Obtaining accurate mean velocity measurements in high Reynolds number turbulent boundary layers using Pitot tubes

This article reports on one component of a larger study on measurement of the zero-pressure-gradient turbulent flat plate boundary layer, in which a detailed investigation was conducted of the suite of corrections required for mean velocity measurements performed using Pitot tubes. In particular, the corrections for velocity shear across the tube and for blockage effects which occur when the tube is in close proximity to the wall were investigated using measurements from Pitot tubes of five different diameters, in two different facilities, and at five different Reynolds numbers ranging from Re_θ = 11 100 to 67 000. Only small differences were found amongst commonly used corrections for velocity shear, but improvements were found for existing near-wall proximity corrections. Corrections for the nonlinear averaging of the velocity fluctuations were also investigated, and the results compared to hot-wire data taken as part of the same measurement campaign. The streamwise turbulence-intensity correction was found to be of comparable magnitude to that of the shear correction, and found to bring the hot-wire and Pitot results into closer agreement when applied to the data, along with the other corrections discussed and refined here

The physiological cost index of walking with a powered knee ankle foot orthosis in subjects with poliomyelitis : A pilot study

Background: A powered knee ankle foot orthosis (KAFO) was developed to provide restriction of knee flexion during stance phase and active flexion and extension of the knee during swing phase of gait. Objectives: The purpose of this study was to determine its effect on the physiological cost index (PCI), walking speed and the distance walked in people with poliomyelitis compared to when walking with a KAFO with drop lock knee joints. Methods: Seven subjects with poliomyelitis volunteered for the study, and undertook gait analysis with both types of KAFO. Results: Walking with the powered KAFO significantly reduced walking speed (p=0.015) and the distance walked (p=0.004), and also it did not improve PCI values (p =0.009) compared to walking with the locked KAFO. Conclusion: Using a powered KAFO did not significantly improve any of the primary outcome measures during walking for poliomyelitis subjects

Dynamic Bioluminescence Imaging: Development of a Physiological Pharmacokinetic Model of Tumor Metabolism

poster abstractBioluminescence (BLI) is a technology which has been studied extensively across multiple genera for more than 90 years. Over this period, BLI has emerged as a powerful noninvasive tool to study tumor localization, growth, and response to therapy due to the relatively recent technological advancements in instrumentation and molecular biology. This technology takes advantage of molecular transfection of the luciferase (LUC) gene from the North American firefly, Photinus pyralis, into human cancer cells, which are then implanted (ectopic or orthotopic) in mice. Oxidation of the exogenously administered substrate D-luciferin by the LUC gene product results in emission of green-yellow photons which are then evaluated in the context of tumor growth and development. Despite the more than 30 years of characterization, there exists a fundamental gap in our knowledge of the underlying PK/PD processes which are at the heart of nearly all BLI interpretation, and has lead to a dogmatic adherence in the literature to numerical methods which are at best simple corollaries of tumor metabolic rate. In an attempt to fill this void, this paper will present a new PK/PD model which takes advantage of the temporal nature of both substrate transport and light evolution. In addition, we will compare these results to traditional non-model based analyses and show how they differ. Lastly we will present OATS (One at A Time) Parameter Sensitivity and Monte Carlo Noise Analysis to characterize the numerical stability and sensitivity of this new model

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

Biogeochemical cycling in the Bering Sea over the onset of major Northern Hemisphere glaciation

The Bering Sea is one of the most biologically productive regions in the marine system and plays a key role in regulating the flow of waters to the Arctic Ocean and into the subarctic North Pacific Ocean. Cores from IODP Expedition 323 to the Bering Sea provide the first opportunity to obtain reconstructions from the region that extend back to the Pliocene. Previous research at Bowers Ridge, south Bering Sea, has revealed stable levels of siliceous productivity over the onset of major Northern Hemisphere Glaciation (NHG) (c. 2.85-2.73 Ma). However, diatom silica isotope records of oxygen (δ18Odiatom) and silicon (δ30Sidiatom) presented here demonstrate that this interval was associated with a progressive increase in the supply of silicic acid to the region, superimposed on shift to a more dynamic environment characterized by colder temperatures and increased sea ice. This concluded at 2.58 Ma with a sharp increase in diatom productivity, further increases in photic zone nutrient availability and a permanent shift to colder sea surface conditions. These transitions are suggested to reflect a gradually more intense nutrient leakage from the subarctic northwest Pacific Ocean, with increases in productivity further aided by increased sea-ice and wind-driven mixing in the Bering Sea. In suggesting a linkage in biogeochemical cycling between the south Bering Sea and subarctic Northwest Pacific Ocean, mainly via the Kamchatka Strait, this work highlights the need to consider the inter-connectivity of these two systems when future reconstructions are carried out in the region

