Extended Photometry for the DEEP2 Galaxy Redshift Survey: A Testbed for Photometric Redshift Experiments

This paper describes a new catalog that supplements the existing DEEP2 Galaxy Redshift Survey photometric and spectroscopic catalogs with ugriz photometry from two other surveys; the Canada-France-Hawaii Legacy Survey (CFHTLS) and the Sloan Digital Sky Survey (SDSS). Each catalog is cross-matched by position on the sky in order to assign ugriz photometry to objects in the DEEP2 catalogs. We have recalibrated the CFHTLS photometry where it overlaps DEEP2 in order to provide a more uniform dataset. We have also used this improved photometry to predict DEEP2 BRI photometry in regions where only poorer measurements were available previously. In addition, we have included improved astrometry tied to SDSS rather than USNO-A2.0 for all DEEP2 objects. In total this catalog contains ~27,000 objects with full ugriz photometry as well as robust spectroscopic redshift measurements, 64% of which have r > 23. By combining the secure and accurate redshifts of the DEEP2 Galaxy Redshift Survey with ugriz photometry, we have created a catalog that can be used as an excellent testbed for future photo-z studies, including tests of algorithms for surveys such as LSST and DES.Comment: 12 pages, 6 figures and 5 tables. Accepted to The Astrophysical Journal Supplement. Catalogs are publicly available at http://deep.ps.uci.edu/DR4/photo.extended.htm

The Economics of Regulations on Hen Housing in California

Beginning January 1, 2015, conventional cage housing for egg-laying hens is scheduled to be prohibited in California. We consider the economic implications of the new hen housing regulations on the California shell egg industry. Our data show that egg production is more costly using noncage systems than conventional cages. The main result of the new regulations will be a drastic reduction in the number of eggs produced in California, a large increase in egg shipments from out of state, little if any change in hen housing for eggs consumed in California, and little change in egg prices in California.animal welfare regulation, hen housing, egg supply, egg prices, egg costs of production, Agribusiness, Agricultural and Food Policy, Agricultural Finance, Consumer/Household Economics, Farm Management, Livestock Production/Industries, Production Economics, Productivity Analysis, Q11, Q18,

Exploring The Distant Universe With Cross-correlation Statistics

Future cosmological surveys will require distance information for an extremely large number of galaxies in order to gain insight into the structure and history of our Universe. Current methods of obtaining accurate distance information such as measuring the redshifts of galaxies via spectroscopy are not feasible for such enormous datasets, mainly due to the long exposure times required. Photometric redshifts, where the redshift is measured using broadband imaging through only a few filters, are a promising avenue of study, although there are inherent limitations to this method making them less understood than spectroscopic redshifts. Understanding these limitations and improving the calibration of photometric redshifts will be very important for future cosmological measurements. This thesis presents tests of a new technique for calibrating photometric redshifts that exploits the clustering of galaxies due to gravitational interaction. This cross-correlation technique uses the measured spatial clustering on the sky of a photometric sample that has only imaging information, with a spectroscopic sample that has secure and accurate redshifts. These tests shows that measurements of this clustering as a function of redshift can be used to accurately reconstruct the true redshift distribution of the photometric sample. In addition, this thesis shows how similar clustering measurements can be used to constrain the contamination of a high redshift candidate sample by low redshift interlopers. Finally it describes a new catalog that combines spectroscopic redshifts and deep photometry that can be used as a testbed for future photo-$z$ studies

New insight into the molecular control of bacterial functional amyloids.

New insight into the molecular control of bacterial functional amyloids. Front. Cell. Infect. Microbiol. 5:33. doi: 10.3389/fcimb.2015.00033 New insight into the molecular control of bacterial functional amyloid

Chance in the Modern Synthesis

The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” or “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. In the following, we first off er a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance

The prevalences of Salmonella Genomic Island 1 variants in human and animal Salmonella Typhimurium DT104 are distinguishable using a Bayesian approach

Throughout the 1990s, there was an epidemic of multidrug resistant Salmonella Typhimurium DT104 in both animals and humans in Scotland. The use of antimicrobials in agriculture is often cited as a major source of antimicrobial resistance in pathogenic bacteria of humans, suggesting that DT104 in animals and humans should demonstrate similar prevalences of resistance determinants. Until very recently, only the application of molecular methods would allow such a comparison and our understanding has been hindered by the fact that surveillance data are primarily phenotypic in nature. Here, using large scale surveillance datasets and a novel Bayesian approach, we infer and compare the prevalence of Salmonella Genomic Island 1 (SGI1), SGI1 variants, and resistance determinants independent of SGI1 in animal and human DT104 isolates from such phenotypic data. We demonstrate differences in the prevalences of SGI1, SGI1-B, SGI1-C, absence of SGI1, and tetracycline resistance determinants independent of SGI1 between these human and animal populations, a finding that challenges established tenets that DT104 in domestic animals and humans are from the same well-mixed microbial population

Severe re‐expansion pulmonary edema after conventional cardiac surgery: Identification and management

Re‐expansion Pulmonary Edema (REPE) is a recognized but rare complication of lung re‐inflation after pathologic collapse or intentional deflation. The presentation of REPE may be highly variable, ranging from a clinically asymptomatic, incidental radiologic finding to acute respiratory failure accompanied by severe, life‐threatening hypoxemia. With the current report, we present a patient with severe aortic insufficiency, severe mitral regurgitation, coronary artery disease, pulmonary hypertension, who underwent aortic valve replacement, mitral valvuloplasty, coronary artery bypass grafting, and developed at the immediate post‐ operative period severe respiratory failure due to REPE, requiring venous‐venous Extracorporeal Membrane Oxygenation (VV‐ECMO).Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149568/1/jocs14057.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149568/2/jocs14057_am.pd

The binding site distance test score: a robust method for the assessment of predicted protein binding sites

We propose a novel method for scoring the accuracy of protein binding site predictions – the Binding-site Distance Test (BDT) score. Recently, the Matthews Correlation Coefficient (MCC) has been used to evaluate binding site predictions, both by developers of new methods and by the assessors for the community wide prediction experiment – CASP8. Whilst being a rigorous scoring method, the MCC does not take into account the actual 3D location of the predicted residues from the observed binding site. Thus, an incorrectly predicted site that is nevertheless close to the observed binding site will obtain an identical score to the same number of nonbinding residues predicted at random. The MCC is somewhat affected by the subjectivity of determining observed binding residues and the ambiguity of choosing distance cutoffs. By contrast the BDT method produces continuous scores ranging between 0 and 1, relating to the distance between the predicted and observed residues. Residues predicted close to the binding site will score higher than those more distant, providing a better reflection of the true accuracy of predictions. The CASP8 function predictions were evaluated using both the MCC and BDT methods and the scores were compared. The BDT was found to strongly correlate with the MCC scores whilst also being less susceptible to the subjectivity of defining binding residues. We therefore suggest that this new simple score is a potentially more robust method for future evaluations of protein-ligand binding site predictions