Physical Sciences and Mathematics Commons^™

Building Academic/Practitioner Teams For Human Rights Projects: Examples, Lessons Learned, And Pitfalls To Avoid, Theresa Harris

Biennial Conference: The Social Practice of Human Rights

Academics are increasingly interested in getting out of their classrooms and labs to contribute their knowledge, expertise, and resources to help communities develop evidence-based policies. In addition to post-election initiatives such as the March for Science and 314 Action, many academics are joining “without borders”-type programs and organizations that connect academics with opportunities to volunteer their time and talents for “social good.”

One of the longest-running of these is On-call Scientists, an initiative of the American Association for the Advancement of Science (AAAS) that connects human rights organizations with pro bono scientists across all fields — life, physical, behavioral, and …

Sustainability For Whom? Place-Makers Of Detroit, Dominica, Ecuador, And Mexico, Emma Gaalaas Mullaney

Sponsored Events -- List

Drawing from more than a decade of work with farmers in rural and urban areas across the Americas, Professor Gaalaas Mullaney highlights some key findings about how small-scale farmers have a big influence on the conservation of cultural and ecological richness in their region. In each of these diverse places, innovative farmers work at the margins of dominant political and economic institutions with only occasional recognition of the value that they produce. What can these farmers teach us about how to cultivate place-based sustainability? How is sustainability related to social and economic justice?

Newest Kid On The Block: Characterization Of The Novel Multidrugresistant Pathogen, Candida Auris, Lindsey Masone, Susanna Mirabelli

Post & Beyond

Candida auris is a novel and emerging fungal pathogen capable of causinginvasive, and often fatal, bloodstream and wound infections in immunocompromised patients. Several outbreaks have been reported in hospitals across the world, including the United States, and predominantly in New York. C.auris exhibits extensive multidrug resistance that has never been seen in any Candida species, and is often misdiagnosed for other Candida species, thus limiting treatment options for patients. Our laboratory obtained 10 C. auris isolates in order to perform in vitro antifungal susceptibility testing and determine the Minimum Inhibitory Concentration (MIC) under Clinical and Laboratory Standards Institute guidelines. …

Analysis Of Complex Vertebrate Genomes: Computational Challenges And Solutions, Jeramiah J. Smith

Commonwealth Computational Summit

No abstract provided.

Adversarial Discriminative Domain Adaptation For Extracting Protein-Protein Interactions From Text, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu

Commonwealth Computational Summit

Relation extraction is the process of extracting structured information from unstructured text. Recently, neural networks (NNs) have produced state-of-art results in extracting protein-protein interactions (PPIs) from text. While multiple corpora have been created to extract PPIs from text, most methods have shown poor cross-corpora generalization. In other words, models trained on one dataset perform poorly on other datasets for the same task. In the case of PPI, the F1 has been shown to vary by as much as 30% between different datasets. In this work, we utilize adversarial discriminative domain adaptation (ADDA) to improve the generalization between the source and …

Discovery Of Sex-Specific Regions In A Salamander Genome, Nataliya Y. Timoshevskaya, Melissa C. Keinath, Jeramiah J. Smith

Commonwealth Computational Summit

Biological Aspects:

Salamander (Ambystoma mexicanum) has a gigantic genome: ~32,000,000,000 bases (10X of size of human genome)

Sex is determined by a pair of morphologically identical chromosomes:

• ZZ in male
• ZW in female

Object:

• Find (if there are any) genomic differences between chromosomes W and Z

Workflow:

1. Sequencing and de novo assembly of the reference salamander genome
2. Alignment of short sequences from male and female genomes to the reference
3. Coverage analysis

Registration And Grouping Algorithms In Protein Nmr Derived Peak Lists And Their Application In Protein Nmr Reference Correction, Andrey Smelter, Xi Chen, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Nuclear magnetic resonance spectroscopy of proteins (protein NMR) is a powerful analytical technique for studying structure and dynamics of proteins. Almost all aspects of protein NMR have been accelerated by the development of software tools that enable the analysis of NMR spectral data and its utilization in studying protein structure and dynamics. This includes software for raw NMR processing, spectral visualization, protein resonance assignment, and structure determination. However, full automation of protein NMR data analysis is still a work in progress and data analysis still requires an expert NMR spectroscopist utilizing an array of software tools.

