Three-Dimensional Turbulence Characteristics of the Bottom Boundary Layer of the Coastal Ocean

The form and dynamics of ocean turbulence are critical to all marine processes; biological, chemical and physical. The three-dimensional turbulence characteristics of the bottom boundary layer of the coastal ocean are examined using a series of 29,991 instantaneous velocity distributions. These data, recorded by a submersible 3D-PTV system at an elevation of 0.64 m above the seabed, represent conditions typical of moderate tidal flows in the coastal ocean. A complexity associated with submersible 3D-PTV in the coastal ocean is that gaps and noise affect the accuracy of the data collected. To accommodate this, a new Physics-Enabled Flow Restoration Algorithm has been tested for the restoration of gappy and noisy velocity measurements where a standard PTV or PIV laboratory set-up (e.g. concentration / size of the particles tracked) is not possible and the boundary and initial conditions are not known a priori. This is able to restore the physical structure of the flow from gappy and noisy data, in accordance with its hydrodynamical basis. In addition to the restoration of the velocity flow field, PEFRA also estimates the maximum possible deviation of the output from the true flow. 3D-PTV measurements show coherent structures, with the hairpin-like vortices highlighted in laboratory measurements and numerical modelling, were frequently present within the logarithmic layer. These exhibit a modal alignment of 8 degrees from the mean flow and a modal elevation of 27 degrees from the seabed, with a mean period of occurrence of 4.3 sec. These appear to straddle sections of zero-mean along-stream velocity, consistent with an interpretation as packets. From these measurements, it is clear that data collected through both laboratory and numerical experiments are directly applicable to geophysical scales – a finding that will enable the fine-scale details of particle transport and pollutant dispersion to be studied in future. Conditional sampling of the Reynolds shear stress (without using Taylor’s hypothesis) reveals that these coherent structures are responsible for the vertical exchange of momentum and, as such, are the key areas where energy is extracted from the mean flow and into turbulence. The present study offers the first assessment of the magnitude of the errors associated with assuming isotropy on shear-based sensors of the TKE dissipation rate and its consequential effect on the Kolmogorov microscale using 3D-PTV data from the bottom boundary layer of the coastal ocean. The results indicate a high degree of spatial variability associated with the low conditions. The averaged data supports the validity of measurements obtained by horizontal and vertical profilers, however along-stream velocity derivatives underestimate the TKE dissipation rate by more than 40% – a factor of two higher than for the equivalent cross-stream and vertical estimates. This has important implications for the deployment of these sensors and the subsequent interpretation of higher-order statistics. Finally, the data have been processed to test four popular sub-grid scale (SGS) stress models and SGS dissipation rate estimates for Large-Eddy Simulations using these in situ experimental data. When the correlation and SGS model coefficients are assessed, the nonlinear model represents the best stress models to use for the present data, consistent with the substantial anisotropy and inhomogeneity associated with these flows. The detailed measurement and analysis of coherent structures in the coastal ocean undertaken therefore supports the development of numerical models and assists with the understanding of all marine processes

The integrin alpha 6 beta 4 is a laminin receptor

In this study, the putative laminin receptor function of the alpha 6 beta 4 integrin was assessed. For this purpose, we used a human cell line, referred to as clone A, that was derived from a highly invasive, colon adenocarcinoma. This cell line, which expresses the alpha 6 beta 4 integrin, adheres to the E8 and not to the P1 fragment of laminin. The adhesion of clone A cells to laminin is extremely rapid with half-maximal adhesion observed at 5 min after plating. Adhesion to laminin is blocked by GoH3, and alpha 6 specific antibody (60% inhibition), as well as by A9, a beta 4 specific antibody (30% inhibition). Most importantly, we demonstrate that alpha 6 beta 4 binds specifically to laminin-Sepharose columns in the presence of either Mg2+ or Mn2+ and it is eluted from these columns with EDTA but not with NaCl. The alpha 6 beta 4 integrin does not bind to collagen-Sepharose, but the alpha 2 beta 1 integrin does bind. Clone A cells do not express alpha 6 beta 1 as evidenced by the following observations: (a) no beta 1 integrin is detected in beta 1 immunoblots of GoH3 immunoprecipitates; and (b) no alpha 6 beta 1 integrin is seen in GoH3 immunoprecipitates of clone A extracts that had been immunodepleted of all beta 4 containing integrin using the A9 antibody. These data establish that laminin is a ligand for the alpha 6 beta 4 integrin and that this integrin can function as a laminin receptor independently of alpha 6 beta 1

