluates the relative effect of formal justice system processing on the interpersonal dynamics of youth peer networks. Using data from the Crossroads Study, a multisite longitudinal sample of first-time adolescent offenders, the current study applies augmented inverse probability weighting and generalized mixed-effects models to estimate the effects of formal processing on friendship selection processes of homophily and withdrawal and …

A Target Enrichment Probe Set For Resolving Phylogenetic Relationships In The Coffee Family, Rubiaceae, Laymon D. Ball, Ana M. Bedoya, Charlotte M. Taylor, Laura P. Lagomarsino

Faculty Publications

Premise: Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often leads to improved phylogenetic resolution at both shallow and deep taxonomic scales; however, a publicly accessible Rubiaceae-specific probe set that allows for comparable phylogenetic inference across clades is lacking. Methods: Here, we use publicly accessible genomic resources to identify putatively single-copy nuclear …