Miracle-dz/UniFAR-FTUs huggingface dataset:
2 Protein Folding on Computational Desktop Grid 2 . 1 Protein Folding with CHARMM

CHARMM is a popularmoleculardynamicscodefor computationalbiology. For many CHARMM applicationssuchasproteinfolding, desktopgridscouldbecomeviablealternati vesto clustersof PCs. In this technicalreport,we presenta prototypeanddiscussthe viability of a protein folding application with CHARMM on the United DevicesMetaProcessor , a platform for widely distributedcomputing. We identify thealgorithmicapproachof proteinfolding asa hybrid searchalgorithmwith best-first,depth-first andbreadth-firstcomponentsandaddresstheissuesof taskschedulingandfault tolerance. Theperformanceevaluationof our systemindicatesthat thecalculationis robustagainsttheheterogeneity of computenodesandlimited communicationcapabilitiestypically found in desktopgrids. We show that thereis aninterestingtradeof betweenaccuracy andtaskparallelismresultingin optimalwork-poolsizefor agivenplatformandagivensimulation.Surprisinglytheplatformheterogeneityof adesktopgrid positively affectsthequality of proteinfolding simulations. Proteinfolding calculationswith CHARMM turn out to be well suitablefor desktopgrids like e.g. the United Devices MetaProcessor . Our software systemcan make a large amountof nearly free compute cyclesavailableto computational biologists.
Multidrug-Resistant Acinetobacter baumannii in Veterinary Clinics, Germany

An increase in prevalence of multidrug-resistant Acinetobacter spp. in hospitalized animals was observed at the Justus-Liebig-University (Germany). Genotypic analysis of 56 isolates during 2000–2008 showed 3 clusters that corresponded to European clones I–III. Results indicate spread of genotypically related strains within and among veterinary clinics in Germany.
Multidrug Resistant Acinetobacter baumannii Biofilms: Evaluation of Phenotypic–Genotypic Association and Susceptibility to Cinnamic and Gallic Acids

Acinetobacter baumannii armed with multidrug resistance (MDR) and biofilm-forming ability is increasingly recognized as an alarming pathogen. A deeper comprehension of the correlation between these two armories is required in circumventing its infections. This study examined the biofilm-forming ability of the isolates by crystal violet staining and the antibiotic susceptibility by broth microdilution method. The genetic basis of the MDR and biofilm-forming phenotypes was screened by polymerase chain reaction. The antimicrobial activities of cinnamic and gallic acids against planktonic cells and biofilms of A. baumannii were investigated, and the findings were confirmed with scanning electron microscopy (SEM). Among 90 A. baumannii isolates, 69 (76.6%) were MDR, and all were biofilm formers; they were classified into weak (12.2%), moderate (53.3%), and strong (34.5%) biofilm formers. Our results underlined a significant association between MDR and enhanced biofilm formation. Genotypically, the presence of blaVIM and blaOXA–23 genes along with biofilm-related genes (ompA, bap, and csuE) was statistically associated with the biofilm-forming abilities. Impressively, both gallic and cinnamic acids could significantly reduce the MDR A. baumannii biofilms with variable degrees dependent on the phenotype–genotype characteristics of the tested isolates. The current findings may possess future therapeutic impact through augmenting antimicrobial arsenal against life-threatening infections with MDR A. baumannii biofilms.
The impact of the 1996 floods on a tidal sand bank in the Knysna estuary, Western Cape : research in action

We report on the cumulative effect of three flood events during October and November 1996, their impact on the intertidal banks of the Salt River estuary and on a single bank in the Knysna middle estuary (19lsupgol/supg01'E; 34 o 04'S) upstream of the railway bridge.We found that where land-derived, medium-to-fine coversand did not exceed 0.03 m, the invertebrate fauna survived and recovered within two years. Burial to a depth of 0.20 m, also over a pre-existing marine bank, affected the fauna so that only 42% of the original numbers were present after two years. At a site 100 m southwest of the other location, where 0.40-0.50 m of land sediment had accumulated over a bank not previously exposed even at neap low tide, only 6.7% of the pre-flood faunal population was evident. Upogebia africanal/Ig (mud prawn), once common on the bank, was absent; Callianassa krausil/Ig (sand prawn) was the only prawn present.
MCCIP Ecosystem Linkages Report Card 2009 Marine non-native species

