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Articles 1 - 30 of 767
Full-Text Articles in Physical Sciences and Mathematics
Production Functions Of Ncaa Men And Women Water Polo Matches, Joey Gullikson, Lewis R. Gale, John Mayberry, Lara Killick, John Kim
Production Functions Of Ncaa Men And Women Water Polo Matches, Joey Gullikson, Lewis R. Gale, John Mayberry, Lara Killick, John Kim
College of the Pacific Faculty Articles
Previous research has adapted the use of economic production functions to estimate the scoring production of teams in professional sports. Most of these studies have focused on professional male team sports, most notably, US baseball, basketball, and association football. This study adds to the literature by utilizing a new and distinctive data set of shooting statistics from 88 men’s and 38 women’s NCAA water polo contests to estimate production functions for United States’ collegiate water polo games and identify the most important variables for predicting margin of victory in such competitions. The results show that shots on goal, average shot …
The Illusion Of Agency In Human–Computer Interaction, Michael Madary
The Illusion Of Agency In Human–Computer Interaction, Michael Madary
College of the Pacific Faculty Articles
This article makes the case that our digital devices create illusions of agency. There are times when users feel as if they are in control when in fact they are merely responding to stimuli on the screen in predictable ways. After the introduction, the second section of the article offers examples of illusions of agency that do not involve human–computer interaction in order to show that such illusions are possible and not terribly uncommon. The third and fourth sections of the article cover relevant work from empirical psychology, including the cues that are known to generate the sense of agency. …
Identification Of Disease-Linked Hyperactivating Mutations In Ube3a Through Large-Scale Functional Variant Analysis, Kellan P. Weston, Xiaoyi Gao, Jinghan Zhao, Kwang Soo Kim, Susan E. Maloney, Jill Gotoff, Sumit Parikh, Yen Chen Leu, Kuen Phon Wu, Marwan Shinawi, Joshua P. Steimel, Joseph S. Harrison, Jason J. Yi
Identification Of Disease-Linked Hyperactivating Mutations In Ube3a Through Large-Scale Functional Variant Analysis, Kellan P. Weston, Xiaoyi Gao, Jinghan Zhao, Kwang Soo Kim, Susan E. Maloney, Jill Gotoff, Sumit Parikh, Yen Chen Leu, Kuen Phon Wu, Marwan Shinawi, Joshua P. Steimel, Joseph S. Harrison, Jason J. Yi
College of the Pacific Faculty Articles
The mechanisms that underlie the extensive phenotypic diversity in genetic disorders are poorly understood. Here, we develop a large-scale assay to characterize the functional valence (gain or loss-of-function) of missense variants identified in UBE3A, the gene whose loss-of-function causes the neurodevelopmental disorder Angelman syndrome. We identify numerous gain-of-function variants including a hyperactivating Q588E mutation that strikingly increases UBE3A activity above wild-type UBE3A levels. Mice carrying the Q588E mutation exhibit aberrant early-life motor and communication deficits, and individuals possessing hyperactivating UBE3A variants exhibit affected phenotypes that are distinguishable from Angelman syndrome. Additional structure-function analysis reveals that Q588 forms a regulatory site …
Specific Splice Junction Detection In Single Cells With Sicilian, Roozbeh Dehghannasiri, Julia E. Olivieri, Ana Damljanovic, Julia Salzman
Specific Splice Junction Detection In Single Cells With Sicilian, Roozbeh Dehghannasiri, Julia E. Olivieri, Ana Damljanovic, Julia Salzman
All Faculty Articles - School of Engineering and Computer Science
Precise splice junction calls are currently unavailable in scRNA-seq pipelines such as the 10x Chromium platform but are critical for understanding single-cell biology. Here, we introduce SICILIAN, a new method that assigns statistical confidence to splice junctions from a spliced aligner to improve precision. SICILIAN is a general method that can be applied to bulk or single-cell data, but has particular utility for single-cell analysis due to that data’s unique challenges and opportunities for discovery. SICILIAN’s precise splice detection achieves high accuracy on simulated data, improves concordance between matched single-cell and bulk datasets, and increases agreement between biological replicates. SICILIAN …