Cosmic biology in perspective

Abstract: A series of astronomical observations obtained over the period 1986 to 2018 supports the idea that life is a cosmic rather than a purely terrestrial or planetary phenomenon. These include (1) the detection of biologically relevant molecules in interstellar clouds and in comets, (2) mid-infrared spectra of interstellar grains and the dust from comets, (3) a diverse set of data from comets including the Rosetta mission showing consistency with biology and (4) the frequency of Earth-like or habitable planets in the Galaxy. We argue that the conjunction of all the available data suggests the operation of cometary biology and interstellar panspermia rather than the much weaker hypothesis of comets being only the source of the chemical building blocks of life. We conclude with specific predictions on the properties expected of extra-terrestrial life if it is discovered on Enceladus, Europa or beyond. A radically different biochemistry elsewhere can be considered as a falsification of the theory of interstellar panspermia

A physics-enabled flow restoration algorithm for sparse PIV and PTV measurements

The gaps and noise present in particle image velocimetry (PIV) and particle tracking velocimetry (PTV) measurements affect the accuracy of the data collected. Existing algorithms developed for the restoration of such data are only applicable to experimental measurements collected under well-prepared laboratory conditions (i.e. where the pattern of the velocity flow field is known), and the distribution, size and type of gaps and noise may be controlled by the laboratory set-up. However, in many cases, such as PIV and PTV measurements of arbitrarily turbid coastal waters, the arrangement of such conditions is not possible. When the size of gaps or the level of noise in these experimental measurements become too large, their successful restoration with existing algorithms becomes questionable. Here, we outline a new physics-enabled flow restoration algorithm (PEFRA), specially designed for the restoration of such velocity data. Implemented as a 'black box' algorithm, where no user-background in fluid dynamics is necessary, the physical structure of the flow in gappy or noisy data is able to be restored in accordance with its hydrodynamical basis. The use of this is not dependent on types of flow, types of gaps or noise in measurements. The algorithm will operate on any data time-series containing a sequence of velocity flow fields recorded by PIV or PTV. Tests with numerical flow fields established that this method is able to successfully restore corrupted PIV and PTV measurements with different levels of sparsity and noise. This assessment of the algorithm performance is extended with an example application to in situ submersible 3D-PTV measurements collected in the bottom boundary layer of the coastal ocean, where the naturally-occurring plankton and suspended sediments used as tracers causes an increase in the noise level that, without such denoising, will contaminate the measurements

The Lantern Vol. 5, No. 3, May 1937

• Dedication • Dr. McClure: An Ursinus Man • Roar, O Wind! • To the Ladies! • The Futility of Dying • The Symbolism of the British Crown • Oh! • It Might Have Been • Treat Yourself? • Three Writers • Hawaii in June • On Being a Twin • Black Magic • Triangle • Who Longs? • A Son Passes • Sing an Old-Fashioned Song • Questioning • An Argument About a Fish • That Morning Eye-Opener • Scoop for the Sun • The Dead Do Not Die Once • Give Us Timehttps://digitalcommons.ursinus.edu/lantern/1010/thumbnail.jp