1 Marine Institute, University of Plymouth, Drake Circus, Plymouth PL4 8AA 2 Sir Alister Hardy Foundation for Ocean Science, The Laboratory, Citadel Hill, The Hoe, Plymouth, PL1 2PB 3 Marine Biological Association, The Laboratory, Citadel Hill, The Hoe, Plymouth, PL1 2PB 4 Ecology Department, Scottish Association for Marine Science (SAMS), Dunstaffnage Marine Laboratory, Oban, Argyll, PA37 1QA 5 Marine Organism Investigations, 3 Marina Village, Ballina, Killaloe, Co Clare, Ireland. 6 FRS Marine Laboratory, PO Box 101, 375 Victoria Road, Aberdeen, AB11 9DB
The Depth of Negative Equity and Mortgage Default Decisions

A central question in the literature on mortgage default is at what point underwater homeowners walk away from their homes even if they can afford to pay. We study borrowers from Arizona, California, Florida, and Nevada who purchased homes in 2006 using non-prime mortgages with 100 percent financing. Almost 80 percent of these borrowers default by the end of the observation period in September 2009. After distinguishing between defaults induced by job losses and other income shocks from those induced purely by negative equity, we find that the median borrower does not strategically default until equity falls to -62 percent of their home's value. This result suggests that borrowers face high default and transaction costs. Our estimates show that about 80 percent of defaults in our sample are the result of income shocks combined with negative equity. However, when equity falls below -50 percent, half of the defaults are driven purely by negative equity. Therefore, our findings lend support to both the "double-trigger" theory of default and the view that mortgage borrowers exercise the implicit put option when it is in their interest.
A finite volume scheme for a Keller–Segel model with additional cross-diffusion

A finite volume scheme for the (Patlak-) Keller-Segel model in two space dimensions with an additional cross-diffusion term in the elliptic equation for the chemical signal is analyzed. The main feature of the model is that there exists a new entropy functional yielding gradient estimates for the cell density and chemical concentration. The main features of the numerical scheme are positivity preservation, mass conservation, entropy stability, and—under additional assumptions—entropy dissipation. The existence of a discrete solution and its numerical convergence to the continuous solution is proved. Furthermore, temporal decay rates for convergence of the discrete solution to the homogeneous steady state is shown using a new discrete logarithmic Sobolev inequality. Numerical examples point out that the solutions exhibit intermediate states and that there exist nonhomogeneous stationary solutions with a finite cell density peak at the domain boundary.
Distributed application configuration, management, and visualization with plush

Support for distributed application management in large-scale networked environments remains in its early stages. Although a number of solutions exist for subtasks of application deployment, monitoring, and maintenance in distributed environments, few tools provide a unified framework for application management. Many of the existing tools address the management needs of a single type of application or service that runs in a specific environment, and these tools are not adaptable enough to be used for other applications or platforms. To this end, we present the design and implementation of Plush, a fully configurable application management infrastructure designed to meet the general requirements of several different classes of distributed applications. Plush allows developers to specifically define the flow of control needed by their computations using application building blocks. Through an extensible resource management interface, Plush supports execution in a variety of environments, including both live deployment platforms and emulated clusters. Plush also uses relaxed synchronization primitives for improving fault tolerance and liveness in failure-prone environments. To gain an understanding of how Plush manages different classes of distributed applications, we take a closer look at specific applications and evaluate how Plush provides support for each.
Implementation of process-integrated waste gas cleaning using activated Lignite