Designed, Highly Expressing, Thermostable Dengue Virus 2 Envelope Protein Dimers Elicit Quaternary Epitope Antibodies, Stephen T. Kudlacek, Stefan Metz, Devina Thiono, Alexander M. Payne, Thanh T.N. Phan, Shaomin Tian, Lawrence J. Forsberg, Jack Mcguire, Ian Selm, Shu Zhang, Ashutosh Tripathy, Joseph S. Harrison, Nathan I. Niceley, Sandrine Soman, Michael K. Mccracken, Gregory D. Gromowski, Richard G. Jarman, Lakshmanane Premkumar, Aravinda M. De Silva, Brian Kuhlman
Designed, Highly Expressing, Thermostable Dengue Virus 2 Envelope Protein Dimers Elicit Quaternary Epitope Antibodies, Stephen T. Kudlacek, Stefan Metz, Devina Thiono, Alexander M. Payne, Thanh T.N. Phan, Shaomin Tian, Lawrence J. Forsberg, Jack Mcguire, Ian Selm, Shu Zhang, Ashutosh Tripathy, Joseph S. Harrison, Nathan I. Niceley, Sandrine Soman, Michael K. Mccracken, Gregory D. Gromowski, Richard G. Jarman, Lakshmanane Premkumar, Aravinda M. De Silva, Brian Kuhlman
College of the Pacific Faculty Articles
Dengue virus (DENV) is a worldwide health burden, and a safe vaccine is needed. Neutralizing antibodies bind to quaternary epitopes on DENV envelope (E) protein homodimers. However, recombinantly expressed soluble E proteins are monomers under vaccination conditions and do not present these quaternary epitopes, partly explaining their limited success as vaccine antigens. Using molecular modeling, we found DENV2 E protein mutations that induce dimerization at low concentrations (<100 pM) and enhance production yield by more than 50-fold. Cross-dimer epitope antibodies bind to the stabilized dimers, and a crystal structure resembles the wild-type (WT) E protein bound to a dimer epitope antibody. Mice immunized with the stabilized dimers developed antibodies that bind to E dimers and not monomers and elicited higher levels of DENV2-neutralizing antibodies compared to mice immunized with WT E antigen. Our findings demonstrate the feasibility of using structure-based design to produce subunit vaccines for dengue and other flaviviruses.
Mechanically Transduced Immunosorbent Assay To Measure Protein-Protein Interactions, Christopher J. Petell, Kathyrn Randene, Michael Pappas, Diego Sandoval, Brian Dstrahl, Joseph S. Harrison, Joshua P. Steimel
Mechanically Transduced Immunosorbent Assay To Measure Protein-Protein Interactions, Christopher J. Petell, Kathyrn Randene, Michael Pappas, Diego Sandoval, Brian Dstrahl, Joseph S. Harrison, Joshua P. Steimel
College of the Pacific Faculty Articles
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus …
Rna Splicing Programs Define Tissue Compartments And Cell Types At Single-Cell Resolution, Julia E. Olivieri, Roozbeh Dehghannasiri, Peter Wang, Sori Jang, Antoine De Morree, Serena Y. Tan, Jingsi Ming, Angela R. Wu, Stephen R. Quake, Mark A. Krasnow, Julia Salzman
Rna Splicing Programs Define Tissue Compartments And Cell Types At Single-Cell Resolution, Julia E. Olivieri, Roozbeh Dehghannasiri, Peter Wang, Sori Jang, Antoine De Morree, Serena Y. Tan, Jingsi Ming, Angela R. Wu, Stephen R. Quake, Mark A. Krasnow, Julia Salzman
All Faculty Articles - School of Engineering and Computer Science
The extent splicing is regulated at single-cell resolution has remained controversial due to both available data and methods to interpret it. We apply the SpliZ, a new statistical approach, to detect cell-type-specific splicing in >110K cells from 12 human tissues. Using 10x data for discovery, 9.1% of genes with computable SpliZ scores are cell-type-specifically spliced, including ubiquitously expressed genes MYL6 and RPS24. These results are validated with RNA FISH, single-cell PCR, and Smart-seq2. SpliZ analysis reveals 170 genes with regulated splicing during human spermatogenesis, including examples conserved in mouse and mouse lemur. The SpliZ allows model-based identification of subpopulations indistinguishable …
