Harvey Mudd College

Moral emotions represent a key element of our human moral apparatus, influencing the link between moral standards and moral behavior. This chapter reviews current theory and research on moral emotions. We first focus on a triad of negatively valenced "self-conscious" emotions-shame, guilt, and embarrassment. As in previous decades, much research remains focused on shame and guilt. We review current thinking on the distinction between shame and guilt, and the relative advantages and disadvantages of these two moral emotions. Several new areas of research are highlighted: research on the domain-specific phenomenon of body shame, styles of coping with shame, psychobiological aspects of shame, the link between childhood abuse and later proneness to shame, and the phenomena of vicarious or "collective" experiences of shame and guilt. In recent years, the concept of moral emotions has been expanded to include several positive emotions-elevation, gratitude, and the sometimes morally relevant experience of pride. Finally, we discuss briefly a morally relevant emotional process-other-oriented empathy.

This paper is based on the premises that the purpose of engineering education is to graduate engineers who can design, and that design thinking is complex. The paper begins by briefly reviewing the history and role of design in the engineering curriculum. Several dimensions of design thinking are then detailed, explaining why design is hard to learn and harder still to teach, and outlining the research available on how well design thinking skills are learned. The currently most-favored pedagogical model for teaching design, project-based learning (PBL), is explored next, along with available assessment data on its success. Two contexts for PBL are emphasized: first-year cornerstone courses and globally dispersed PBL courses. Finally, the paper lists some of the open research questions that must be answered to identify the best pedagogical practices of improving design learning, after which it closes by making recommendations for research aimed at enhancing design learning.

Summary When studying convergence of measures, an important issue is the choice of probability metric. We provide a summary and some new results concerning bounds among some important probability metrics/distances that are used by statisticians and probabilists. Knowledge of other metrics can provide a means of deriving bounds for another one in an applied problem. Considering other metrics can also provide alternate insights. We also give examples that show that rates of convergence can strongly depend on the metric chosen. Careful consideration is necessary when choosing a metric.

Using the method of images, we examine the three boundary conditions commonly applied to the surface of a semi-infinite turbid medium. We find that the image-charge configurations of the partial-current and extrapolated-boundary conditions have the same dipole and quadrupole moments and that the two corresponding solutions to the diffusion equation are approximately equal. In the application of diffusion theory to frequency-domain photon-migration (FDPM) data, these two approaches yield values for the scattering and absorption coefficients that are equal to within 3%. Moreover, the two boundary conditions can be combined to yield a remarkably simple, accurate, and computationally fast method for extracting values for optical parameters from FDPM data. FDPM data were taken both at the surface and deep inside tissue phantoms, and the difference in data between the two geometries is striking. If one analyzes the surface data without accounting for the boundary, values deduced for the optical coefficients are in error by 50% or more. As expected, when aluminum foil was placed on the surface of a tissue phantom, phase and modulation data were closer to the results for an infinite-medium geometry. Raising the reflectivity of a tissue surface can, in principle, eliminate the effect of the boundary. However, we find that phase and modulation data are highly sensitive to the reflectivity in the range of 80-100%, and a minimum value of 98% is needed to mimic an infinite-medium geometry reliably. We conclude that noninvasive measurements of optically thick tissue require a rigorous treatment of the tissue boundary, and we suggest a unified partial-current--extrapolated boundary approach.

Based on the full BABAR data sample, we report improved measurements of the ratios $\mathcal{R}({D}^{(*)})=\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\tau}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\tau}})/\mathcal{B}(\overline{B}\ensuremath{\rightarrow}{D}^{(*)}{\ensuremath{\ell}}_{\ensuremath{\ell}}^{\ensuremath{-}}{\overline{\ensuremath{\nu}}}_{\ensuremath{\ell}})$, where $\ensuremath{\ell}$ is either $e$ or $\ensuremath{\mu}$. These ratios are sensitive to new physics contributions in the form of a charged Higgs boson. We measure $\mathcal{R}(D)=0.440\ifmmode\pm\else\textpm\fi{}0.058\ifmmode\pm\else\textpm\fi{}0.042$ and $\mathcal{R}({D}^{*})=0.332\ifmmode\pm\else\textpm\fi{}0.024\ifmmode\pm\else\textpm\fi{}0.018$, which exceed the standard model expectations by $2.0\ensuremath{\sigma}$ and $2.7\ensuremath{\sigma}$, respectively. Taken together, our results disagree with these expectations at the $3.4\ensuremath{\sigma}$ level. This excess cannot be explained by a charged Higgs boson in the type II two-Higgs-doublet model.