Extragenic suppressor mutations in ΔripA disrupt stability and function of LpxA

Abstract Background Francisella tularensis is a Gram-negative bacterium that infects hundreds of species including humans, and has evolved to grow efficiently within a plethora of cell types. RipA is a conserved membrane protein of F. tularensis, which is required for growth inside host cells. As a means to determine RipA function we isolated and mapped independent extragenic suppressor mutants in ∆ripA that restored growth in host cells. Each suppressor mutation mapped to one of two essential genes, lpxA or glmU, which are involved in lipid A synthesis. We repaired the suppressor mutation in lpxA (S102, LpxA T36N) and the mutation in glmU (S103, GlmU E57D), and demonstrated that each mutation was responsible for the suppressor phenotype in their respective strains. We hypothesize that the mutation in S102 altered the stability of LpxA, which can provide a clue to RipA function. LpxA is an UDP-N-acetylglucosamine acyltransferase that catalyzes the transfer of an acyl chain from acyl carrier protein (ACP) to UDP-N-acetylglucosamine (UDP-GlcNAc) to begin lipid A synthesis. Results LpxA was more abundant in the presence of RipA. Induced expression of lpxA in the ΔripA strain stopped bacterial division. The LpxA T36N S102 protein was less stable and therefore less abundant than wild type LpxA protein. Conclusion These data suggest RipA functions to modulate lipid A synthesis in F. tularensis as a way to adapt to the host cell environment by interacting with LpxA.http://deepblue.lib.umich.edu/bitstream/2027.42/110509/1/12866_2014_Article_336.pd

Morphine Attenuates fNIRS Signal Associated With Painful Stimuli in the Medial Frontopolar Cortex (medial BA 10)

Functional near infrared spectroscopy (fNIRS) is a non-invasive optical imaging method that provides continuous measure of cortical brain functions. One application has been its use in the evaluation of pain. Previous studies have delineated a deoxygenation process associated with pain in the medial anterior prefrontal region, more specifically, the medial Brodmann Area 10 (BA 10). Such response to painful stimuli has been consistently observed in awake, sedated and anesthetized patients. In this study, we administered oral morphine (15 mg) or placebo to 14 healthy male volunteers with no history of pain or opioid abuse in a crossover double blind design, and performed fNIRS scans prior to and after the administration to assess the effect of morphine on the medial BA 10 pain signal. Morphine is the gold standard for inhibiting nociceptive processing, most well described for brain effects on sensory and emotional regions including the insula, the somatosensory cortex (the primary somatosensory cortex, S1, and the secondary somatosensory cortex, S2), and the anterior cingulate cortex (ACC). Our results showed an attenuation effect of morphine on the fNIRS-measured pain signal in the medial BA 10, as well as in the contralateral S1 (although observed in a smaller number of subjects). Notably, the extent of signal attenuation corresponded with the temporal profile of the reported plasma concentration for the drug. No clear attenuation by morphine on the medial BA 10 response to innocuous stimuli was observed. These results provide further evidence for the role of medial BA 10 in the processing of pain, and also suggest that fNIRS may be used as an objective measure of drug-brain profiles independent of subjective reports

Electronic learning can facilitate student performance in undergraduate surgical education: a prospective observational study

BACKGROUND: Our institution recently introduced a novel internet accessible computer aided learning (iCAL) programme to complement existing surgical undergraduate teaching methods. On graduation of the first full cycle of undergraduate students to whom this resource was available we assessed the utility of this new teaching facility. METHOD: The computer programme prospectively records usage of the system on an individual user basis. We evaluated the utilisation of the web-based programme and its impact on class ranking changes from an entry-test evaluation to an exit examination in surgery. RESULTS: 74.4% of students were able to access iCAL from off-campus internet access. The majority of iCAL usage (64.6%) took place during working hours (08:00–18:00) with little usage on the weekend (21.1%). Working hours usage was positively associated with improvement in class rank (P = 0.025, n = 148) but out-of hours usage was not (P = 0.306). Usage during weekdays was associated with improved rank (P = 0.04), whereas weekend usage was not (P = 0.504). There were no significant differences in usage between genders (P = 0.3). Usage of the iCAL system was positively correlated with improvement in class rank from the entry to the exit examination (P = 0.046). Students with lower ranks on entry examination, were found to use the computer system more frequently (P = 0.01). CONCLUSION: Electronic learning complements traditional teaching methods in undergraduate surgical teaching. Its is more frequently used by students achieving lower class ranking with traditional teaching methods, and this usage is associated with improvements in class ranking