Clinical and Genetic Re-Evaluation of Inherited Retinal Degeneration Pedigrees following Initial Negative Findings on Panel-Based Next Generation Sequencing

Although rare, inherited retinal degenerations (IRDs) are the most common reason for blind registration in the working age population. They are highly genetically heterogeneous (>300 known genetic loci), and confirmation of a molecular diagnosis is a prerequisite for many therapeutic clinical trials and approved treatments. First-tier genetic testing of IRDs with panel-based next-generation sequencing (pNGS) has a diagnostic yield of ≈70–80%, leaving the remaining more challenging cases to be resolved by second-tier testing methods. This study describes the phenotypic reassessment of patients with a negative result from first-tier pNGS and the rationale, outcomes, and cost of second-tier genetic testing approaches. Removing non-IRD cases from consideration and utilizing case-appropriate second-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees, bringing the overall resolve rate to 92% (388/423). At present, pNGS remains the most cost-effective first-tier approach for the molecular assessment of diverse IRD populations Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology), and genetic (i.e., single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner.     

Evaluation of a statewide foodborne illness complaint surveillance system in Minnesota, 2000 through 2006

Foodborne outbreaks are detected by recognition of similar illnesses among persons with a common exposure or by identification of case clusters through pathogen-specific surveillance. PulseNet USA has created a national framework for pathogen-specific surveillance, but no comparable effort has been made to improve surveillance of consumer complaints of suspected foodborne illness. The purpose of this study was to characterize the complaint surveillance system in Minnesota and to evaluate its use for detecting outbreaks. Minnesota Department of Health foodborne illness surveillance data from 2000 through 2006 were analyzed for this study. During this period, consumer complaint surveillance led to detection of 79% of confirmed foodborne outbreaks. Most norovirus infection outbreaks were detected through complaints. Complaint surveillance also directly led or contributed to detection of 25% of salmonellosis outbreaks. Eighty-one percent of complainants did not seek medical attention. The number of ill persons in a complainant's party was significantly associated with a complaint ultimately resulting in identification of a foodborne outbreak. Outbreak confirmation was related to a complainant's ability to identify a common exposure and was likely related to the process by which the Minnesota Department of Health chooses complaints to investigate. A significant difference (P < 0.001) was found in incubation periods between complaints that were outbreak associated (median, 27 h) and those that were not outbreak associated (median, 6 h). Complaint systems can be used to detect outbreaks caused by a variety of pathogens. Case detection for foodborne disease surveillance in Minnesota happens through a multitude of mechanisms. The ability to integrate these mechanisms and carry out rapid investigations leads to improved outbreak detection.     

Landscape-scale modeling of water quality in Lake Superior and Lake Michigan watersheds: How useful are forest-based indicators?

The Great Lakes watersheds have an important influence on the water quality of the nearshore environment, therefore, watershed characteristics can be used to predict what will be observed in the streams. We used novel landscape information describing the forest cover change, along with forest census data and established land cover data to predict total phosphorus and turbidity in Great Lakes streams. In Lake Superior, we modeled increased phosphorus as a function of the increase in the proportion of persisting forest, forest disturbed during 2000–2009, and agricultural land, and we modeled increased turbidity as a function of the increase in the proportion of persisting forest, forest disturbed during 2000–2009, agricultural land, and urban land. In Lake Michigan, we modeled increased phosphorus as a function of ecoregion, decrease in the proportion of forest disturbed during 1984–1999 and watershed storage, and increase in the proportion of urban land, and we modeled increased turbidity as a function of ecoregion, increase in the proportion of forest disturbed during 2000–2009, and decrease in the proportion softwood forest. We used these relationships to identify priority areas for restoration in the Lake Superior basin in the southwestern watersheds, and in west central and southwest watersheds of the Lake Michigan basin. We then used the models to estimate water quality in watersheds without observed instream data to prioritize those areas for management. Prioritizing watersheds will aid effective management of the Great Lakes watershed and result in efficient use of restoration funds, which will lead to improved nearshore water quality.     

