Pattern formation with a conservation law

Pattern formation in systems with a conserved quantity is considered by studying the appropriate amplitude equations. The conservation law leads to a large-scale neutral mode that must be included in the asymptotic analysis for pattern formation near onset. Near a stationary bifurcation, the usual Ginzburg--Landau equation for the amplitude of the pattern is then coupled to an equation for the large-scale mode. These amplitude equations show that for certain parameters all roll-type solutions are unstable. This new instability differs from the Eckhaus instability in that it is amplitude-driven and is supercritical. Beyond the stability boundary, there exist stable stationary solutions in the form of strongly modulated patterns. The envelope of these modulations is calculated in terms of Jacobi elliptic functions and, away from the onset of modulation, is closely approximated by a sech profile. Numerical simulations indicate that as the modulation becomes more pronounced, the envelope broadens. A number of applications are considered, including convection with fixed-flux boundaries and convection in a magnetic field, resulting in new instabilities for these systems

Pattern formation with a conservation law

Pattern formation in systems with a conserved quantity is considered by studying the appropriate amplitude equations. The conservation law leads to a large-scale neutral mode that must be included in the asymptotic analysis for pattern formation near onset. Near a stationary bifurcation, the usual Ginzburg--Landau equation for the amplitude of the pattern is then coupled to an equation for the large-scale mode. These amplitude equations show that for certain parameters all roll-type solutions are unstable. This new instability differs from the Eckhaus instability in that it is amplitude-driven and is supercritical. Beyond the stability boundary, there exist stable stationary solutions in the form of strongly modulated patterns. The envelope of these modulations is calculated in terms of Jacobi elliptic functions and, away from the onset of modulation, is closely approximated by a sech profile. Numerical simulations indicate that as the modulation becomes more pronounced, the envelope broadens. A number of applications are considered, including convection with fixed-flux boundaries and convection in a magnetic field, resulting in new instabilities for these systems

Conformation of Polypyrimidine Tract Binding Protein in Solution

SummaryThe polypyrimidine tract binding protein (PTB) is an RNA binding protein that normally functions as a regulator of alternative splicing but can also be recruited to stimulate translation initiation by certain picornaviruses. High-resolution structures of the four RNA recognition motifs (RRMs) that make up PTB have previously been determined by NMR. Here, we have used small-angle X-ray scattering to determine the low-resolution structure of the entire protein. Scattering patterns from full-length PTB and deletion mutants containing all possible sequential combinations of the RRMs were collected. All constructs were found to be monomeric in solution. Ab initio analysis and rigid-body modeling utilizing the high-resolution models of the RRMs yielded a consistent low-resolution model of the spatial organization of domains in PTB. Domains 3 and 4 were found to be in close contact, whereas domains 2 and especially 1 had loose contacts with the rest of the protein

High resolution Late-glacial and early-Holocene summer air temperature records from Scotland inferred from Chironomid assemblages

Lateglacial and early-Holocene mean July air temperatures have been reconstructed, using a chironomid-based inference model, from lake-sediment sequences from Abernethy Forest, in the eastern Highlands of Scotland, and Loch Ashik, on the Isle of Skye in north-west Scotland. Chronology for Abernethy Forest was derived from radiocarbon dates of terrestrial plant macrofossils deposited in the lake sediments. Chronology for Loch Ashik was derived from tephra layers of known ages, the first age-depth model of this kind. Chironomid-inferred temperatures peak early in the Lateglacial Interstadial and then gradually decline by about 1 °C to the beginning of the Younger Dryas (YD). At Abernethy Forest, the Lateglacial Interstadial is punctuated by three centennial-scale cold oscillations which appear to be synchronous with the Greenland Interstadial events GI-1d, when temperatures at Abernethy fell by 5.9 °C, GI-1c, when temperatures fell by 2.3 °C, and GI-1b, when temperatures fell by 2.8 °C. At Loch Ashik only the oscillation correlated with GI-1d is clearly defined, when temperatures fell by 3.8 °C. The start of the YD is clearly marked at both sites when temperatures fell by 5.5 °C at Abernethy Forest and 2.8 °C at Loch Ashik. A warming trend is apparent during the late-YD at Abernethy Forest but at Loch Ashik late-YD temperatures became very cold, possibly influenced by its close proximity to the Skye ice-field. The rapidly rising temperatures at the YD – Holocene transition occur about 300 years earlier at both sites than changes in sediment lithology and loss-on-ignition. The temperature trends at both sites are broadly similar, although between-site differences may result from the influence of local factors. Similar climate trends are found at other sites in the northern British Isles. However, the British summer temperature records differ in detail from trends in the oxygen-isotope records from the Greenland ice-cores and from other chironomid-inferred temperature records available from Scandinavia, north-west Europe and central Europe, which suggest important differences in the influence of climatic forcing at regional scales.publishedVersio