Co-Evolutionary Analysis Suggests A Role For Tlr9 In Papillomavirus Restriction, Kelly King, Brendan B. Larsen, Sophie Gryseeis, Cécile Richet, Simona Kraberger, Robert Jackson, Michael Worobey, Joseph S. Harrison, Arvind Varsani, Koenraad Van Doorslaer
Co-Evolutionary Analysis Suggests A Role For Tlr9 In Papillomavirus Restriction, Kelly King, Brendan B. Larsen, Sophie Gryseeis, Cécile Richet, Simona Kraberger, Robert Jackson, Michael Worobey, Joseph S. Harrison, Arvind Varsani, Koenraad Van Doorslaer
College of the Pacific Faculty Articles
Upon infection, DNA viruses can be sensed by pattern recognition receptors (PRRs) leading to the activation of type I and III interferons, aimed at blocking infection. Therefore, viruses must inhibit these signaling pathways, avoid being detected, or both. Papillomavirus virions are trafficked from early endosomes to the Golgi apparatus and wait for the onset of mitosis to complete nuclear entry. This unique subcellular trafficking strategy avoids detection by cytoplasmic PRRs, a property that may contribute to establishment of infection. However, as the capsid uncoats within acidic endosomal compartments, the viral DNA may be exposed to detection by toll-like receptor (TLR) …
In Silico Apc/C Substrate Discovery Reveals Cell Cycle-Dependent Degradation Of Uhrf1 And Other Chromatin Regulators, Jennifer L. Franks, Raquel C. Martinez-Chacin, Xianxi Wang, Rochelle L. Tiedemann, Thomas Bonacci, Rajarshi Choudhury, Derek L. Bolhuis, Taylor P. Enrico, Ryan D. Mouery, Jeffrey S. Damrauer, Feng Yan, Joseph S. Harrison, M. Ben Major, Katherine A. Hoadley, Aussie Suzuki, Scott B. Rothbart, Nicholas G. Brown, Michael J. Emanuele
In Silico Apc/C Substrate Discovery Reveals Cell Cycle-Dependent Degradation Of Uhrf1 And Other Chromatin Regulators, Jennifer L. Franks, Raquel C. Martinez-Chacin, Xianxi Wang, Rochelle L. Tiedemann, Thomas Bonacci, Rajarshi Choudhury, Derek L. Bolhuis, Taylor P. Enrico, Ryan D. Mouery, Jeffrey S. Damrauer, Feng Yan, Joseph S. Harrison, M. Ben Major, Katherine A. Hoadley, Aussie Suzuki, Scott B. Rothbart, Nicholas G. Brown, Michael J. Emanuele
College of the Pacific Faculty Articles
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and critical regulator of cell cycle progression. Despite its vital role, it has remained challenging to globally map APC/C substrates. By combining orthogonal features of known substrates, we predicted APC/C substrates in silico. This analysis identified many known substrates and suggested numerous candidates. Unexpectedly, chromatin regulatory proteins are enriched among putative substrates, and we show experimentally that several chromatin proteins bind APC/C, oscillate during the cell cycle, and are degraded following APC/C activation, consistent with being direct APC/C substrates. Additional analysis revealed detailed mechanisms of ubiquitylation for UHRF1, a key chromatin …
Optical Properties And Composition Of Viscous Organic Particles Found In The Southern Great Plains, Matthew Fraund, Daniel Bonanno, Swarup China, Don Q. Pham, Daniel Veghte, Johannes Weis, Gourihar Kulkarni, Ken Teske, Mary K. Gilles, Alexander Laskin, Ryan C. Moffet
Optical Properties And Composition Of Viscous Organic Particles Found In The Southern Great Plains, Matthew Fraund, Daniel Bonanno, Swarup China, Don Q. Pham, Daniel Veghte, Johannes Weis, Gourihar Kulkarni, Ken Teske, Mary K. Gilles, Alexander Laskin, Ryan C. Moffet
Department of Chemistry Student Articles
Atmospheric high-viscosity organic particles (HVOPs) were observed in samples of ambient aerosols collected in April and May 2016 in the Southern Great Plains of the United States. These particles were apportioned as either airborne soil organic particles (ASOPs) or tar balls (TBs) from biomass burning based on spetro-microscopic imaging and assessments of meteorological records of smoke and precipitation data. Regardless of their apportionment, the number fractions of HVOPs were positively correlated (R2=0.85) with increased values of absorption Ångström exponent (AAE) measured in situ for ambient aerosol at the site. Extending this correlation to 100 % HVOPs yields an …
