Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens.

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species

Survey of Stormwater BMP Maintenance Practices

Many stormwater management manuals and guidance documents have stated the importance and estimated frequency of maintenance for stormwater best management practices (BMPs), but few have documented the actual frequency and intensity of maintenance required to maintain a desired level of performance and efficiency. Increased attention to mass balance, numerical goals, total maximum daily loads (TMDLs), and non-degradation requirements has created the need for more emphasis on BMP maintenance in order to meet permitting and reporting requirements. The purpose of this paper is to advance short and long-term maintenance considerations so as to develop more realistic maintenance plans. To do so, we conducted a national literature search for maintenance costs and developed, distributed, analyzed the results of a detailed municipal public works survey. The specific goals of the survey were to identify and inventory stormwater BMP O&M efforts and costs. Survey questionnaires were sent to 106 cities with 28 responses received. The survey related to the following topics: number of BMPs in the city, frequency of BMP inspections, average staff-hours spent per routine inspection/maintenance, complexity of BMP maintenance, most frequent causes of performance deterioration within BMPs, and cost of non-routine maintenance activities. The results of the survey revealed that most (89%) cities perform routine maintenance once per year or less. Staff-hours per year ranged from one to four hours for most stormwater BMPs and but were significantly more for rain gardens (one to sixteen hours per year) and wetlands (one to nine hours per year). The most common causes of performance deterioration were sediment buildup and litter/debris for most stormwater BMPs. Respondents indicated that the removal of accumulated sediment incurred the largest cost of all BMP maintenance activities

Iron-Enhanced Swale Ditch Checks for Phosphorus Retention

Iron-enhanced ditch checks in roadside swales were developed specifically for capturing dissolved phosphorus and dissolved metals from roadway runoff in both urban and agricultural environments. One iron-enhanced ditch check constructed along CR 15 (formerly TH 5) in Stillwater, Minnesota, was monitored during 40 storm events from 2016 to 2018. The iron-enhanced sand filter insert generally captured phosphate, yielding lower phosphate concentrations and mass load reductions that varied between 22% and 50% during several events. However, the cumulative phosphate retention in the filter insert decreased from 42% in 2015 to 30% in 2016, 25% in 2017, and 23% in 2018. The filter insert was not an effective retention device for dissolved copper and zinc. The overall ditch check’s performance, although unexceptional in 2016 and 2017, appeared to improve in 2018. Sampling issues likely contributed to the low performance measured until 2017. The 2018 water sample collection method provided a better estimate of the ditch check’s performance and roughly matched that of the filter insert. Synthetic runoff testing supported the level of treatment achieved during storm events. Phosphate load from the degrading topsoil and the overutilization of the bottom filter media most likely affected overall treatment performance. Design improvements and recommended maintenance actions were developed based on the lessons learned from field monitoring. The iron-enhanced ditch check can improve net phosphate retention through roadside swales, as long as the recommended maintenance actions are performed as scheduled.Natarajan, Poornima; Gulliver, John S; Weiss, Peter T. (2019). Iron-Enhanced Swale Ditch Checks for Phosphorus Retention. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/208692

Free energy for parameterized Polyakov loops in SU(2) and SU(3) lattice gauge theory

We present a study of the free energy of parameterized Polyakov loops P in SU(2) and SU(3) lattice gauge theory as a function of the parameters that characterize P. We explore temperatures below and above the deconfinement transition, and for our highest temperatures T > 5 T_c we compare the free energy to perturbative results.Comment: Minor changes. Final version to appear in JHE

Monitoring an Iron-Enhanced Sand Filter Trench for the Capture of Phosphate from Stormwater Runoff

This monitoring project was performed on an iron enhanced sand filtration (IESF) trench in the City of Prior Lake. Water from the pond and IESF trench discharges into a wetland that ultimately drains into Upper Prior Lake. In 2002, Upper Prior Lake was listed on Minnesota’s 303(d) List of Impaired Waters for nutrient/eutrophication biological indicators with aquatic recreation being impaired. Water quality has been reduced due to excessive phosphorus loading. According to the TMDL implementation plan developed for Spring Lake and Upper Prior Lake, the total phosphorus load must be reduced by 83% and 41%, respectively, to meet water quality goals. Overall, for 28 monitored natural rainfall/runoff events from 2013-2015, the IESF trench removed 26% of the phosphate mass load it received, though after non-routine maintenance in August 2014 the performance improved to 45% phosphate mass load reduction. These results indicate the importance of maintenance. A newer installation was previously monitored, and found to retain 71% of the phosphate (Erickson and Gulliver 2010). Most of the overall phosphate load reduction was achieved during larger events that had comparatively high influent phosphate concentrations (32.3 – 125.2 μg/L) and mass loads. Many small events in this investigation with low influent phosphate concentrations (3.8 – 38.4 μg/L) or mass loads exhibited negative removal (i.e., effluent mass load > influent mass load). The high effluent phosphate concentrations are suspected to be caused by the degradation of floating plants (primarily duckweed) that were deposited on the surface of the filter trench. As mentioned above, nonroutine maintenance to remove this material resulted in substantial performance improvement. After this maintenance, positive removal was observed for influent concentrations ranging from 6.3 – 44.1 μg/L. Detailed results, maintenance activities, design and operating & maintenance recommendations, and lessons learned are given within this report.U.S. Environmental Protection Agency Section 319 Program Minnesota Pollution Control Agenc