The relationship between forest cover and diet quality:a case study of rural southern Malawi

Peer reviewedPublisher PD

Observations of Rapid Disk-Jet Interaction in the Microquasar GRS 1915+105

We present evidence that ~ 30 minute episodes of jet formation in the Galactic microquasar GRS 1915+105 may sometimes entirely be a superposition of smaller, faster phenomena. We base this conclusion on simultaneous X-ray and infrared observations in July 2002, using the Rossi X-ray Timing Explorer and the Palomar 5 meter telescope. On two nights, we observed quasi-periodic infrared flares from GRS 1915+105, each accompanied by a set of fast oscillations in the X-ray light curve (indicating an interaction between the jet and accretion disk). In contrast to similar observations in 1997, we find that the duration of each X-ray cycle matches the duration of its accompanying infrared flare, and we observed one instance in which an isolated X-ray oscillation occurred at the same time as a faint infrared "subflare" (of duration ~ 150 seconds) superimposed on one of the main flares. From these data, we are able to conclude that each X-ray oscillation had an associated faint infrared flare and that these flares blend together to form, and entirely comprise, the ~ 30 minute events we observed. Part of the infrared emission in 1997 also appears to be due to superimposed small flares, but it was overshadowed by infrared-bright ejections associated with the appearance of a sharp "trigger" spike in each X-ray cycle that were not present in 2002. We also study the evolution of the X-ray spectrum and find significant differences in the high energy power law component, which was strongly variable in 1997 but not in 2002. Taken together, these observations reveal the diversity of ways in which the accretion disk and jet in black hole systems are capable of interacting and solidify the importance of the trigger spike for large ejections to occur on ~ 30 minute timescales in GRS 1915+105.Comment: 17 pages, 9 figures; accepted for publication in The Astrophysical Journa

The PDK1-Rsk signaling pathway controls Langerhans cell proliferation and patterning

Langerhans cells (LC), the dendritic cells of the epidermis, are distributed in a distinctive regularly spaced array. In the mouse, the LC array is established in the first few days of life from proliferating local precursors, but the regulating signaling pathways are not fully understood. We found that mice lacking the kinase phosphoinositide-dependent kinase 1 selectively lack LC. Deletion of the phosphoinositide-dependent kinase 1 target kinases, ribosomal S6 kinase 1 (Rsk1) and Rsk2, produced a striking perturbation in the LC network: LC density was reduced 2-fold, but LC size was increased by the same magnitude. Reduced LC numbers in Rsk1/2?/? mice was not due to accelerated emigration from the skin but rather to reduced proliferation at least in adults. Rsk1/2 were required for normal LC patterning in neonates, but not when LC were ablated in adults and replaced by bone marrow–derived cells. Increased LC size was an intrinsic response to reduced LC numbers, reversible on LC emigration, and could be observed in wild type epidermis where LC size also correlated inversely with LC density. Our results identify a key signaling pathway needed to establish a normal LC network and suggest that LC might maintain epidermal surveillance by increasing their “footprint” when their numbers are limite

