Untouchable Fullness: Male Friendship in the novels of Willa Cather and D.H. Lawrence

Senior Project submitted to The Division of Languages and Literature of Bard Colleg

Lexicographic Sensitivity Functions for Nonsmooth Models in Mathematical Biology

Systems of ordinary differential equations (ODEs) may be used to model a wide variety of real-world phenomena in biology and engineering. Classical sensitivity theory is well-established and concerns itself with quantifying the responsiveness of such models to changes in parameter values. By performing a sensitivity analysis, a variety of insights can be gained into a model (and hence, the real-world system that it represents); in particular, the information gained can uncover a system\u27s most important aspects, for use in design, control or optimization of the system. However, while the results of such analysis are desirable, the approach that classical theory offers is limited to the case of ODE systems whose right-hand side functions are at least once continuously differentiable. This requirement is restrictive in many real-world systems in which sudden changes in behavior are observed, since a sharp change of this type often translates to a point of nondifferentiability in the model itself. To contend with this issue, recently-developed theory employing a specific class of tools called lexicographic derivatives has been shown to extend classical sensitivity results into a broad subclass of locally Lipschitz continuous ODE systems whose right-hand side functions are referred to as lexicographically smooth. In this thesis, we begin by exploring relevant background theory before presenting lexicographic sensitivity functions as a useful extension of classical sensitivity functions; after establishing the theory, we apply it to two models in mathematical biology. The first of these concerns a model of glucose-insulin kinetics within the body, in which nondifferentiability arises from a biochemical threshold being crossed within the body; the second models the spread of rioting activity, in which similar nonsmooth behavior is introduced out of a desire to capture a tipping point behavior where susceptible individuals suddenly begin to join a riot at a quicker rate after a threshold riot size is crossed. Simulations and lexicographic sensitivity functions are given for each model, and the implications of our results are discussed

Wild-type Caenorhabditis elegans isolates exhibit distinct gene expression profiles in response to microbial infection

The soil-dwelling nematode Caenorhabditis elegans serves as a model system to study innate immunity against microbial pathogens. C. elegans have been collected from around the world, where they, presumably, adapted to regional microbial ecologies. Here we use survival assays and RNA-sequencing to better understand how two isolates from disparate climates respond to pathogenic bacteria. We found that, relative to N2 (originally isolated in Bristol, UK), CB4856 (isolated in Hawaii), was more susceptible to the Gram-positive microbe, Staphylococcus epidermidis, but equally susceptible to Staphylococcus aureus as well as two Gram-negative microbes, Providencia rettgeri and Pseudomonas aeruginosa. We performed transcriptome analysis of infected worms and found gene-expression profiles were considerably different in an isolate-specific and microbe-specific manner. We performed GO term analysis to categorize differential gene expression in response to S. epidermidis. In N2, genes that encoded detoxification enzymes and extracellular matrix proteins were significantly enriched, while in CB4856, genes that encoded detoxification enzymes, C-type lectins, and lipid metabolism proteins were enriched, suggesting they have different responses to S. epidermidis, despite being the same species. Overall, discerning gene expression signatures in an isolate by pathogen manner can help us to understand the different possibilities for the evolution of immune responses within organisms

Vitamin B12 Regulates Glial Migration and Synapse Formation through Isoform-Specific Control of PTP-3/LAR PRTP Expression

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.Vitamin B12 is known to play critical roles during the development and aging of the brain, and vitamin B12 deficiency has been linked to neurodevelopmental and degenerative disorders. However, the underlying molecular mechanisms of how vitamin B12 affects the development and maintenance of the nervous system are still unclear. Here, we report that vitamin B12 can regulate glial migration and synapse formation through control of isoform-specific expression of PTP-3/LAR PRTP (leukocyte-common antigen-related receptor-type tyrosine-protein phosphatase). We found the uptake of diet-supplied vitamin B12 in the intestine to be critical for the expression of a long isoform of PTP-3 (PTP-3A) in neuronal and glial cells. The expression of PTP-3A cell autonomously regulates glial migration and synapse formation through interaction with an extracellular matrix protein NID-1/nidogen 1. Together, our findings demonstrate that isoform-specific regulation of PTP-3/ LAR PRTP expression is a key molecular mechanism that mediates vitamin-B12-dependent neuronal and glial development.NIH P40 OD010440Holland Trice AwardsNIH R01 NS09417NIH R01NS10563

