Minimal seeds for shear flow turbulence: using nonlinear transient growth to touch the edge of chaos

We propose a general strategy for determining the minimal finite amplitude isturbance to trigger transition to turbulence in shear flows. This involves constructing a variational problem that searches over all disturbances of fixed initial amplitude, which respect the boundary conditions, incompressibility and the Navier--Stokes equations, to maximise a chosen functional over an asymptotically long time period. The functional must be selected such that it identifies turbulent velocity fields by taking significantly enhanced values compared to those for laminar fields. We illustrate this approach using the ratio of the final to initial perturbation kinetic energies (energy growth) as the functional and the energy norm to measure amplitudes in the context of pipe flow. Our results indicate that the variational problem yields a smooth converged solution providing the amplitude is below the threshold amplitude for transition. This optimal is the nonlinear analogue of the well-studied (linear) transient growth optimal. At and above this threshold, the optimising search naturally seeks out disturbances that trigger turbulence by the end of the period, and convergence is then practically impossible. The first disturbance found to trigger turbulence as the amplitude is increased identifies the `minimal seed' for the given geometry and forcing (Reynolds number). We conjecture that it may be possible to select a functional such that the converged optimal below threshold smoothly converges to the minimal seed at threshold. This seems at least approximately true for our choice of energy growth functional and the pipe flow geometry chosen here.Comment: 27 pages, 19 figures, submitted to JF

Networks and the epidemiology of infectious disease

The science of networks has revolutionised research into the dynamics of interacting elements. It could be argued that epidemiology in particular has embraced the potential of network theory more than any other discipline. Here we review the growing body of research concerning the spread of infectious diseases on networks, focusing on the interplay between network theory and epidemiology. The review is split into four main sections, which examine: the types of network relevant to epidemiology; the multitude of ways these networks can be characterised; the statistical methods that can be applied to infer the epidemiological parameters on a realised network; and finally simulation and analytical methods to determine epidemic dynamics on a given network. Given the breadth of areas covered and the ever-expanding number of publications, a comprehensive review of all work is impossible. Instead, we provide a personalised overview into the areas of network epidemiology that have seen the greatest progress in recent years or have the greatest potential to provide novel insights. As such, considerable importance is placed on analytical approaches and statistical methods which are both rapidly expanding fields. Throughout this review we restrict our attention to epidemiological issues

Data Recovery Excavations at the Snakeskin Bluff Site (41GU177), Guadalupe County, Texas