Numerous investigations made during the last few years have substantially extended the knowledge of environmental pollutants and their impact on Nature and Man. This knowledge and the growing environmental awareness of the population have caused environmental requirements to be constantly tightened and legislation introduced to prescribe lower emission limits. It is in particular the emissions of toxic organic compounds such as polychlorinated dioxins and furans as well as heavy metals which have been gaining importance in the industrial countries worldwide due to the increasing amounts of residues being incinerated and the application of recycling processes. Since primary measures alone do not permit sufficient reduction in emissions, additional cleaning systems have to be installed. In this context, process solutions are being sought which allow the gases to be cleaned in a technically efficient and inexpensive way. A cleaning measure covering all emission-relevant pollutants is adsorption using carbon-containing adsorbents such as activated lignite or activated carbon which are comparatively easy to integrate into dedusting, scrubbing and absorption processes. By contrast with adsorption in separate waste gas cleaning processes, which has been common practice to date, and thanks to extensive investigations and plant optimisations, entrained-phase adsorption can now be operated as a process-integrated low-cost and highly efficient technology. The latter can as a rule be confined to the simple injection of pulverised sorbents into the raw gas flow of existing dedusting units. For some years, process-integrated adsorption by means of activated lignite has been state of the art and has been successfully implemented in the most varied applications. Different systems are taken as an example to illustrate that the adsorption of emission-relevant pollutants dioxins, furans and heavy metals using activated lignite in an entrained-dust cloud with downstream dedusting units, such as fabric filters, electrostatic precipitators and scrubbers, is a technically efficient and at the same time reasonably priced emission reduction technology. With a production capacity of 200,000 t/a, RWE Power AG, Germany, is Europe's biggest producer of activated lignite for the adsorptive cleaning of furnace waste gases. RWE Power is the market leader for these applications in Europe. The reason for this is the low-priced production of this activated lignite as a mass product in large quantities which has at the same time good adsorption properties comparable with those of high-grade activated carbon. This activated lignite is produced in four grain sizes and can be supplied for any possible adsorption technique. Around the world approx. 500 systems are operating with activated lignite for waste gas cleaning.
Testing Sediment Connectivity at the Experimental SPA2 Basin, Sicily (Italy)

The concept of sediment delivery can be used as a measure of sediment connectivity, and it can be linked to the structural connectivity (morphological unit, slope length, slope steepness, travel time) of a basin and to the hydrological connectivity (rainfall–runoff processes at morphological unit scale). In this paper, the sediment connectivity concept was tested at basin scale applying SEdiment Delivery Distributed model, which takes into account the hillslope sediment transport, and using sediment yield measurements carried out at SPA2 experimental basin (Sicily, Italy). For the SPA2 basin discretized into morphological units, the SEdiment Delivery Distributed model was first calibrated at event scale using the sediment yield measurements carried out at the outlet of the experimental basin in the period April 2000–March 2015. The model calibration was used to determine the relationships useful for estimating the unique coefficient βe of the model appearing in the expression used to calculate the sediment delivery ratio of each morphological unit. The developed analysis allowed establishing that the functional connectivity is dependent on the magnitude of erosion events, and for low events the sediment connectivity is only governed by its structural component. Then, at annual scale, the model was calibrated for the period 2000–2015, and relationships for the estimate of the coefficient βa taking into account the intensity of erosion events occurring in each year were determined. Finally, a physical interpretation of β coefficient at the two temporal scales (βe, βa) and its link to sediment connectivity was proposed. Copyright © 2017 John Wiley & Sons, Ltd.
Mineralogy of some foraminifera as related to their classification and ecology