Ag and Ag–Mn nanowire catalysts for alkaline fuel cells

Low loadings of Ag and Ag–Mn nanowire catalysts were applied to the surface of a CNT-base electrode. The catalyzed electrodes had a 60 mV larger onset potential and promoted the ORR via the direct 4 electron pathway. The Ag/CNT, Ag–Mn/CNT, and CNT samples produced a Tafel slope of about 70 mV/decade which confirmed the ORR activation was limited by the migration of oxygen molecules to active surface sites. The catalytic performance of the Ag and Ag–Mn nanowires was also comparable to that of a bulk catalyst but at a much lower loading. Electrochemical test results showed that the Ag and Ag–Mn catalysts exhibited similar performance. The Ag–Mn nanowire catalysts were synthesized using a unique electroless deposition procedure to co-deposit Ag and Mn. ICP confirmed that 2 to 9 at% Mn was present in the nanowires. XPS and XRD analysis showed that the Ag–Mn nanowires were composed of Mn in solid solution with Ag and a thin surface layer containing MnO and MnO₂. The Ag–Mn nanowires were expected to be the most active. The equivalent performance between Ag and Ag–Mn samples was attributed to the presence of inactive MnO and low concentrations of MnO₂ in the nanowires. Although MnO₂ is known to be active towards the ORR, the dominant Mn species in the nanowires was MnO.     

A music symbols recognition method using pattern matching along with integrated projection and morphological operation techniques

Multimedia Tools and Applications - Optical Music Recognition (OMR) can be divided into three main phases: (i) staff line detection and removal. The goal of this phase is to detect and to remove...     

A 40 keV cyclotron for radioisotope dating

We have built and begun testing a small low energy negative ion cyclotron for direct detection of ¹⁴C. At present, the cyclotron is operated in a high resolution mode at the 31st harmonic, with 1–2 kV on the dees. The high harmonic and a minimum number of turns of approximately 100, should give a fwhm mass resolution of about $\text{1}\text{30000}$ — sufficient to suppress the background from molecular ions such as ¹³CH^?. Background such as scattered ions of ¹²C^? and ¹³C^? should be totally suppressed by the cyclotron acceleration process. (At the 88″ cyclotron at LBL we found that ions only 1% off-resonance are suppressed by more than a factor of 10¹⁷.) A miniature Cs sputter source located at the center of the cyclotron is expected to provide more than 1 μA of negative carbon ions. Negative ions are used in order to eliminate the interference from ¹⁴N. Unlike high energy cyclotrons, focussing is obtained solely from the axial components of the accelerating electric field. The magnetic field is kept flat to within 1 part in 10⁴ in order to maintain exact isochronism throughout the several thousand accelerating rf cycles. The low final energy of 40 keV eliminates any danger from radiation or need for shielding, and the final orbit radius of only 10.5 cm, reduce the size and cost of the machine to that of conventional mass spectrometers.     

Apple quality,storage, and washing treatments affect patulin levels in apple cider

Patulin is a mycotoxin produced primarily by Penicillium expansum, a mold responsible for rot in apples and other fruits. The growth of this fungus and the production of patulin are common in fruit that has been damaged. However, patulin can be detected in visibly sound fruit. The purpose of this project was to determine how apple quality, storage, and washing treatments affect patulin levels in apple cider. Patulin was not detected in cider pressed from fresh tree-picked apples (seven cultivars) but was found at levels of 40.2 to 374 microg/liter in cider pressed from four cultivars of fresh ground-harvested (dropped) apples. Patulin was not detected in cider pressed from culled tree-picked apples stored for 4 to 6 weeks at 0 to 2 degrees C but was found at levels of 0.97 to 64.0 microg/liter in cider pressed from unculled fruit stored under the same conditions. Cider from controlled-atmosphere-stored apples that were culled before pressing contained 0 to 15.1 microg of patulin per liter, while cider made from unculled fruit contained 59.9 to 120.5 microg of patulin per liter. The washing of ground-harvested apples before pressing reduced patulin levels in cider by 10 to 100%, depending on the initial patulin levels and the type of wash solution used. These results indicate that patulin is a good indicator of the quality of the apples used to manufacture cider. The avoidance of ground-harvested apples and the careful culling of apples before pressing are good methods for reducing patulin levels in cider.     