While manual resonance assignment …

The Lamprey Genome: Illuminating Genomic Change Across Eons And Embryogenesis, Jeramiah J. Smith, Courtney K. M. Waterbury, Melissa C. Keinath, Cody B. Saraceno, Vladimir A. Timoshevskiy, Nataliya Y. Timoshevskaya

Commonwealth Computational Summit

The lamprey genome provides unique insights into both the deep evolutionary history of vertebrate genomes and the maintenance of genome structure/integrity over development. The lamprey lineage diverged from all other vertebrates approximately 500 million years ago. As such, comparisons between lamprey and other vertebrates permit reconstruction of ancient duplication and rearrangement events that defined the fundamental architecture and gene content of all extant vertebrate genomes. Lamprey also undergoes programmatic changes genome structure that result in the physical elimination of ~20% of its genomic DNA (~0.5Gb from a ~2 Gb genome) from all somatic cell lineages during early embryonic development. Here, …

Aberrant Coordination Geometries Discovered In Most Abundant Metalloproteins, Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Metalloproteins play crucial biochemical roles in our body and are essential across all domains of life. The structural environment around a metal ion, especially the coordination geometry (CG), is both sequentially and functionally relevant. Studies of the metalloprotein’s CG will greatly help alleviate the imbalance between the ample sequence data available and the insufficient knowledge on protein functions. Current methodologies in characterizing metalloproteins’ CG consider only previously reported CG (canonical CG) models based primarily on nonbiological chemical context. Exceptions to these canonical CG models can greatly hamper the ability to characterize metalloproteins both structurally and functionally.

Use Of Hpc To Analyze Changes In Gene Expression During Fruit Fly Spermiogenesis, Sepideh Dadkhah, Douglas A. Harrison, Jeramiah J. Smith

Commonwealth Computational Summit

In the fruit fly, Drosophila melanogaster, JAK/STAT signaling during spermiogenesis is known to play a crucial role in the maintenance of stem cells of the testis. Recent studies in our lab have shown that activation of the JAK/STAT pathway in somatic cyst cells is also required for the later stages of spermiogenesis like individualization.

The main goal of this project is to characterize the events downstream of JAK/STAT signaling in spermiogenesis and more specifically to determine the mechanism by which JAK/STAT activation regulates individualization, a later stage in spermiogenesis where 64 individual spermatids are formed from a 64-interconnected spermatid …

Heads And Tails, Julie Simons

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Cellular Automaton Modeling Approach To Chestnut Blight Canker Development, Samuel Iselin

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Turning Monitoring Data Into Simple Population Growth Models: Getting Your Ducks In A Row, Holly Gaff

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Model Selection And Permanence In A Stochastic Integrated Pest Management Model, Timothy Comar, Olcay Akman, Daniel Hrozencik

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Agent-Based Model For Integrated Pest Management With Periodic Control Strategies, Timothy Comar, Elizabeth Rodriguez

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Yeast Cell Cycle And Metabolism Can Be Coupled In Nontrivial Ways., Todd Young

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Stochastic And Deterministic Multigroup Epidemiology, Jordan Hasler, Chris Chang, Ananya Yammanuru, Lewis Oh, Esther Matthew, Mounisha Kovour

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Behavior Response Of Antlion Larvae To Alternating Magnetic Fields, Lindsey Wagner, Caleb L. Adams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Critical Firing Rate In Synchronous Transitions Of Coupled Neurons, Annabelle Shaffer, Epaminondas Rosa, Rosangela Follmann

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Kinetics Of Type I Interferons During Influenza A Virus Infection, Margaret A. Myers

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Handicap Principle Implies Emergence Of Dimorphic Ornaments, Sara Clifton, Daniel M. Abrams, Rosemary I. Braun

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Should I Get A Flu Shot? How Well Did This Go Last Year?, Winfried Just, David Gerberry, Ying Xin

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling Cdc42 Oscillation In Fission Yeast, Bin Xu

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

One Tick, Two Tick, Two Pathogens, Oh No! Am I Sick?, Caleb L. Adams

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling Microtubule-Based Transport In The Frog Egg Cell, Maria-Veronica Ciocanel

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Food Web Control And Synchronization Using A Robust Feedback, Hector Puebla, Mariana Rodriguez-Jara, Cesar S. Lopez-Monsalvo, Eliseo Hernandez-Martinez, Alejandra Velasco-Perez

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

A Model Of Dengue Transmission With Wolbachia-Free And Wolbachia-Infected Mosquitoes, Iftikhar Ahmed

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Effects Of Evolution On Food Web Diversity And Abundance, Rosalyn Rael

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Modeling The Influence Of El Niño On Parasite Transmission In Sand Crab Populations And Seabird Abundance Along The California Coast, James Peirce, Olcay Akman, Abou Seck

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Role Of Intermittent Preventive Treatment For Malaria In Saving Lives And Promoting Drug Resistance, Carrie Manore

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.