Framework programmable platform for the advanced software development workstation. Integration mechanism design document

The Framework Programmable Software Development Platform (FPP) is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by this model, this system development framework will take advantage of an integrated operating environment to automate effectively the management of the software development process so that costly mistakes during the development phase can be eliminated

Caenorhabditis elegans voltage-gated calcium channel subunits UNC-2 and UNC-36 and the calcium-dependent kinase UNC-43/CaMKII regulate neuromuscular junction morphology

The conserved Caenorhabditis elegans proteins NID-1/nidogen and PTP-3A/LAR-RPTP function to efficiently localize the presynaptic scaffold protein SYD-2/α-liprin at active zones. Loss of function in these molecules results in defects in the size, morphology and spacing of neuromuscular junctions

Framework Programmable Platform for the advanced software development workstation: Framework processor design document

The design of the Framework Processor (FP) component of the Framework Programmable Software Development Platform (FFP) is described. The FFP is a project aimed at combining effective tool and data integration mechanisms with a model of the software development process in an intelligent integrated software development environment. Guided by the model, this Framework Processor will take advantage of an integrated operating environment to provide automated support for the management and control of the software development process so that costly mistakes during the development phase can be eliminated

Reconstructing the Hopfield network as an inverse Ising problem

We test four fast mean field type algorithms on Hopfield networks as an inverse Ising problem. The equilibrium behavior of Hopfield networks is simulated through Glauber dynamics. In the low temperature regime, the simulated annealing technique is adopted. Although performances of these network reconstruction algorithms on the simulated network of spiking neurons are extensively studied recently, the analysis of Hopfield networks is lacking so far. For the Hopfield network, we found that, in the retrieval phase favored when the network wants to memory one of stored patterns, all the reconstruction algorithms fail to extract interactions within a desired accuracy, and the same failure occurs in the spin glass phase where spurious minima show up, while in the paramagnetic phase, albeit unfavored during the retrieval dynamics, the algorithms work well to reconstruct the network itself. This implies that, as a inverse problem, the paramagnetic phase is conversely useful for reconstructing the network while the retrieval phase loses all the information about interactions in the network except for the case where only one pattern is stored. The performances of algorithms are studied with respect to the system size, memory load and temperature, sample-to-sample fluctuations are also considered.Comment: 8 pages, 3 figure

Joint gravitational wave -- gamma-ray burst detection rates in the aftermath of GW170817

The observational follow-up campaign of the gravitational wave (GW) multi-messenger event GW170817/GRB170817A has shown that the prompt $\gamma$-rays are consistent with a relativistic structured jet observed from a wide viewing angle $\gtrsim 20$\deg. We perform Bayesian inference using the data from early and late EM observations to determine the jet profile of GRB170817A assuming a structured jet model. We use the geometric dependence on the burst luminosity to produce a short duration gamma-ray burst (sGRB) efficiency function with redshift, which folded in with binary neutron star detection rate, allows us to estimate the future joint GW/sGRB detection rates for LIGO and Virgo detectors. We show that, if the jet structured profile of GRB170817A is a relatively common feature of sGRBs, then there is a realistic probability of another off-axis coincident detection during the third aLIGO/Virgo observing run (O3). We also find that up to 4 yr$^{-1}$ joint events may be observed during the advanced LIGO run at design sensitivity and up to 10 yr$^{-1}$ by the upgraded advanced LIGO configuration A+. We show that the detection efficiencies for wide-angled sGRB emissions will be limited by GRB satellites as the GW detection range increases through proposed upgrades. Therefore, although the number of coincident detections will increase with GW detector sensitivity, the relative proportion of detected binary neutron stars with $\gamma$-ray counterparts will decrease; 11\% for O3 down to 2\% during A+.Comment: Updated to final accepted MNRAS versio