Evidence from previous and present studies indicates that the mineralogical nature of secreted calcareous shells of Foraminifera is principally a genetic characteristic. Mineral content is probably affected, but not determined entirely, by environmental influences. Most genera are wholly calcitic. Relatively few genera are wholly aragonitic and they probably belong to two closely related families. X-ray diffraction studies of 131 genera, having calcareous shells, in 29 families of Recent Foraminifera have shown varying amounts of Mg substitution for Ca in their shells. Certain of the calcitic shells are consistently characterized by low Mg content (0-5 mol % MgCO 3 [or 0-4.3 weight %) and others consistently characterized by high Mg content (10 mol % or higher MgCO 3 [8.6 weight %]); relatively few fall into the intermediate group. A natural division of the genera of Foraminifera, related to Mg content, is indicated. With certain few exceptions, calcitic genera whose shells have high Mg content are restricted to twelve families and those whose shells have low Mg content are restricted to ten other families. Two families seem to belong in an intermediate group. Shells from two families are aragonitic in nature, hence are very low (
Wave Power Resource Investigations in New Zealand

Electricorp Production is funding a resource Investigation to determine the feasibility of using wave power to generate electricity. At least four different wave generation systems are commercially available. The New Zealand wave power Is greatest south of the South Island where estimates predict the average wave power will exceed 100 kW/m. Electricorp Production has founded the deployment of a wave rider buoy off the south of the South Island to measure the wave resource In detail. This buoy was deployed In February 1989 for about one year in a depth of about 100m and about 30 km off the coast. Land based microseismic recordings are processed and related to the wave energy (In particular the swell).
Amniotic Fluid Embolism

Amniotic fluid embolism is one of the most catastrophic complications of pregnancy. First described in 1941, the condition is exceedingly rare and the exact pathophysiology is still unknown. The etiology was thought to be embolic in nature, but more recent evidence suggests an immunologic basis. Common presenting symptoms include dyspnea, nonreassuring fetal status, hypotension, seizures, and disseminated intravascular coagulation. Early recognition of amniotic fluid embolism is critical to a successful outcome. However, despite intensive resuscitation, outcomes are frequently poor for both infant and mother. Recently, aggressive and successful management of amniotic fluid embolism with recombinant factor VIIa and a ventricular assist device, inhaled nitric oxide, cardiopulmonary bypass and intraaortic balloon pump with extracorporeal membrane oxygenation have been reported and should be considered in select cases.
Construction and characterization of a bacterial artificial chromosome library of Sorghum bicolor.

The construction of representative large insert DNA libraries is critical for the analysis of complex genomes. The predominant vector system for such work is the yeast artificial chromosome (YAC) system. Despite the success of YACs, many problems have been described including: chimerism, tedious steps in library construction and low yields of YAC insert DNA. Recently a new E.coli based system has been developed, the bacterial artificial chromosome (BAC) system, which offers many potential advantages over YACs. We tested the BAC system in plants by constructing an ordered 13,440 clone sorghum BAC library. The library has a combined average insert size, from single and double size selections, of 157 kb. Sorghum inserts of up to 315 kb were isolated and shown to be stable when grown for over 100 generations in liquid media. No chimeric clones were detected as determined by fluorescence in situ hybridization of ten BAC clones to metaphase and interphase S.bicolor nuclei. The library was screened with six sorghum probes and three maize probes and all but one sorghum probe hybridized to at least one BAC clone in the library. To facilitate chromosome walking with the BAC system, methods were developed to isolate the proximal ends of restriction fragments inserted into the BAC vector and used to isolate both the left and right ends of six randomly selected BAC clones. These results demonstrate that the S. bicolor BAC library will be useful for several physical mapping and map-based cloning applications not only in sorghum but other related cereal genomes, such as maize. Furthermore, we conclude that the BAC system is suitable for most large genome applications, is more 'user friendly' than the YAC system, and will likely lead to rapid progress in cloning biologically significant genes from plants.
Gain Enhancement for Circularly Polarized SIW Frequency Beam Scanning Antenna Using a Phase-Correcting Grating Cover