On behalf of Central Texas Regional Water Supply Corporation (CTRWSC) and VRRSP Consultants, LLC, SWCA Environmental Consultants (SWCA) conducted archaeological data recovery excavations at multicomponent site 41GU177 (the Snakeskin Bluff Site) within the proposed alignment of the Vista Ridge Regional Water Supply Project (Vista Ridge) in Guadalupe County, Texas. Investigations were conducted in compliance with Section 106 of the National Historic Preservation Act (NHPA) (54 United States Code [USC] 306108) and its implementing regulations (36 Code of Federal Regulations [CFR] 800), in anticipation of a Nationwide Permit 12 from the U.S. Army Corps of Engineers (USACE) in accordance with Section 404 of the Clean Water Act. In addition, the work is subject to compliance with the Antiquities Code of Texas (ACT), as the Vista Ridge Project will be ultimately owned by CTRWSC, a political subdivision of the State of Texas. The Vista Ridge project will involve construction of an approximately 140-mile-long, 60-inch-diameter water pipeline from north-central San Antonio, Bexar County, to Deanville, Burleson County, Texas. The of area of potential effects (APE) for the Phase I survey efforts included the proposed centerline alignment and a 100-foot-wide corridor (50 feet on either side of centerline), as well as temporary and permanent construction easements, and aboveground facilities, such as pump stations and the northern and southern termini sites. Between June 2015 and March 2018 the cultural resources inventory identified 78 cultural resources (i.e., 64 archaeological sites and 14 isolated finds). Included in that inventory was site 41GU177, originally discovered on August 31, 2015 on the west bank of the Guadalupe River. Site 41GU177 is a stratified prehistoric site on the western high bank of the Guadalupe River southeast of New Braunfels, Texas near the community of McQueeney. The site contains components deposited intermittently from approximately the Late Archaic to Transitional Archaic periods through Late Prehistoric times. The primary components investigated in the excavations span the final Late Archaic period and into the Austin phase of the Late Prehistoric, a timeframe from approximately 2,600 to 900 years ago. The field investigations, conducted between October 2016 and December 2017, included intensive shovel testing, geomorphological study with mechanical excavations, and subsequent hand excavations. This report presents the results of the data recovery investigations conducted from November–December 2017. The survey results and testing results have been previously reported on (Acuña et al. 2016; Rodriguez et al. 2017); the testing results are also presented in Appendix A. SWCA’s work at 41GU177 was conducted under the ACT. The state regulations mandate the evaluation of the site’s eligibility for designation as a State Antiquities Landmark (SAL) or for listing on the National Register of Historic Places (NRHP). The survey and testing investigations were conducted under ACT Permit No. 7295, and the subsequent data recovery was completed under Permit No. 8231. Brandon S.Young served as initial Principal Investigator (PI) on both permits and Christina Nielsen took over asPI on the permits for the final reporting stages of the project. Overall, 34.1 m3 of sediment was excavated from the site during the data recovery through both traditional and feature-focused unit excavations. During these excavations, approximately 22 m2 of Late Prehistoric components were exposed, consisting of rock-lined hearths and 6,496 artifacts. The Late Prehistoric artifacts included Edwards points, Perdiz points, a Fresno point, ceramics, bifaces, an end scraper, a shell bead, various informal lithic tools, ground stone, choppers, debitage, and faunal remains. The Late Prehistoric component was approximately 40–80 cm thick. No cultural features were identified within the underlying Archaic components of the site; however, 3,421 artifacts were recovered including a Zephyr point, bifaces, ground stone, various informal lithic tools, choppers, debitage, and faunal remains. The Transitional Archaic component was approximately 35–60 cm thick; however, the underlying Archaic (and possible older) components were not defined. The excavations were limited to the right-of-way, and consequently the exposure afforded only a partial glimpse of the overall site. Based on the assemblage, the site is interpreted as a logistical base camp as indicated by both formal and informal tool forms and site furniture. Small groups exploited the abundance of lithic raw material and riparian zone resources, making forays into the landscape to hunt and forage. A total of four radiocarbon dates from the Late Prehistoric components reveal several short-term encampments over the course of several centuries from approximately 600 to 1200 B.P. (A.D. 750 to 1350). The Toyah Phase component has some noted disturbances (especially towards the ground surface), but good integrity from where the radiocarbon sample was collected. The Austin Phase component is vertically and horizontally discrete, contains a substantial amount of archaeological materials, and the site structure and radiocarbon dates suggests multiple, discrete occupations. The data recovery investigations at the Snakeskin Bluff site sought to address environmental, technological, chronological, and adaptive changes during the transition from Archaic to Late Prehistoric. As mentioned, the overall artifact and feature recovery at the site was low and disturbances and mixing of components was noted, especially within the upper deposits of the site. Disturbances within the Late Prehistoric Toyah Phase were most prevalent in the eastern portions of the site. The Late Prehistoric Austin Phase component contained intact, well-preserved archaeological deposits containing preserved flora and faunal material, cooking features, and diagnostic implements. The Transitional Archaic (and older) occupations were difficult to characterize, due to limited quantities of temporal diagnostic artifacts, lack of cultural features, and low artifact recovery. Despite these limitations, the data recovered from the cultural components show diachronic shifts between the technological and foraging strategies of the Archaic and Late Prehistoric. In concurrence with the 2016–2017 testing recommendations, the Snakeskin Bluff site is considered eligible for designation as an SAL and for the NRHP. Although not all cultural components of the site were stratigraphically discrete, the Late Prehistoric Austin Phase component revealed intact, well-preserved archaeological deposits that significantly contributed to our understanding of Late Prehistoric patterns. Given the sensitive nature of the cultural deposits at 41GU177, the main concern following the completion of data recovery excavations was the prevention of significant surface and subsurface impacts to the site during clearing and pipeline construction. As such, SWCA developed a site monitoring protocol; methods and results of the monitoring efforts are provided in Appendix H. Contributing components beyond the impact area will not be affected and will be preserved by avoidance; however, it is important to note that these investigations mitigated the project-specific effects, not the entire site. Any future project that could impact the site’s deeper deposits, or those beyond the current right-of-way, warrant further consideration to assess the possibilities for additional contributing components. With these considerations, no further work is recommended