Kras Ubiquitination At Lysine 104 Retains Exchange Factor Regulation By Dynamically Modulating The Conformation Of The Interface, Guowei Yin, Jerry Zhang, Vinay Nair, Vinh Truong, Angelo Chaia, Johnny Petela, Joseph S. Harrison, Alemayehu A. Gorfe, Sharon L. Campbell
Kras Ubiquitination At Lysine 104 Retains Exchange Factor Regulation By Dynamically Modulating The Conformation Of The Interface, Guowei Yin, Jerry Zhang, Vinay Nair, Vinh Truong, Angelo Chaia, Johnny Petela, Joseph S. Harrison, Alemayehu A. Gorfe, Sharon L. Campbell
College of the Pacific Faculty Articles
RAS proteins function as highly regulated molecular switches that control cellular growth. In addition to regulatory proteins, RAS undergoes a number of posttranslational modifications (PTMs) that regulate its activity. Lysine 104, a hot spot for multiple PTMs, is a highly conserved residue that forms key interactions that stabilize the RAS helix-2(H2)/helix-3(H3) interface. Mutation at 104 attenuates interaction with guanine nucleotide exchange factors (GEFs), whereas ubiquitination at lysine 104 retains GEF regulation. To elucidate how ubiquitination modulates RAS function, we generated monoubiquitinated KRAS at 104 using chemical biology approaches and conducted biochemical, NMR, and computational analyses. We find that ubiquitination promotes …
The Carbon Emissions Of Wind Power; A Study Of Emissions Of Windmill In The Panhandle Of Texas, Rahim Khoie, Antonio Calderon
The Carbon Emissions Of Wind Power; A Study Of Emissions Of Windmill In The Panhandle Of Texas, Rahim Khoie, Antonio Calderon
All Faculty Presentations - School of Engineering and Computer Science
The 2008 through 2016 were the years of implementation of increasingly restrictive regulatory policies on climate change, and particularly on carbon emissions by coal-burning power plants. Some of these regulations were imposed by states (in the form of Renewable Portfolio Standards, RPS) and majority of them were imposed by Obama Administration. These regulations, among other factors, resulted in a significant drop in the U.S. total emissions; 12% drop from 2007 to 2016. The current Administration has taken several actions in reversing, relaxing, or repealing many of these regulations, and particularly regulations on use of coal in electricity generation. In this …
Exploring An Active Learning Focus In A Liberal Arts Engineering Curriculum, David Robert Bruce, Sebastian Dziallas
Exploring An Active Learning Focus In A Liberal Arts Engineering Curriculum, David Robert Bruce, Sebastian Dziallas
All Faculty Presentations - School of Engineering and Computer Science
Fulbright University Vietnam is Vietnam's first not-for-profit, independent university with a focus on liberal arts, sciences and engineering undergraduate programs. The curriculum is built on integration of these programs and incorporates active learning and experiential learning activities in courseware design. Experiential learning activities include student led research, examination of user centered design, and observational analysis of the environment. Active learning activities include think-pair-sharing, flipped classrooms, and sticky-note clustering. Complimentary to the active learning and experiential learning emphasis, the integration of engineering with liberal arts affords incorporation of concepts encompassing student-centric learning and allows community rather than content-based exploration of concepts. …
Positive Effects Of A Small Grant For Creation Of Open Education Resources, Cherian Mathews
Positive Effects Of A Small Grant For Creation Of Open Education Resources, Cherian Mathews
All Faculty Presentations - School of Engineering and Computer Science
Open educational resources have been shown to have the potential to improve student learning outcomes while lowering student costs associated with curricular materials. University competitively awarded small grants of $2500 to encourage faculty to create or adopt Open Educational Resources (OER) to help reduce student costs or enhance the student learning experience. This paper outlines how the grant award was used to create open tutorial resources and lab materials that helped students independently learn to use the simulation software Simulink in conjunction with a Digital Signal Processing course. Students were required to review the OER materials and complete the lab …