A planar circularly polarized (CP) frequency beam scanning Fabry–Perot resonator antenna (FPRA) with enhanced gain property is presented in this paper. The antenna consists of two layers. The CP substrate integrated waveguide (SIW) beam scanning leaky-wave antenna (LWA) is used as the feeding antenna. It provides good impedance matching and stable radiation pattern over the working band. Then, partially reflecting surface (PRS) layer is introduced to improve the gain property by using a single substrate with metal patches array printed on both top and bottom surfaces. After comparisons among four patch types, circular patch type is chosen. It is an ideal choice for CP antenna because of its completely symmetrical structure along $\varphi $ -plane and gentler phase slope. Parameter analysis is made for better understanding of the working principle. Finally, the antenna is fabricated and measured for verification. It shows that the main beam scans from −38° to 28° within the operating frequency band from 9.1 to 14.6 GHz (or 47.8%). The 3-dB axial ratio (AR) bandwidth is from 10.2 to 13.5 GHz (or 28.7%). Maximum gain is 14.6 dBic, and 3-dB gain bandwidth is from 11 to 14 GHz (or 26.1%). Gain enhancement of about 3.3 ~ 6 dB is achieved, compared with the unloaded type. Due to the advantages of high gain, CP beam-scanning capability, and easy fabrication, this method is a good option to design antennas in wireless communication and radar systems.
Proceedings of the 13th International Conference on Extending Database Technology

The papers in this volume were presented at the 13th International Conference on Extending Database Technology (EDBT 2010), held in Lausanne, Switzerland, March 22--26, 2010. Starting last year, EDBT is held jointly with the ICDT (International Conference on Database Theory) conference. This year, the conference research track received a total of 307 submissions, out of which 54 were accepted. This amounts to an acceptance rate of about 18 %, confirming the reputation of the EDBT conference as being quite selective! The program committee consisted of 75 members, leading to 12--13 articles to be reviewed by each PC member. While such load is not per se inconsistent with previous editions of EDBT or other prestigious conferences such as, e.g., SIGMOD or VLDB, some reviewers found this quite a heavy load, and significant care had to be taken to ensure appropriate external reviewers or load re-balancing. The submissions were thoroughly discussed, typically as soon as three reviews were available for the paper, even if this was before the review submission deadline; overall, 444 comments were exchanged through the electronic submission tool (EasyChair). The chair is particularly grateful to the PC members which have taken the time to carefully consider papers and debate each other's arguments. Given the high number of interesting submissions, the PC has worked with the chair to select the best submissions, and did not consider issues such as the overall balance of various database research areas in the conference program. Thus, the proceedings you are holding now reflect the best and most interesting works submitted to our conference, and you can consider the way they split over various topics as a snapshot of the state of our research community as of September 2009.
The role of mannose receptor during experimental leishmaniasis

The primary host cells for Leishmania replication are macrophages (MP). Several molecules on the surface of professional phagocytic cells have been implicated in the initial process of parasite internalization and initiation of signaling pathways. These pattern recognition receptors distinguish molecular patterns on pathogen surfaces. Mannose receptor (MR), specifically, recognizes mannose residues on the surface of Leishmania parasites. We studied the role of MR in the pathogenesis of experimental cutaneous and visceral leishmaniasis using MR‐deficient [MR‐knockout (KO)] C57BL/6 mice. MR‐deficient MP exhibied a comparable infection rate and cytokine production. In the absence of MR, the clinical course of Leishmania major and Leishmania donovani infections was similar in MR‐KO and wild‐type mice (MR‐WT). Furthermore, immunohistochemistry of cutaneous lesions from MR‐KO and MR‐WT mice revealed no differences in lesion architecture or cell components. Inhibition of MP responses is a hallmark of Leishmania infection; our data demonstrate further that host MR is not essential for blocking IFN‐γ/LPS‐induced IL‐12 production and MAPK activation by Leishmania. Thus, we conclude that the MR is not essential for host defense against Leishmania infection or regulation of IL‐12 production.