Discrimination in the Workplace: Evidence from a Civil War in Peru

Few events give the opportunity to observe the full range of human behavior as wars do. In the case of civil wars in ethnically-mixed societies, the distribution of violence across various segments of the population can provide evidence on the extent and nature of discrimination. As in the case of markets, identifying discrimination in the warplace is challenging. There is uncertainty on the reconstruction of events as well as the rationale behind the violence. We use a unique data set collected by the Peruvian Truth and Reconciliation Commission on war crimes during the 1980's to show that there is evidence of taste-based discrimination by agents of the state towards ethnic minorities and women. The evidence is robust to different assumptions on the logic of repression and missing data problems. Working Paper 07-3

Measurement of the direct energy gap of coherently strained Sn_xGe_(1–x)/Ge(001) heterostructures

The direct energy gap has been measured for coherently strained Sn_xGe_(1–x) alloys on Ge(001) substrates with 0.035 < x < 0.115 and film thickness 50–200 nm. The energy gap determined from infrared transmittance data for coherently strained Sn_xGe_(1–x) alloys indicates a large alloy contribution and a small strain contribution to the decrease in direct energy gap with increasing Sn composition. These results are consistent with a deformation potential model for changes in the valence and conduction band density of states with coherency strain for this alloy system

Use Permits: A Hedonistic Approach Applied to Farmland in the Southeastern US

In the State of Georgia, any agricultural producer who wishes to pump more than 100,000 gallons of water a day for crop irrigation is required to have an irrigation permit. The permit stays with the land and in the event of sale the permit is transferred with the property. Until recently, permits were essentially granted freely to all applicants in the Flint River water basin, without limit. In 1999, however, with increasing demand for water from growing urban Atlanta and several years of drought in the Southeast, the state of Georgia placed a moratorium on the issuance of agricultural water permits in the Flint River basin. This research exploits this policy change within a hedonic pricing framework to estimate the value of irrigation rights in the Southeast US. While the value of irrigation rights has been studied extensively in the western US, differences in property rights and legal regimes, as well as a lack of established water-rights markets in the East, leave us with little information regarding the value of irrigation rights in this setting. Working Paper 06-4

Pattern-based phylogenetic distance estimation and tree reconstruction

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic accuracy of our method, and to conduct a comprehensive comparison of existing alignment-free methods (freely available as Python package decaf+py at http://www.bioinformatics.org.au), we have created a dataset of reference trees covering a wide range of phylogenetic distances. Amino acid sequences were evolved along the trees and input to the tested methods; from their calculated distances we infered trees whose topologies we compared to the reference trees. We find our pattern-based method statistically superior to all other tested alignment-free methods on this dataset. We also demonstrate the general advantage of alignment-free methods over an approach based on automated alignments when sequences violate the assumption of collinearity. Similarly, we compare methods on empirical data from an existing alignment benchmark set that we used to derive reference distances and trees. Our pattern-based approach yields distances that show a linear relationship to reference distances over a substantially longer range than other alignment-free methods. The pattern-based approach outperforms alignment-free methods and its phylogenetic accuracy is statistically indistinguishable from alignment-based distances.Comment: 21 pages, 3 figures, 2 table

Detection of Structure in Infrared-Dark Clouds with Spitzer: Characterizing Star Formation in the Molecular Ring

We have conducted a survey of a sample of infrared-dark clouds (IRDCs) with the Spitzer Space Telescope in order to explore their mass distribution. We present a method for tracing mass using dust absorption against the bright Galactic background at 8 microns. The IRDCs in this sample are comprised of tens of clumps, ranging in sizes from 0.02 to 0.3 pc in diameter and masses from 0.5 to a few 10 Msun, the broadest dynamic range in any clump mass spectrum study to date. Structure with this range in scales confirms that IRDCs are the the precursors to stellar clusters in an early phase of fragmentation. Young stars are distributed in the vicinity of the IRDCs, but the clumps are typically not associated with stars and appear pre-stellar in nature. We find an IRDC clump mass spectrum with a slope of 1.76 +/- 0.05 for masses from 30 to 3000 Msun. This slope is consistent with numerous studies, culled from a variety of observational techniques, of massive star formation regions and is close to the mass function of Galactic stellar clusters and star clusters in other galaxies. We assert that the shape of the mass function is an intrinsic and universal feature of massive star formation regions, that are the birth sites of stellar clusters. As these clouds evolve and their constituent clumps fragment, the mass spectrum will steepen and eventually assume the form of the core mass function that is observed locally.Comment: Accepted to ApJ. 37 pages, 24 figures. Full-resolution versions of the figures are available at http://www.astro.lsa.umich.edu/~seragan/ftp/irdc_figs