Global Biobank Engine: Enabling Genotype-Phenotype Browsing For Biobank Summary Statistics, Gregory Mcinnes, Yosuke Tanigawa, Chris Deboever, Adam Lavertu, Julia E. Olivieri, Matthew Aguirre, Manuel A. Rivas
Global Biobank Engine: Enabling Genotype-Phenotype Browsing For Biobank Summary Statistics, Gregory Mcinnes, Yosuke Tanigawa, Chris Deboever, Adam Lavertu, Julia E. Olivieri, Matthew Aguirre, Manuel A. Rivas
All Faculty Articles - School of Engineering and Computer Science
Summary: Large biobanks linking phenotype to genotype have led to an explosion of genetic association studies across a wide range of phenotypes. Sharing the knowledge generated by these resources with the scientific community remains a challenge due to patient privacy and the vast amount of data. Here, we present Global Biobank Engine (GBE), a web-based tool that enables exploration of the relationship between genotype and phenotype in biobank cohorts, such as the UK Biobank. GBE supports browsing for results from genome-wide association studies, phenome-wide association studies, gene-based tests and genetic correlation between phenotypes. We envision GBE as a platform that …
Quantitative Capabilities Of Stxm To Measure Spatially Resolved Organic Volume Fractions Of Mixed Organic ∕ Inorganic Particles, Matthew Fraund, Tim Park, Daniel Bonanno, Don Q. Pham, Ryan C. Moffet
Quantitative Capabilities Of Stxm To Measure Spatially Resolved Organic Volume Fractions Of Mixed Organic ∕ Inorganic Particles, Matthew Fraund, Tim Park, Daniel Bonanno, Don Q. Pham, Ryan C. Moffet
Department of Chemistry Student Articles
Scanning transmission X-ray microscopy coupled with near-edge X-ray absorption and fine structure (STXM-NEXAFS) spectroscopy can be used to characterize the morphology and composition of aerosol particles. Here, two inorganic ∕ organic systems are used to validate the calculation of organic volume fraction (OVF) and determine the level of associated error by using carbon K-edge STXM data at 278, 285.4, 288.6, and 320 eV. Using the mixture of sodium chloride and sucrose as one system and ammonium sulfate and sucrose as another, three solutions were made with 10:1, 1:1, and 1:10 mass ratios (inorganic to organic). The OVFs of the organic-rich …
Evolution Of Portulacineae Marked By Gene Tree Conflict And Gene Family Expansion Associated With Adaptation To Harsh Environments, Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W. Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia E. Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas C. Majure, Urs Eggli, Stephen A. Smith
Evolution Of Portulacineae Marked By Gene Tree Conflict And Gene Family Expansion Associated With Adaptation To Harsh Environments, Ning Wang, Ya Yang, Michael J. Moore, Samuel F. Brockington, Joseph F. Walker, Joseph W. Brown, Bin Liang, Tao Feng, Caroline Edwards, Jessica Mikenas, Julia E. Olivieri, Vera Hutchison, Alfonso Timoneda, Tommy Stoughton, Raúl Puente, Lucas C. Majure, Urs Eggli, Stephen A. Smith
All Faculty Articles - School of Engineering and Computer Science
Several plant lineages have evolved adaptations that allow survival in extreme and harsh environments including many families within the plant clade Portulacineae (Caryophyllales) such as the Cactaceae, Didiereaceae, and Montiaceae. Here, using newly generated transcriptomic data, we reconstructed the phylogeny of Portulacineae and examined potential correlates between molecular evolution and adaptation to harsh environments. Our phylogenetic results were largely congruent with previous analyses, but we identified several early diverging nodes characterized by extensive gene tree conflict. For particularly contentious nodes, we present detailed information about the phylogenetic signal for alternative relationships. We also analyzed the frequency of gene duplications, confirmed …
Larval Food Limitation In A Speyeria Butterfly (Nymphalidae): How Many Butterflies Can Be Supported?, Ryan I. Hill, Cassidi E. Rush, John Mayberry
Larval Food Limitation In A Speyeria Butterfly (Nymphalidae): How Many Butterflies Can Be Supported?, Ryan I. Hill, Cassidi E. Rush, John Mayberry