1 The Method of Logical Effort 2 Design Examples 3 Deriving the Method of Logical Effort 4 Calculating the Logical Effort of Gates 5 Calibrating the Model 6 Asymmetric Logic Gates 7 Unequal Rising and Falling Delays 8 Circuit Families 9 Forks of Amplifiers 10 Branches and Interconnect 11 Wide Structures 12 Conclusions A Cast of Characters B Reference process parameters C Logical Effort Tools D Solutions

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.

The most efficient dye-sensitized solar cells (DSSCs) have had essentially the same configuration (nanoparticle TiO2 sensitized with [Ru(4,4′-dicarboxy-2,2′-bipyridine)2(NCS)2] in contact with I3−/I−) for the last 17 years. In this article we outline the strategies for improving each of the three major photo-relevant components of a DSSC, review literature reports consistent with these strategies and suggest future directions. Finally we explore the potential of future generation DSSCs for advancing energy-conversion performance.

Three structural models of amorphous carbon with differing percentages of threefold- and fourfold-coordinated atoms were constructed and analyzed, along with a purely four-coordinated amorphous Ge model which was scaled to diamond bond lengths. The radial distribution function and interference function, $F(k)$, of the model containing 14% four-coordinated atoms were in best agreement with the experimental results of Boiko et al., although the functions containing 48% four-coordinated atoms were in best agreement with the results of Kakinoki et al. The unavoidable planar nature of the entirely three-coordinated model caused its $F(k)$ to be in poor agreement with experiment. Raman and vibrational density-of-states (DOS) spectra were also calculated for the models. The presence of disorder in the three-coordinated model produced a downward shift in frequency of the principal Raman peak and DOS band edge from the position seen in graphite. With the addition of four-coordinated atoms, there was a gradual transition from graphitelike spectra to diamondlike spectra, rather than spectra with a mixture of distinct features typical of graphite and diamond. In addition, there was a further downward shift in frequency of the main Raman peak and in that of the "disorder peak" seen in microcrystalline and amorphous carbon. The spectra of the model containing 14% four-coordinated carbon was in best agreement with recent Raman scattering experiments. These results suggest a structure for amorphous carbon consisting of three-coordinated planar regions with occasional four-coordinated atoms allowing changes in orientation of the planes. The positions of the peaks in the spectra suggest that the proportion of four-coordinated atoms is not likely to exceed 10%.

Mathematical models of tumor-immune interactions provide an analytic framework in which to address specific questions about tumor-immune dynamics. We present a new mathematical model that describes tumor-immune interactions, focusing on the role of natural killer (NK) and CD8+ T cells in tumor surveillance, with the goal of understanding the dynamics of immune-mediated tumor rejection. The model describes tumor-immune cell interactions using a system of differential equations. The functions describing tumor-immune growth, response, and interaction rates, as well as associated variables, are developed using a least-squares method combined with a numerical differential equations solver. Parameter estimates and model validations use data from published mouse and human studies. Specifically, CD8+ T-tumor and NK-tumor lysis data from chromium release assays as well as in vivo tumor growth data are used. A variable sensitivity analysis is done on the model. The new functional forms developed show that there is a clear distinction between the dynamics of NK and CD8+ T cells. Simulations of tumor growth using different levels of immune stimulating ligands, effector cells, and tumor challenge are able to reproduce data from the published studies. A sensitivity analysis reveals that the variable to which the model is most sensitive is patient specific, and can be measured with a chromium release assay. The variable sensitivity analysis suggests that the model can predict which patients may positively respond to treatment. Computer simulations highlight the importance of CD8+ T-cell activation in cancer therapy.