Band gap reduction in GaNSb alloys due to the anion mismatch

The structural and optoelectronic properties in GaNxSb1–x alloys (0<=x<0.02) grown by molecular-beam epitaxy on both GaSb substrates and AlSb buffer layers on GaAs substrates are investigated. High-resolution x-ray diffraction (XRD) and reciprocal space mapping indicate that the GaNxSb1–x epilayers are of high crystalline quality and the alloy composition is found to be independent of substrate, for identical growth conditions. The band gap of the GaNSb alloys is found to decrease with increasing nitrogen content from absorption spectroscopy. Strain-induced band-gap shifts, Moss-Burstein effects, and band renormalization were ruled out by XRD and Hall measurements. The band-gap reduction is solely due to the substitution of dilute amounts of highly electronegative nitrogen for antimony, and is greater than observed in GaNAs with the same N content

An Extreme X-ray Disk Wind in the Black Hole Candidate IGR J17091-3624

{\it Chandra} spectroscopy of transient stellar-mass black holes in outburst has clearly revealed accretion disk winds in soft, disk--dominated states, in apparent anti-correlation with relativistic jets in low/hard states. These disk winds are observed to be highly ionized, dense, and to have typical velocities of $\sim$1000 km/s or less projected along our line of sight. Here, we present an analysis of two {\it Chandra} High Energy Transmission Grating spectra of the Galactic black hole candidate IGR J17091$-$3624 and contemporaneous EVLA radio observations, obtained in 2011. The second {\it Chandra} observation reveals an absorption line at 6.91$\pm$0.01 keV; associating this line with He-like Fe XXV requires a blue-shift of $9300^{+500}_{-400}$ km/s (0.03$c$, or the escape velocity at 1000 R$_{Schw}$). This projected outflow velocity is an order of magnitude higher than has previously been observed in stellar-mass black holes, and is broadly consistent with some of the fastest winds detected in active galactic nuclei. A potential feature at 7.32 keV, if due to Fe XXVI, would imply a velocity of $\sim 14600$ km/s (0.05$c$), but this putative feature is marginal. Photoionization modeling suggests that the accretion disk wind in IGR J17091$-$3624 may originate within 43,300 Schwarzschild radii of the black hole, and may be expelling more gas than accretes. The contemporaneous EVLA observations strongly indicate that jet activity was indeed quenched at the time of our {\it Chandra} observations. We discuss the results in the context of disk winds, jets, and basic accretion disk physics in accreting black hole systems.Comment: 6 pages, 2 figures, Accepted to ApJLetter

The REFOLD database: a tool for the optimization of protein expression and refolding

A large proportion of proteins expressed in Escherichia coli form inclusion bodies and thus require renaturation to attain a functional conformation for analysis. In this process, identifying and optimizing the refolding conditions and methodology is often rate limiting. In order to address this problem, we have developed REFOLD, a web-accessible relational database containing the published methods employed in the refolding of recombinant proteins. Currently, REFOLD contains >300 entries, which are heavily annotated such that the database can be searched via multiple parameters. We anticipate that REFOLD will continue to grow and eventually become a powerful tool for the optimization of protein renaturation. REFOLD is freely available at

