Nonlinear forecasting of the generalised Kuramoto-Sivashinsky equation

We study the emergence of pattern formation and chaotic dynamics in the one-dimensional (1D) generalized Kuramoto-Sivashinsky (gKS) equation by means of a time-series analysis, in particular a nonlinear forecasting method which is based on concepts from chaos theory and appropriate statistical methods. We analyze two types of temporal signals, a local one and a global one, finding in both cases that the dynamical state of the gKS solution undergoes a transition from high dimensional chaos to periodic pulsed oscillations through low dimensional deterministic chaos with increasing the control parameter of the system. Our results demonstrate that the proposed nonlinear forecasting methodology allows to elucidate the dynamics of the system in terms of its predictability properties

Flatness-based feed-forward control of an HVDC power transmission network

Abstract-An efficient and well-established technology for power transmission across long distances is high voltage direct current transmission (HVDC). However, HVDC is up to now almost completely limited to peer-to-peer connections or networks with peers situated closely to each other. This contribution introduces the flatness-based design of a feedforward control of tree-like, i.e. cycle-free, HVDC transmission networks comprising two or more converter stations. The resulting control concept allows a flexible determination of the power distribution within the network. Furthermore, effects like power losses and delays due to wave propagation, which are related especially to long transmission lines, can be easily taken into account. Numerical simulations for an example network are included to prove the value of the results

Sidescan Sonar Image, Surficial Geologic Interpretation, and Bathymetry of the Long Island Sound Sea Floor off Hammonasset Beach State Park, Connecticut

Ongoing research by the U.S. Geological Survey (USGS) in Long Island Sound, a major East Coast estuary surrounded by the most densely populated region of the United States, is building upon cooperative research with the State of Connecticut that was initiated in 1982. During the initial phase of this cooperative program, geologic framework studies in Long Island Sound were completed and results published (Lewis and Needell, 1987; Needell and others, 1987; Lewis and Stone, 1991). Emphasis of the present program in Long Island Sound is shifting from framework studies toward studies of the sediment distribution, processes that control this sediment distribution, nearshore environmental concerns, and the relation of benthic community structures to the sea-floor geology. Because of the enormous surrounding population, large inputs of anthropogenic wastes (e.g., fertilizer and sewage) and toxic chemicals have produced stresses on the environment of the Sound, causing degradation and potential loss of benthic habitats (Long Island Sound Study, 1994). To examine this problem, we are constructing sidescan sonar mosaics (complete-coverage acoustic images) of the sea floor within areas of special interest, such as in areas affected by seasonal hypoxia like the Norwalk survey or near major coastal resources like the Hammonasset Beach survey (fig.1). The mosaic that we have constructed off Hammonasset Beach State Park and which is presented herein allows insight into the geological variability of the sea floor, which is one of the primary controls of benthic habitat diversity. It also provides a detailed framework for future research, monitoring, and management activities, and it improves our understanding of the complex processes that control the distribution of bottom sediments, benthic habitats, and associated infaunal community structures off one of the most significant coastal recreational facilities within the State of Connecticut. Because precise information on environmental setting is important to the selection of sampling sites and to the accurate interpretation of point measurements, the sidescan sonar mosaics also act as base maps for subsequent sedimentological, geochemical, and infaunal sampling and bottom photography

Hare: a file system for non-cache-coherent multicores

Hare is a new file system that provides a POSIX-like interface on multicore processors without cache coherence. Hare allows applications on different cores to share files, directories, and file descriptors. The challenge in designing Hare is to support the shared abstractions faithfully enough to run applications that run on traditional shared-memory operating systems, with few modifications, and to do so while scaling with an increasing number of cores. To achieve this goal, Hare must support features (such as shared file descriptors) that traditional network file systems don't support, as well as implement them in a way that scales (e.g., shard a directory across servers to allow concurrent operations in that directory). Hare achieves this goal through a combination of new protocols (including a 3-phase commit protocol to implement directory operations correctly and scalably) and leveraging properties of non-cache-coherent multiprocessors (e.g., atomic low-latency message delivery and shared DRAM). An evaluation on a 40-core machine demonstrates that Hare can run many challenging Linux applications (including a mail server and a Linux kernel build) with minimal or no modifications. The results also show these applications achieve good scalability on Hare, and that Hare's techniques are important to achieving scalability.Quanta Computer (Firm

Functional cardiac fibroblasts derived from human pluripotent stem cells via second heart field progenitors

Cardiac fibroblasts (CFs) play critical roles in heart development, homeostasis, and disease. The limited availability of human CFs from native heart impedes investigations of CF biology and their role in disease. Human pluripotent stem cells (hPSCs) provide a highly renewable and genetically defined cell source, but efficient methods to generate CFs from hPSCs have not been described. Here, we show differentiation of hPSCs using sequential modulation of Wnt and FGF signaling to generate second heart field progenitors that efficiently give rise to hPSC-CFs. The hPSC-CFs resemble native heart CFs in cell morphology, proliferation, gene expression, fibroblast marker expression, production of extracellular matrix and myofibroblast transformation induced by TGFβ1 and angiotensin II. Furthermore, hPSC-CFs exhibit a more embryonic phenotype when compared to fetal and adult primary human CFs. Co-culture of hPSC-CFs with hPSC-derived cardiomyocytes distinctly alters the electrophysiological properties of the cardiomyocytes compared to co-culture with dermal fibroblasts. The hPSC-CFs provide a powerful cell source for research, drug discovery, precision medicine, and therapeutic applications in cardiac regeneration.J.L.C. received funding from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior and Fundação de Amparo à Pesquisa do Distrito Federal. The work was funded by NIH R01 HL129798 (T.J.K.); NIH U01 HL134764 (T.J.K.); S10RR025644 (T.J.K.); and the UW Institute for Clinical and Translational Research, grant UL1TR000427, from the Clinical and Translational Science Award of the NCATS/NIH.S

