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

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

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

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

The seasonal cycle of ocean-atmosphere CO2 Flux in Ryder Bay, West Antarctic Peninsula

Approximately 15 million km2 of the Southern Ocean is seasonally ice covered, yet the processes affecting carbon cycling and gas exchange in this climatically important region remain inadequately understood. Here, 3 years of dissolved inorganic carbon (DIC) measurements and carbon dioxide (CO2) fluxes from Ryder Bay on the west Antarctic Peninsula (WAP) are presented. During spring and summer, primary production in the surface ocean promotes atmospheric CO2 uptake. In winter, higher DIC, caused by net heterotrophy and vertical mixing with Circumpolar Deep Water, results in outgassing of CO2 from the ocean. Ryder Bay is found to be a net sink of atmospheric CO2 of 0.59–0.94 mol C m−2 yr−1 (average of 3 years). Seasonal sea ice cover increases the net annual CO2 uptake, but its effect on gas exchange remains poorly constrained. A reduction in sea ice on the WAP shelf may reduce the strength of the oceanic CO2 sink in this region

Driven Tunneling Dynamics: Bloch-Redfield Theory versus Path Integral Approach

In the regime of weak bath coupling and low temperature we demonstrate numerically for the spin-boson dynamics the equivalence between two widely used but seemingly different roads of approximation, namely the path integral approach and the Bloch-Redfield theory. The excellent agreement between these two methods is corroborated by a novel efficient analytical high-frequency approach: it well approximates the decay of quantum coherence via a series of damped coherent oscillations. Moreover, a suitably tuned control field can selectively enhance or suppress quantum coherence.Comment: 4 pages including 3 figures, submitted for publicatio

Ácidos grasos como marcadores de las relaciones tróficas entre el sestón, el zooplancton crustáceo y el sifonóforo Nanomia cara en Georges Basin y el cañón Oceanographer (NO Atlántico)

[EN] Fatty acid concentrations expressed as percentages of total fatty acid pools in seston, stage V copepodites of Calanus finmarchicus, adults of the euphausiid Meganyctiphanes norvegica, and the physonect siphonophore Nanomia cara were used to elucidate trophic links in Georges Basin and Oceanographer Canyon in September 2003. Seston at both locations was refractory and comprised mainly of saturated fatty acids. Phytoplankton did not contribute significantly to the fatty acid composition of seston or higher trophic levels. Only four fatty acids, i.e. 14:0, 16:0, 16:1 (n–7) and 18:1 (n–7), were transferred from seston to C. finmarchicus or M. norvegica, which suggested weak trophic interactions. Fatty acids transferred from the two species of crustaceans to N. cara included the same four fatty acids, along with three polyunsaturated fatty acids found in relatively high concentrations in both crustaceans, i.e. 20:3 (n–6), 20:5 (n–3) and 22:6 (n–3). In addition, 18:1 (n–9), which occurred in relatively high concentrations only in M. norvegica, and 18:0 and 18:2 (n–6), which were found in low concentrations in both crustaceans, also appeared to be transferred to N. cara. Overall, fatty acid trophic markers proved useful for identifying trophic links to N. cara[ES] En este estudio se utilizaron las concentraciones de ácidos grasos (expresadas como porcentajes) para identificar posibles relaciones tróficas entre el seston, el estadio V (copepoditos) de Calanus finmarchicus, los adultos del eufáusido Meganyctiphanes norvegica, y el sifonóforo fisonecto Nanomia cara en Georges Basin y el cañón submarino Oceanographer durante Septiembre de 2003. En ambos lugares el seston era muy refractario y compuesto básicamente por ácidos grasos saturados. El fitoplancton no contribuyó de forma significativa a la composición de ácidos grasos del seston o de niveles tróficos superiores. Sólo cuatro ácidos grasos [14:0, 16:0, 16:1 (n–7) y 18:1 (n–7)] se transfirieron potencialmente del seston a C. finmarchicus o M. norvegica, lo que sugiere una débil conexión trófica entre estos eslabones de la cadena. Los ácidos grasos transferidos de las dos especies de zooplancton crustáceo a N. cara incluyen los mismos descritos más arriba y otros tres ácidos grasos poliinsaturados [20:3 (n–6), 20:5 (n–3) y 22:6 (n–3)] encontrados en concentraciones relativamente elevadas en ambos crustáceos. Además, tanto el 18:1 (n–9) (encontrado en elevadas concentraciones en M. norvegica) y los 18:0 y 18:2 (n–6) (encontrados en bajas concentraciones en ambas especies de crustáceos) se transfieren a N. cara. Los ácidos grasos demuestran ser una herramienta útil para identificar conexiones tróficas en N. caraA grant to MJY from the National Science Foundation (NSF-0002493), the European Project EUROGEL, and USDA CRIS Project FLA-FAS-03978 supported this workPeer reviewe