On the Use of Neural Text Generation for the Task of Optical Character Recognition

Optical Character Recognition (OCR), is extraction of textual data from scanned text documents to facilitate their indexing, searching, editing and to reduce storage space. Although OCR systems have improved significantly in recent years, they still suffer in situations where the OCR output does not match the text in the original document. Deep learning models have contributed positively to many problems but their full potential to many other problems are yet to be explored. In this paper we propose a post-processing approach based on the application deep learning to improve the accuracy of OCR system (minimizing the error rate).We report on the use of neural network language models to accomplish the task of correcting incorrectly predicted characters/words by OCR systems. We applied our approach to the IAM handwriting database. Our proposed approach delivers significant accuracy improvement of 20:41% in F-score, 10:86% in character level comparison using Levenshtein distance and 20:69% in document level comparison over previously reported context based OCR empirical results of IAM handwriting database

Sleep duration partially accounts for race differences in diurnal cortisol dynamics

Objective: Emerging research demonstrates race differences in diurnal cortisol slope, an indicator of hypothalamic-pituitary-adrenocortical (HPA)-axis functioning associated with morbidity and mortality, with African Americans showing flatter diurnal slopes than their White counterparts. Sleep characteristics are associated with both race and with HPA-axis functioning. The present report examines whether sleep duration may account for race differences in cortisol dynamics. Method: Participants were 424 employed African American and White adults (mean age = 42.8 years, 84.2% White, 53.6% female) with no cardiovascular disease (Adult Health and Behavior Project—Phase 2 [AHAB-II] cohort, University of Pittsburgh). Cortisol slope was calculated using 4 salivary cortisol readings, averaged over each of 4 days. Demographic (age, sex), psychosocial (socioeconomic status [SES], affect, discrimination), and health behaviors (smoking, alcohol use, physical activity) variables were used as covariates, and sleep (self-report and accelerometry) was also assessed. Results: African Americans had flatter slopes than Whites (F(1, 411) = 10.45, B = .02, p = .001) in models adjusting for demographic, psychosocial, and health behavior covariates. Shorter actigraphy-assessed total sleep time was a second significant predictor of flatter cortisol slopes (F(1, 411) = 25.27, B = −.0002, p \u3c .0001). Total sleep time partially accounted for the relationship between race and diurnal slope [confidence interval = .05 (lower = .014, upper .04)]. Conclusions: African Americans have flatter diurnal cortisol slopes than their White counterparts, an effect that may be partially attributable to race differences in nightly sleep duration. Sleep parameters should be considered in further research on race and cortisol. (PsycINFO Database Record (c) 2017 APA, all rights reserved

A non-canonical scaffold-type E3 ligase complex mediates protein UFMylation

Protein UFMylation, i.e., post‐translational modification with ubiquitin‐fold modifier 1 (UFM1), is essential for cellular and endoplasmic reticulum homeostasis. Despite its biological importance, we have a poor understanding of how UFM1 is conjugated onto substrates. Here, we use a rebuilding approach to define the minimal requirements of protein UFMylation. We find that the reported cognate E3 ligase UFL1 is inactive on its own and instead requires the adaptor protein UFBP1 to form an active E3 ligase complex. Structure predictions suggest the UFL1/UFBP1 complex to be made up of winged helix (WH) domain repeats. We show that UFL1/UFBP1 utilizes a scaffold‐type E3 ligase mechanism that activates the UFM1‐conjugating E2 enzyme, UFC1, for aminolysis. Further, we characterize a second adaptor protein CDK5RAP3 that binds to and forms an integral part of the ligase complex. Unexpectedly, we find that CDK5RAP3 inhibits UFL1/UFBP1 ligase activity in vitro. Results from reconstituting ribosome UFMylation suggest that CDK5RAP3 functions as a substrate adaptor that directs UFMylation to the ribosomal protein RPL26. In summary, our reconstitution approach reveals the biochemical basis of UFMylation and regulatory principles of this atypical E3 ligase complex