Oxidation of H2S by iron oxides in unsaturated conditions

Previous studies have demonstrated that gas-phase H2S can immobilize certain redox-sensitive contaminants (e.g., Cr, U, Tc) in vadose zone environments. A key issue for effective and efficient delivery of H2S in these environments is the reactivity of the gas with indigenous iron oxides. To elucidate the factors that control the transport of H2S in the vadose zone, laboratory column experiments were conducted to identify reaction mechanisms and measure rates of H2S oxidation by iron oxide-coated sands using several carrier gas compositions (N2, air, and O2) and flow rates. Most experiments were conducted using ferrihydrite-coated sand. Additional studies were conducted with goethite- and hematite-coated sand and a natural sediment. Selective extractions were conducted at the end of each column experiment to determine the mass balance of the reaction products. XPS was used to confirm the presence of the reaction products. For column experiments in which ferrihydrite-coated sand was the substrate and N2 was the carrier gas, the major H2S oxidation products were FeS and elemental sulfur (mostly S8(0), represented as S(0) for simplicity) at ratios that were consistent with the stoichiometry of the postulated reactions. When air or O2 were used as the carrier gas, S(0) became the dominant reaction product along with FeS2 and smaller amounts of FeS, sulfate, and thiosulfate. A mathematical model of reactive transport was used to test the hypothesis that S(0) forming on the iron oxide surfaces reduces access of H2S to the reactive surface. Several conceptual models were assessed in the context of the postulated reactions with the final model based on a linear surface poisoning model and fitted reaction rates. These results indicate that carrier gas selection is a critical consideration with significant tradeoffs for remediation objectives.     

Prenatal cocaine, alcohol, and undernutrition differentially alter mineral and protein content in fetal rats

Alcohol exposure and undernutrition during pregnancy have been associated with altered fetal body composition. Recent observations suggest that cocaine exposure during pregnancy may impair delivery of nutrients to the fetus and could thereby alter body growth and composition. Such effects are important because they can adversely influence physical and neural development. Consequently, we investigated the dose-dependent effects of cocaine on fetal body composition in an animal (rat) model and compared such effects with those caused by prenatal alcohol exposure and undernutrition. Pregnant Sprague-Dawley rats received either 20, 30, 40, or 50 mg/kg cocaine HCl (SC) twice daily from gestation days 7 through 19. Pair-fed (undernutrition) and untreated control groups and a group receiving 3.0 g/kg alcohol (PO) twice daily served as comparison groups (n = 11 to 14/group). Females were sacrificed on gestation day 20. One male and one female fetus was removed from each dam. The fetuses were minced, dehydrated, defatted, and analyzed for content of protein and the minerals Zn, Ca, Fe, Mg, K, and Na. In terms of concentration per unit of fat-free dry solids, male fetuses in the cocaine groups showed significant decreases in protein compared to untreated controls (15+/-3 to 20+/-2 mg/g vs. 24+/-4 mg/g, p = 0.01). There was a significant treatment effect for Ca (p < 0.05), reflecting a trend for decreased Ca concentrations in the fetuses of the cocaine and undernutrition groups. Male fetuses in the alcohol group had significantly elevated Mg levels compared to male fetuses in the other groups (3.0+/-0.8 vs. 1.0+/-0.2 to 2.3+/-0.7 mg/g, p < 0.05). There were some sex differences, with female fetuses having significantly lower concentrations of Mg, Fe, K, and higher protein concentrations than male fetuses. Although the effects were few and modest, these results suggest that prenatal cocaine, alcohol, and undernutrition can differentially alter fetal body weight and composition and, therefore, adversely influence fetal development.     

Synthesis and differential properties of creatine analogues as inhibitors for human creatine kinase isoenzymes

Fourteen new creatine analogues, all with a guanidine function and either a polar or an apolar group instead of the creatine carboxylic function, were tested as potential inhibitors for human creatine kinase by kinetic analysis of their effects on the reaction rate. Only compounds bearing an apolar aromatic moiety, which was spaced from the guanidine function by at least two bonds, proved to have a significant inhibitory activity and showed a mixed-type inhibition similar to that of creatine. Among these compounds 2,6-dichlorobenzylguanidine (Ki = 5.6 mM and 39.8 mM for muscle-type and brain-type creatine kinases, respectively) and 3-(2,6-dichlorophenyl)propylguanidine (Ki = 15 mM and 4.5 mM) were the more potent inhibitors and showed a significant isoenzyme selectivity between muscle- and brain-type creatine kinases. Our results are in agreement with recent data that suggest the location of a hydrophobic pocket near the guanidine-binding domain of the enzyme. The observed selectivity in isoenzyme inhibition may be useful to study structural differences in catalytic centers.