Nutrient adequacy during weight loss interventions: a randomized study in women comparing the dietary intake in a meal replacement group with a traditional food group

<p>Abstract</p> <p>Background</p> <p>Safe and effective weight control strategies are needed to stem the current obesity epidemic. The objective of this one-year study was to document and compare the macronutrient and micronutrient levels in the foods chosen by women following two different weight reduction interventions.</p> <p>Methods</p> <p>Ninety-six generally healthy overweight or obese women (ages 25–50 years; BMI 25–35 kg/m²) were randomized into a Traditional Food group (TFG) or a Meal Replacement Group (MRG) incorporating 1–2 meal replacement drinks or bars per day. Both groups had an energy-restricted goal of 5400 kJ/day. Dietary intake data was obtained using 3-Day Food records kept by the subjects at baseline, 6 months and one-year. For more uniform comparisons between groups, each diet intervention consisted of 18 small group sessions led by the same Registered Dietitian.</p> <p>Results</p> <p>Weight loss for the 73% (n = 70) completing this one-year study was not significantly different between the groups, but was significantly different (p ≤ .05) within each group with a mean (± standard deviation) weight loss of -6.1 ± 6.7 kg (TFG, n = 35) vs -5.0 ± 4.9 kg (MRG, n = 35). Both groups had macronutrient (Carbohydrate:Protein:Fat) ratios that were within the ranges recommended (50:19:31, TFG vs 55:16:29, MRG). Their reported reduced energy intake was similar (5729 ± 1424 kJ, TFG vs 5993 ± 2016 kJ, MRG). There was an improved dietary intake pattern in both groups as indicated by decreased intake of saturated fat (≤ 10%), cholesterol (<200 mg/day), and sodium (< 2400 mg/day), with increased total servings/day of fruits and vegetables (4.0 ± 2.2, TFG vs 4.6 ± 3.2, MRG). However, the TFG had a significantly lower dietary intake of several vitamins and minerals compared to the MRG and was at greater risk for inadequate intake.</p> <p>Conclusion</p> <p>In this one-year university-based intervention, both dietitian-led groups successfully lost weight while improving overall dietary adequacy. The group incorporating fortified meal replacements tended to have a more adequate essential nutrient intake compared to the group following a more traditional food group diet. This study supports the need to incorporate fortified foods and/or dietary supplements while following an energy-restricted diet for weight loss.</p

Dynamics of 5-carboxylcytosine during hepatic differentiation: potential general role for active demethylation by DNA repair in lineage specification

Patterns of DNA methylation (5-methylcytosine, 5mC) are rearranged during differentiation contributing to the regulation of cell type-specific gene expression. TET proteins oxidise 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Both 5fC and 5caC can be recognised and excised from DNA by thymine-DNA glycosylase (TDG) followed by the subsequent incorporation of unmodified cytosine into the abasic site via the base excision repair (BER) pathway. We previously demonstrated that 5caC accumulates during lineage specification of neural stem cells (NSCs) suggesting that such active demethylation pathway is operative in this system, however it is still unknown if TDG/BER-dependent demethylation is utilised during other types of cellular differentiation. Here we analyse dynamics of the global levels of 5hmC and 5caC during differentiation of human pluripotent stem cells (hPSCs) towards hepatic endoderm. We show that, similar to differentiating NSCs, 5caC transiently accumulates during hepatic differentiation. The levels of 5caC increase during specification of foregut, peak at the stage of hepatic endoderm commitment and drop in differentiating cells concurrently with the onset of expression of Alpha Fetoprotein, a marker of committed hepatic progenitors. Moreover, we show that 5caC accumulates at promoter regions of several genes expressed during hepatic specification at differentiation stages corresponding to the commencement of their expression. Our data indicate that transient 5caC accumulation is a common feature of two different types (neural/glial and endoderm/hepatic) of cellular differentiation. This suggests that oxidation of 5mC may represent a general mechanism of rearrangement of 5mC profiles during lineage specification of somatic cells in mammals