A model for estimating time-variant rainfall infiltration as a function of antecedent surface moisture and hydrologic soil type

Recent research indicates that the use of remote sensing techniques for the measurement of near surface soil moisture could be practical in the not too distant future. Other research shows that infiltration rates, especially for average or frequent rainfall events, are extremely sensitive to the proper definition and consideration of the role of the soil moisture at the beginning of the rainfall. Thus, it is important that an easy to use, but theoretically sound, rainfall infiltration model be available if the anticipated remotely sensed soil moisture data is to be optimally utilized for hydrologic simulation. A series of numerical experiments with the Richards' equation for an array of conditions anticipated in watershed hydrology were used to develop functional relationships that describe temporal infiltration rates as a function of soil type and initial moisture conditions

An evaluation of DNA-damage response and cell-cycle pathways for breast cancer classification

Accurate subtyping or classification of breast cancer is important for ensuring proper treatment of patients and also for understanding the molecular mechanisms driving this disease. While there have been several gene signatures proposed in the literature to classify breast tumours, these signatures show very low overlaps, different classification performance, and not much relevance to the underlying biology of these tumours. Here we evaluate DNA-damage response (DDR) and cell cycle pathways, which are critical pathways implicated in a considerable proportion of breast tumours, for their usefulness and ability in breast tumour subtyping. We think that subtyping breast tumours based on these two pathways could lead to vital insights into molecular mechanisms driving these tumours. Here, we performed a systematic evaluation of DDR and cell-cycle pathways for subtyping of breast tumours into the five known intrinsic subtypes. Homologous Recombination (HR) pathway showed the best performance in subtyping breast tumours, indicating that HR genes are strongly involved in all breast tumours. Comparisons of pathway based signatures and two standard gene signatures supported the use of known pathways for breast tumour subtyping. Further, the evaluation of these standard gene signatures showed that breast tumour subtyping, prognosis and survival estimation are all closely related. Finally, we constructed an all-inclusive super-signature by combining (union of) all genes and performing a stringent feature selection, and found it to be reasonably accurate and robust in classification as well as prognostic value. Adopting DDR and cell cycle pathways for breast tumour subtyping achieved robust and accurate breast tumour subtyping, and constructing a super-signature which contains feature selected mix of genes from these molecular pathways as well as clinical aspects is valuable in clinical practice.Comment: 28 pages, 7 figures, 6 table

A two-phase approach for detecting recombination in nucleotide sequences

Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer picture of the phylogenetic relationships among different gene sequences or genomes. Nevertheless, detecting recombination events can be a daunting task, as the performance of different recombinationdetecting approaches can vary, depending on evolutionary events that take place after recombination. We recently evaluated the effects of postrecombination events on the prediction accuracy of recombination-detecting approaches using simulated nucleotide sequence data. The main conclusion, supported by other studies, is that one should not depend on a single method when searching for recombination events. In this paper, we introduce a two-phase strategy, applying three statistical measures to detect the occurrence of recombination events, and a Bayesian phylogenetic approach in delineating breakpoints of such events in nucleotide sequences. We evaluate the performance of these approaches using simulated data, and demonstrate the applicability of this strategy to empirical data. The two-phase strategy proves to be time-efficient when applied to large datasets, and yields high-confidence results.Comment: 5 pages, 3 figures. Chan CX, Beiko RG and Ragan MA (2007). A two-phase approach for detecting recombination in nucleotide sequences. In Hazelhurst S and Ramsay M (Eds) Proceedings of the First Southern African Bioinformatics Workshop, 28-30 January, Johannesburg, 9-1

Dual-Career Couples in Academia : Does Wage Growth Suffer When One’s Partner Works for the Same University?

Extending the literature on monopsony in academic labor markets, we find that faculty pay is inversely related to seniority in both cross-sectional and longitudinal data sets for a large public university in the United States. Fixed-effects results indicate that the negative relationship cannot be explained by lower quality of senior faculty. Arguing that mobility costs are higher when both partners work for the same university, we allow monopsony power to vary by employment status of partner. We find that pay of male faculty is negatively and significantly related to the number of years the partner has been employed by the university and that the penalty is greater when couples are hired together.Monopsony, academic labor market

Quantitative Prediction of miRNA-mRNA Interaction Based on Equilibrium Concentrations

MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental condition