College of the Pacific Faculty Articles
For herbivorous insects the importance of larval food plants is obvious, yet the role of host abundance and density in conservation are relatively understudied. Populations of Speyeria butterflies across North America have declined and Speyeria adiaste is an imperiled species endemic to the southern California Coast Ranges. In this paper, we study the link between the food plant Viola purpurea quercetorum and abundance of its herbivore Speyeria adiaste clemencei to better understand the butterfly’s decline and aid in restoration of this and other Speyeria species. To assess the degree to which the larval food plant limits adult abundance of S. …
Use Of Standardized Patient Simulations To Assess Impact Of Motivational Interviewing Training On Social--Emotional Development, Suzanne M. Galal, Deepti Vyas, John Mayberry, Ed Rogan
Use Of Standardized Patient Simulations To Assess Impact Of Motivational Interviewing Training On Social--Emotional Development, Suzanne M. Galal, Deepti Vyas, John Mayberry, Ed Rogan
College of the Pacific Faculty Articles
The objective of this study was to assess the impact of motivational interviewing (MI) training on students’ social–emotional development. Two simulations using standardized patients (SP) were conducted within a smoking cessation module. Students first completed a 4 h self-study module focused on smoking cessation tools and general counseling techniques. Faculty then administered a 15-item rubric focused on students’ self-assessment of their verbal/non-verbal communication, social–emotional competence and MI skills. Students then participated in a smoking cessation counseling session with an SP. SPs used the same rubric to assess student performance. Teaching assistants (TAs) observed and assessed the students using the same …
A Linked Coptic Dictionary Online, Frank Feder, Maxim Kupreyev, Emma Manning, Caroline T. Schroeder, Amir Zeldes
A Linked Coptic Dictionary Online, Frank Feder, Maxim Kupreyev, Emma Manning, Caroline T. Schroeder, Amir Zeldes
College of the Pacific Faculty Presentations
We describe a new project publishing a freely available online dictionary for Coptic. The dictionary encompasses comprehensive cross-referencing mechanisms, including linking entries to an online scanned edition of Crum’s Coptic Dictionary, internal cross-references and etymological information, translated searchable definitions in English, French and German, and linked corpus data which provides frequencies and corpus look-up for headwords and multiword expressions. Headwords are available for linking in external projects using a REST API. We describe the challenges in encoding our dictionary using TEI XML and implementing linking mechanisms to construct a Web interface querying frequency information, which draw on NLP tools to …
P62-Dependent Phase Separation Of Patient-Derived Keap1 Mutations And Nrf2, E. W. Cloer, P. F. Siesser, E. M. Cousins, D Goldfarb, D. D. Mowrey, Joseph S. Harrison, S. J. Weir, N. V. Dokholyan, M. B. Major
P62-Dependent Phase Separation Of Patient-Derived Keap1 Mutations And Nrf2, E. W. Cloer, P. F. Siesser, E. M. Cousins, D Goldfarb, D. D. Mowrey, Joseph S. Harrison, S. J. Weir, N. V. Dokholyan, M. B. Major
College of the Pacific Faculty Articles
Cancer-derived loss-of-function mutations in the KEAP1 tumor suppressor gene stabilize the NRF2 transcription factor, resulting in a pro-survival gene expression program that alters cellular metabolism and neutralizes oxidative stress. In a recent genotype-phenotype study, we classified 40% of KEAP1 mutations as ANCHOR mutants. By immunoprecipitation, these mutants bind more NRF2 than wild-type KEAP1 and ubiquitylate NRF2, but are incapable of promoting NRF2 degradation. BioID-based protein interaction studies confirmed increased abundance of NRF2 within the KEAP1 ANCHOR mutant complexes with no other statistically significant changes to the complexes. Discrete molecular dynamic simulation modeling and limited proteolysis suggest that the ANCHOR mutations …
Reconsidering Downwind Operation By Analysis Of The Nrel Phase Vi Data, Scott Larwood, Raymond Chow