Dissipative Landau-Zener transitions of a qubit: bath-specific and universal behavior

We study Landau-Zener transitions in a qubit coupled to a bath at zero temperature. A general formula is derived that is applicable to models with a non-degenerate ground state. We calculate exact transition probabilities for a qubit coupled to either a bosonic or a spin bath. The nature of the baths and the qubit-bath coupling is reflected in the transition probabilities. For diagonal coupling, when the bath causes energy fluctuations of the diabatic qubit states but no transitions between them, the transition probability coincides with the standard LZ probability of an isolated qubit. This result is universal as it does not depend on the specific type of bath. For pure off-diagonal coupling, by contrast, the tunneling probability is sensitive to the coupling strength. We discuss the relevance of our results for experiments on molecular nanomagnets, in circuit QED, and for the fast-pulse readout of superconducting phase qubits.Comment: 16 pages, 8 figure

Permeable Pavements in Cold Climates: State of the Art and Cold Climate Case Studies

This document is an extensive review of full-depth permeable pavements including porous asphalt, pervious concrete, and permeable interlocking concrete pavers (PICP). Also included is a brief section on articulated concrete blocks/mats. The main topics, which have been divided into chapters, include structural and mix design, hydrologic design, hydraulic performance (i.e. infiltration capacity), maintenance needs/frequency/actions, the impact of permeable pavement on water quality, results of a highway shoulder feasibility study, knowledge gaps, and several cold climate case studies from the United States and Canada. While progress has recently been made with the relatively new permeable pavement technology, researchers have also identified many unresolved issues that are not well understood. These include a methodology to measure subgrade infiltration rates, filling data gaps related to structural integrity, construction, and related issues associated with permeable pavements, determining what maintenance activities are most effective on various pavement types and how frequently specific maintenance actions should be performed, a better understanding of the processes involved in the observed reduction of contaminant concentrations in stormwater flowing through permeable pavements, and a better understanding of the performance of permeable pavements over a time frame that better corresponds with a life-span of 20 years

The influence of iron status and genetic polymorphisms in the HFE gene on the risk for postoperative complications after bariatric surgery: a prospective cohort study in 1,064 patients

<p>Abstract</p> <p>Background</p> <p>Gastric bypass surgery is a highly effective therapy for long-term weight loss in severely obese patients, but carries significant perioperative risks including infection, wound dehiscence, and leaks from staple breakdown. Iron status can affect immune function and wound healing, thus may influence peri-operative complications. Common mutations in the HFE gene, the gene responsible for the iron overload disorder hereditary hemochromatosis, may impact iron status.</p> <p>Methods</p> <p>We analyzed 1064 extremely obese Caucasian individuals who underwent open and laparoscopic Roux-n-Y gastric bypass surgery at the Geisinger Clinic. Serum iron, ferritin, transferrin, and iron binding capacity were measured pre-operatively. All patients had intra-operative liver biopsies and were genotyped for the C282Y and H63D mutations in the HFE gene. Associations between surgical complications and serum iron measures, HFE gene status, and liver iron histology were determined.</p> <p>Results</p> <p>We found that increased serum iron and transferrin saturation were present in patients with any post-operative complication, and that increased serum ferritin was also increased in patients with major complications. Increased serum transferrin saturation was also associated with wound complications in open RYGB, and transferrin saturation and ferritin with prolonged lengths of stay. The presence of 2 or more HFE mutations was associated with overall complications as well as wound complications in open RYGB. No differences were found in complication rates between those with stainable liver iron and those without.</p> <p>Conclusion</p> <p>Serum iron status and HFE genotype may be associated with complications following RYGB surgery in the extremely obese.</p