The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods

A recent workshop entitled The Family Name as Socio-Cultural Feature and Genetic Metaphor: From Concepts to Methods was held in Paris in December 2010, sponsored by the French National Centre for Scientific Research (CNRS) and by the journal Human Biology. This workshop was intended to foster a debate on questions related to the family names and to compare different multidisciplinary approaches involving geneticists, historians, geographers, sociologists and social anthropologists. This collective paper presents a collection of selected communications

Cross-resistance to elvitegravir and dolutegravir in 502 patients failing on raltegravir: a French national study of raltegravir-experienced HIV-1-infected patients

OBJECTIVES: The objectives of this study were to determine the prevalence and patterns of resistance to integrase strand transfer inhibitors (INSTIs) in patients experiencing virological failure on raltegravir-based ART and the impact on susceptibility to INSTIs (raltegravir, elvitegravir and dolutegravir). PATIENTS AND METHODS: Data were collected from 502 treatment-experienced patients failing a raltegravir-containing regimen in a multicentre study. Reverse transcriptase, protease and integrase were sequenced at failure for each patient. INSTI resistance-associated mutations investigated were those included in the last ANRS genotypic algorithm (v23). RESULTS: Among the 502 patients, at failure, median baseline HIV-1 RNA (viral load) was 2.9 log10 copies/mL. Patients had been previously exposed to a median of five NRTIs, one NNRTI and three PIs. Seventy-one percent harboured HIV-1 subtype B and the most frequent non-B subtype was CRF02_AG (13.3%). The most frequent mutations observed were N155H/S (19.1%), Q148G/H/K/R (15.4%) and Y143C/G/H/R/S (6.7%). At failure, viruses were considered as fully susceptible to all INSTIs in 61.0% of cases, whilst 38.6% were considered as resistant to raltegravir, 34.9% to elvitegravir and 13.9% to dolutegravir. In the case of resistance to raltegravir, viruses were considered as susceptible to elvitegravir in 11% and to dolutegravir in 64% of cases. High HIV-1 viral load at failure (P < 0.001) and low genotypic sensitivity score of the associated treatment with raltegravir (P < 0.001) were associated with the presence of raltegravir-associated mutations at failure. Q148 mutations were selected more frequently in B subtypes versus non-B subtypes (P = 0.004). CONCLUSIONS: This study shows that a high proportion of viruses remain susceptible to dolutegravir in the case of failure on a raltegravir-containing regimen

Implementing a genomic data management system using iRODS in the Wellcome Trust Sanger Institute

<p>Abstract</p> <p>Background</p> <p>Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence data. A good data management system therefore needs to be implemented and integrated into the current WTSI infrastructure. Such a system enables good management of the IT infrastructure of the sequencing pipeline and allows biologists to track their data.</p> <p>Results</p> <p>We have chosen a data grid system, iRODS (Rule-Oriented Data management systems), to act as the data management system for the WTSI. iRODS provides a rule-based system management approach which makes data replication much easier and provides extra data protection. Unlike the metadata provided by traditional file systems, the metadata system of iRODS is comprehensive and allows users to customize their own application level metadata. Users and IT experts in the WTSI can then query the metadata to find and track data.</p> <p>The aim of this paper is to describe how we designed and used (from both system and user viewpoints) iRODS as a data management system. Details are given about the problems faced and the solutions found when iRODS was implemented. A simple use case describing how users within the WTSI use iRODS is also introduced.</p> <p>Conclusions</p> <p>iRODS has been implemented and works as the production system for the sequencing pipeline of the WTSI. Both biologists and IT experts can now track and manage data, which could not previously be achieved. This novel approach allows biologists to define their own metadata and query the genomic data using those metadata.</p

Late Pleistocene and Early Holocene Sea-Level History and Glacial Retreat Interpreted from Shell-Bearing Marine Deposits of Southeastern Alaska, USA

We leverage a data set of \u3e720 shell-bearing marine deposits throughout southeastern Alaska (USA) to develop updated relative sea-level curves that span the past ~14,000 yr. This data set includes site location, elevation, description when avail-able, and 436 14C ages, 45 of which are published here for the first time. Our sea-level curves suggest a peripheral forebulge developed west of the retreating Cordilleran Ice Sheet (CIS) margin between ca. 17,000 and 10,800 calibrated yr B.P. By 14,870 ± 630 to 12,820 ± 340 cal. yr B.P., CIS mar-gins had retreated from all of southeastern Alaska’s fjords, channels, and passages. At this time, isolated or stranded ice caps existed on the islands, with alpine or tidewater glaciers in many valleys. Paleoshorelines up to 25 m above sea level mark the maximum elevation of transgression in the southern portion of the study region, which was achieved by 11,000 ± 390 to 10,500 ± 420 cal. yr B.P. The presence of Pacific sardine (Sardinops sagax) and the abundance of charcoal in sediments that date between 11,000 ± 390 and 7630 ± 90 cal. yr B.P. suggest that both ocean and air temperatures in southeastern Alaska were relatively warm in the early Holocene. The sea-level and paleoenvironmental reconstruction presented here can inform future investigations into the glacial, volcanic, and archaeological history of southeastern Alaska