Intact carcasses as enrichment for large felids: Effects on on- and off-exhibit behaviors

Reducing stereotypic behaviors in captive animals is a goal for zoological institutions worldwide, and environmental enrichment is one tool commonly used to meet that end. Behavioral needs associated with feeding, however, are often neglected in large carnivores. To address these needs, I tested the effects of calf carcasses as enrichment for large felids. Over 14 weeks, I provided nine animals with up to seven intact carcasses. The cats were housed at Toledo Zoo, Potawatomi Zoo, and Binder Park Zoo. Animals were observed off and on exhibit for changes in feeding, natural, stereotypic, active, and inactive behaviors. I compared treatment behaviors with behaviors observed during a baseline period in which the animals were fed traditional processed diets. For these nine cats, carcass provision decreased off-exhibit stereotypic behaviors but had little impact on on-exhibit behaviors. Zoo Biol 21:37–47, 2002. © 2002 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34915/1/10033_ftp.pd

Canonical A-to-I and C-to-U RNA Editing Is Enriched at 3′UTRs and microRNA Target Sites in Multiple Mouse Tissues

RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Enzymes that catalyze RNA editing are required for life, and defects in RNA editing are associated with many diseases. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. Here, we demonstrate that canonical RNA editing (A-to-I and C-to-U) occurs in liver, white adipose, and bone tissues of the laboratory mouse, and we show that apparent non-canonical editing (all other possible base substitutions) is an artifact of current high-throughput sequencing technology. Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3′ UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing

Dynamic Bioluminescence Imaging: Development of a Physiological Pharmacokinetic Model of Tumor Metabolism

poster abstractBioluminescent imaging (BLI) has proven to be a valuable tool for the study of cellular biology and therapeutic response in a wide array of tumor types. Several BLI analytical approaches have been developed to assess tumor function and growth, all with the primary assumption that substrate concentrations saturate the luciferase enzyme. Recent work suggests that when D-luciferin is administered over the range from 75-600mg/kg, target tissue concentrations of D-luciferin are well below the Km of luciferase for the reaction, and, that the pharmacokinetics of D-luciferin significantly impact observed emission rates. To address the concentration and PK concerns, we developed a three compartment physiologically based pharmacokinetic (PhPK) model for D-luciferin including oxidation by luciferase via Michaelis-Menten kinetics. The model was applied to dynamically acquired BLI in NOD/SCID mice with ectopic luciferase-transfected SF767 tumors. The current PhPK model estimates tumor volume, tumor substrate metabolism (M ̅), tumor blood flow (Vb) and substrate extraction from the blood (Er). Studies were conducted using intraperitoneal, subcutaneous and intravenous routes of administration of 150 mg/kg of D-luciferin, where dynamic BLI was conducted weekly for four weeks. The D-luciferin concentration in tumor tissue, determined immediately after the last imaging session, was found to be approximately 8-fold below the reported Km for the reaction across all routes of administration, supporting the need for a PhPK modeling approach for analyzing BLI data. The model-predicted tumor volumes increased over time and were highly correlated with caliper-measured tumor volumes (y=1.984x, R2=0.980, p<0.0001). Tumor D-luciferin metabolism was found to increase exponentially over the 4 weeks, while blood flow decreased over this same interval, a finding which is consistent with the interpretation of a Warburg effect. When tumor M ̅ was compared with the traditional measures of peak emission (Cmax) and area under the curve (AUC), it was found that metabolism increased exponentially with increases in either Cmax (y=92.7exp(8E-11x), R2= 0.997) or AUC ( y=86.4exp(5E-14x), R2= 0.989), suggesting that Cmax and AUC may substantially underestimate the magnitude of tumor metabolism. The present PhPK model of D-luciferin distribution and metabolism overcomes limitations in the Cmax and AUC approaches caused by incorrect substrate: enzyme concentration assumptions, and thus provides a more reliable estimate of tumor burden, growth, and therapeutic response