Reconsidering Downwind Operation By Analysis Of The Nrel Phase Vi Data, Scott Larwood, Raymond Chow
All Faculty Articles - School of Engineering and Computer Science
Data are presented comparing upwind versus downwind operation of the National Renewable Energy Laboratory’s Phase VI wind turbine. Power was not reduced as expected for downwind, which may be attributed to inboard three-dimensional effects. Average flap bending loads were reduced with downwind coning and compared well with prediction. Fatigue loads were increased with downwind; however, fatigue was mitigated with a tower shroud. The shroud needs to align with the freestream, demonstrated by an increase in fatigue loads from a 10° shroud misalignment. Pressure data were acquired in the tower wake at the rotor location with and without the shroud. The …
Comparative Biochemical Analysis Of Uhrf Proteins Reveals Molecular Mechanisms That Uncouple Uhrf2 From Dna Methylation Maintenance, Robert M. Vaughan, Bradley M. Dickson, Evan M. Cornett, Joseph S. Harrison, Brian Kuhlman, Scott B. Rothbart
Comparative Biochemical Analysis Of Uhrf Proteins Reveals Molecular Mechanisms That Uncouple Uhrf2 From Dna Methylation Maintenance, Robert M. Vaughan, Bradley M. Dickson, Evan M. Cornett, Joseph S. Harrison, Brian Kuhlman, Scott B. Rothbart
College of the Pacific Faculty Articles
UHRF1 is a histone- and DNA-binding E3 ubiquitin ligase that functions with DNMT1 to maintain mammalian DNA methylation. UHRF1 facilitates DNMT1 recruitment to replicating chromatin through a coordinated mechanism involving histone and DNA recognition and histone ubiquitination. UHRF2 shares structural homology with UHRF1, but surprisingly lacks functional redundancy to facilitate DNA methylation maintenance. Molecular mechanisms uncoupling UHRF2 from DNA methylation maintenance are poorly defined. Through comprehensive and comparative biochemical analysis of recombinant human UHRF1 and UHRF2 reader and writer activities, we reveal conserved modes of histone PTM recognition but divergent DNA binding properties. While UHRF1 and UHRF2 diverge in their …
The Circles Of Apollonius, Christopher D. Goff
The Circles Of Apollonius, Christopher D. Goff
College of the Pacific Faculty Presentations
After creating an eye-catching logo for the San Joaquin Math Teachers’ Circle, we decided to spend a session studying it. Our investigation evolved into a journey covering over 2000 years of mathematics history, beginning with a lost work created by Apollonius, moving to a problem posed by a princess, and arriving in the strange world of fractals.
Elemental Mixing State Of Aerosol Particles Collected In Central Amazonia During Goamazon2014/15, Matthew Fraund, Don Q. Pham, Daniel Bonanno, Tristan H. Harder, Bingbing Wang, Joel Brito, Suzane S. De Sa, Samara Carbone, Swarup China, Paulo Artaxo, Scot T. Martin, Christopher Pöhlker, Meinrat O. Andreae, Alexander Laskin, Mary K. Gilles, Ryan C. Moffet
Elemental Mixing State Of Aerosol Particles Collected In Central Amazonia During Goamazon2014/15, Matthew Fraund, Don Q. Pham, Daniel Bonanno, Tristan H. Harder, Bingbing Wang, Joel Brito, Suzane S. De Sa, Samara Carbone, Swarup China, Paulo Artaxo, Scot T. Martin, Christopher Pöhlker, Meinrat O. Andreae, Alexander Laskin, Mary K. Gilles, Ryan C. Moffet
Department of Chemistry Student Articles
Two complementary techniques, Scanning Transmission X-ray Microscopy/Near Edge Fine Structure spectroscopy (STXM/NEXAFS) and Scanning Electron Microscopy/Energy Dispersive X-ray spectroscopy (SEM/EDX), have been quantitatively combined to characterize individual atmospheric particles. This pair of techniques was applied to particle samples at three sampling sites (ATTO, ZF2, and T3) in the Amazon basin as part of the Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) field campaign during the dry season of 2014. The combined data was subjected to k-means clustering using mass fractions of the following elements: C, N, O, Na, Mg, P, S, Cl, K, Ca, Mn, Fe, Ni, and …
Some Tricks In Parameter Selection For Extreme Learning Machine, Weipeng Cao, Jinzhu Gao, Zhong Ming, Shubin Cai