Body temperature (T(b)) profoundly affects the fitness of ectotherms. Many ectotherms use behavior to control T(b) within narrow levels. These temperatures are assumed to be optimal and therefore to match body temperatures (Trmax) that maximize fitness (r). We develop an optimality model and find that optimal body temperature (T(o)) should not be centered at Trmax but shifted to a lower temperature. This finding seems paradoxical but results from two considerations relating to Jensen's inequality, which deals with how variance and skew influence integrals of nonlinear functions. First, ectotherms are not perfect thermoregulators and so experience a range of T(b). Second, temperature-fitness curves are asymmetric, such that a T(b) higher than Trmax depresses fitness more than will a T(b) displaced an equivalent amount below Trmax. Our model makes several predictions. The magnitude of the optimal shift (Trmax - To) should increase with the degree of asymmetry of temperature-fitness curves and with T(b) variance. Deviations should be relatively large for thermal specialists but insensitive to whether fitness increases with Trmax ("hotter is better"). Asymmetric (left-skewed) T(b) distributions reduce the magnitude of the optimal shift but do not eliminate it. Comparative data (insects, lizards) support key predictions. Thus, "suboptimal" is optimal.

INTRODUCTION Control of mosquito vectors has historically proven to be an effective means of eliminating malaria. Human malaria is transmitted only by mosquitoes in the genus Anopheles , but not all species within the genus, or even all members of each vector species, are efficient malaria vectors. Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. RATIONALE This variation in vectorial capacity suggests an underlying genetic/genomic plasticity that results in variation of key traits determining vectorial capacity within the genus. Sequencing the genome of Anopheles gambiae , the most important malaria vector in sub-Saharan Africa, has offered numerous insights into how that species became highly specialized to live among and feed upon humans and how susceptibility to mosquito control strategies is determined. Until very recently, similar genomic resources have not existed for other anophelines, limiting comparisons to individual genes or sets of genomic markers with no genome-wide data to investigate attributes associated with vectorial capacity across the genus. RESULTS We sequenced and assembled the genomes and transcriptomes of 16 anophelines from Africa, Asia, Europe, and Latin America, spanning ~100 million years of evolution and chosen to represent a range of evolutionary distances from An. gambiae , a variety of geographic locations and ecological conditions, and varying degrees of vectorial capacity. Genome assembly quality reflected DNA template quality and homozygosity. Despite variation in contiguity, the assemblies were remarkably complete and searches for arthropod-wide single-copy orthologs generally revealed few missing genes. Genome annotation supported with RNA sequencing transcriptomes yielded between 10,738 and 16,149 protein-coding genes for each species. Relative to Drosophila, the closest dipteran genus for which equivalent genomic resources exist, Anopheles exhibits a dynamic genomic evolutionary profile. Comparative analyses show a fivefold faster rate of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses in Anopheles . Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes. We also document evidence of variation in important reproductive phenotypes, genes controlling immunity to Plasmodium malaria parasites and other microbes, genes encoding cuticular and salivary proteins, and genes conferring metabolic insecticide resistance. This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts. CONCLUSIONS Anopheline mosquitoes exhibit a molecular evolutionary profile very distinct from Drosophila , and their genomes harbor strong evidence of functional variation in traits that determine vectorial capacity. These 16 new reference genome assemblies provide a foundation for hypothesis generation and testing to further our understanding of the diverse biological traits that determine vectorial capacity. Geography, vector status, and molecular phylogeny of the 16 newly sequenced anopheline mosquitoes and selected other dipterans. The maximum likelihood molecular phylogeny of all sequenced anophelines and two mosquito outgroups was constructed from the aligned protein sequences of 1085 single-copy orthologs. Shapes between branch termini and species names indicate vector status and are colored according to geographic ranges depicted on the map.