Some Tricks In Parameter Selection For Extreme Learning Machine, Weipeng Cao, Jinzhu Gao, Zhong Ming, Shubin Cai
All Faculty Presentations - School of Engineering and Computer Science
Extreme learning machine (ELM) is a widely used neural network with random weights (NNRW), which has made great contributions to many fields. However, the relationship between the parameters and the performance of ELM has not been fully investigated yet, i.e. the impact of the number of hidden layer nodes, the randomization range of the weights between the input layer and hidden layer, the randomization range of the threshold of hidden nodes, and the type of activation functions. In this paper, eight benchmark functions are used to study this relationship. We have some interesting findings, such as more hidden layer nodes …
A First Look At The Year In Computing, Sebastian Dziallas, Sally Fincher, Colin G. Johnson, Ian Utting
A First Look At The Year In Computing, Sebastian Dziallas, Sally Fincher, Colin G. Johnson, Ian Utting
All Faculty Presentations - School of Engineering and Computer Science
In this paper, we discuss students' expectations and experiences in the first term of the Year in Computing, a new programme for non-computing majors at the University of Kent, a public research university in the UK. We focus on the effect of students' home discipline on their experiences in the programme and situate this work within the context of wider efforts to make the study of computing accessible to a broader range of students. Copyright is held by the owner/author(s).
Alan Turing: The Man Behind The Machine, Christopher D. Goff
Alan Turing: The Man Behind The Machine, Christopher D. Goff
College of the Pacific Faculty Presentations
No abstract provided.
Hemi-Methylated Dna Regulates Dna Methylation Inheritance Through Allosteric Activation Of H3 Ubiquitylation By Uhrf1, Joseph S. Harrison, Evan M. Cornett, Dennis Goldfarb, Paul A. Darosa, Zimeng M. Li, Feng Yan, Bradley M. Dickson, Angela H. Guo, Daniel V. Cantu, Lilia Kaustov, Peter J. Brown, Cheryl H. Arrowsmith, Dorothy A. Erie, Michael B. Major, Rachel E. Klevit, Krzysztof Krajewski, Brian Kuhlman, Brian D. Strahl, Scott B. Rothbart
Hemi-Methylated Dna Regulates Dna Methylation Inheritance Through Allosteric Activation Of H3 Ubiquitylation By Uhrf1, Joseph S. Harrison, Evan M. Cornett, Dennis Goldfarb, Paul A. Darosa, Zimeng M. Li, Feng Yan, Bradley M. Dickson, Angela H. Guo, Daniel V. Cantu, Lilia Kaustov, Peter J. Brown, Cheryl H. Arrowsmith, Dorothy A. Erie, Michael B. Major, Rachel E. Klevit, Krzysztof Krajewski, Brian Kuhlman, Brian D. Strahl, Scott B. Rothbart
College of the Pacific Faculty Articles
The epigenetic inheritance of DNA methylation requires UHRF1, a histone- and DNA-binding RING E3 ubiquitin ligase that recruits DNMT1 to sites of newly replicated DNA through ubiquitylation of histone H3. UHRF1 binds DNA with selectivity towards hemi-methylated CpGs (HeDNA); however, the contribution of HeDNA sensing to UHRF1 function remains elusive. Here, we reveal that the interaction of UHRF1 with HeDNA is required for DNA methylation but is dispensable for chromatin interaction, which is governed by reciprocal positive cooperativity between the UHRF1 histone- and DNA-binding domains. HeDNA recognition activates UHRF1 ubiquitylation towards multiple lysines on the H3 tail adjacent to the …
The Ebb And Flow Of Official Calls In Water Polo, James Graham, John Mayberry
The Ebb And Flow Of Official Calls In Water Polo, James Graham, John Mayberry
College of the Pacific Faculty Articles
Defensive fouls play an important role in elite men’s water polo generating over half of all goals. Despite their importance, little is known about the relationship between foul calling patterns and other game-state variables in the sport. Here we apply a sequence of hierarchical mixed logistic regression models on data from major tournaments in 2012–2014 to study such relationships and find a number of significant biases in foul calling rates. Offensive teams who are winning/tied are about 31% less likely to draw a defensive foul and 32% more likely to get called for an offensive foul than teams who are …