Within the adiabatic approximation, time-dependent density functional theory yields only single excitations. Near states of double excitation character, the exact exchange–correlation kernel has a strong dependence on frequency. We derive the exact frequency-dependent kernel when a double excitation mixes with a single excitation, well separated from the other excitations, in the limit that the electron–electron interaction is weak. Building on this, we construct a nonempirical approximation for the general case, and illustrate our results on a simple model.

Two independent methods are presented for the nonperturbative calculation of the electronic coupling matrix element (Hab) for electron transfer reactions using ab initio electronic structure theory. The first is based on the generalized Mulliken–Hush (GMH) model, a multistate generalization of the Mulliken Hush formalism for the electronic coupling. The second is based on the block diagonalization (BD) approach of Cederbaum, Domcke, and co-workers. Detailed quantitative comparisons of the two methods are carried out based on results for (a) several states of the system Zn2OH2+ and (b) the low-lying states of the benzene–Cl atom complex and its contact ion pair. Generally good agreement between the two methods is obtained over a range of geometries. Either method can be applied at an arbitrary nuclear geometry and, as a result, may be used to test the validity of the Condon approximation. Examples of nonmonotonic behavior of the electronic coupling as a function of nuclear coordinates are observed for Zn2OH2+. Both methods also yield a natural definition of the effective distance (rDA) between donor (D) and acceptor (A) sites, in contrast to earlier approaches which required independent estimates of rDA, generally based on molecular structure data.

The Raman scattering from various model structures for amorphous silicon is computed. It is shown that the width of the ``optic peak'' increases roughly linearly with the rms bond-angle distortion \ensuremath{\Delta}${\ensuremath{\theta}}_{b}$ of the network. The experimentally observed linewidths lead to 7.7\ifmmode^\circ\else\textdegree\fi{}\ensuremath{\le}\ensuremath{\Delta}${\ensuremath{\theta}}_{b}$\ensuremath{\le}10.5\ifmmode^\circ\else\textdegree\fi{}. The smaller linewidths (and hence angles) correspond to networks that have been annealed at higher temperatures. These results are consistent with model-building experience which shows that it is impossible to construct fully bonded amorphous networks with \ensuremath{\Delta}${\ensuremath{\theta}}_{b}$\ensuremath{\le}6.6\ifmmode^\circ\else\textdegree\fi{}.

The conditions for validity and the limitations of experiments intended to simulate astrophysical hydrodynamics are discussed, with application to some ongoing experiments. For systems adequately described by the Euler equations, similarity criteria required for properly scaled experiments are identified. The conditions for the applicability of the Euler equations are formulated, based on the analysis of localization, heat conduction, viscosity, and radiation. Other considerations involved in such a scaling, including its limitations at small spatial scales, are discussed. The results are applied to experiments aimed at simulating three-dimensional hydrodynamics during supernova explosions and hydrodynamic instabilities in young supernova remnants. In addition, hydrodynamic situations with significant radiative effects are discussed.

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We present a competition model of cancer tumor growth that includes both the immune system response and drug therapy. This is a four‐population model that includes tumor cells, host cells, immune cells, and drug interaction. We analyze the stability of the drug‐free equilibria with respect to the immune response in order to look for target basins of attraction. One of our goals was to simulate qualitatively the asynchronous tumor‐drug interaction known as “Jeffs phenomenon.” The model we develop is successful in generating this asynchronous response behavior. Our other goal was to identify treatment protocols that could improve standard pulsed chemotherapy regimens. Using optimal control theory with constraints and numerical simulations, we obtain new therapy protocols that we then compare with traditional pulsed periodic treatment. The optimal control generated therapies produce larger oscillations in the tumor population over time. However, by the end of the treatment period, total tumor size is smaller than that achieved through traditional pulsed therapy, and the normal cell population suffers nearly no oscillations.

Systema Naturae includes representatives of every major lineage of the animal phylum Cnidaria. However, Linnaeus did not classify the members of the phylum as is now done, and the diversity of the group is not well represented. We contrast the Linnaean perspective on cnidarian diversity with the modern, phylogenetic perspective. For each order, we detail diversity at the family level, providing phylogenetic context where possible.

BACKGROUND: This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. RESULTS: The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. CONCLUSIONS: Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.