bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of the Meshing of Trochoidal Profiles With Clearances
Authors: Ivanović Lozica , Devedžić Goran , Ćuković Saša , Mirić Nenad
Published: March 2012

This paper explains development of the general mathematical model of trochoidal gearing that can be applied for gerotor pumps and cyclo reducers. The model analyzes geometry and physics of the gearing pair in trochoidal pump where the outer gear has one tooth more than the inner gear. The inner gear profile is described by peritrochoid equidistance and the outer gear profile by circular arc. Mathematical model of gearing with clearances is based on the principle of an ideal profile development. Minimum clearance height between teeth profiles in relation to instantaneous gear ratio is determined. The influence of gear profile geometrical parameters on gearing process, clearance height change, and pulsation of drive moment is analyzed and presented in numerical examples. Obtained results can be used for the design of the trochoidal gearing where accurate and silent operation is required.
Impact of Layered Soil on Foundation Heat Transfer for Slab-On Grade Floors
Authors: Khaled Nizar , Rouissi Khaled , Krarti Moncef
Published: March 2012

This paper presents an analytical solution associated with the steady-periodic heat transfer for a typical slab-on-grade floor building foundation in contact with a nonhomogeneous soil medium. In particular, the solution accounts for the impact of the above-grade wall thickness on the ground-coupled heat transfer. The interzone temperature estimation profile (ITPE) technique is utilized to obtain the analytical solution to determine soil temperature distributions and to estimate foundation heat loss/gain from slab-on-grade floors. In this paper, the impact of the nonhomogeneous soil properties on the transient foundation heat transfer is investigated for various slab configurations and soil thermal properties. The presented solution presents the first ITPE analytical solution for building foundation coupled with layered soil medium. The results indicate that nonhomogeneous soil properties have a significant effect on soil temperature distribution and on total slab heat loss. In particular, it is found that an error of up to 20% in estimating total slab heat transfer can be incurred if homogeneous soil medium is considered instead of a two-layered ground.
Radiative Heat Transfer Analysis in Plasmonic Nanofluids for Direct Solar Thermal Absorption
Authors: Lee Bong Jae , Park Keunhan , Walsh Timothy , Xu Lina
Published: March 2012

The present study reports a novel concept of a direct solar thermal collector that harnesses the localized surface plasmon of metallic nanoparticles suspended in water. At the plasmon resonance frequency, the absorption and scattering from the nanoparticle can be greatly enhanced via the coupling of the incident radiation with the collective motion of electrons in metal. However, the surface plasmon induces strong absorption with a sharp peak due to its resonant nature, which is not desirable for broad-band solar absorption. In order to achieve the broad-band absorption, we propose a direct solar thermal collector that has four types of gold-nanoshell particles blended in the aquatic solution. Numerical simulations based on the Monte Carlo algorithm and finite element analysis have shown that the use of blended plasmonic nanofluids can significantly enhance the solar collector efficiency with an extremely low particle concentration (e.g., approximately 70% for a 0.05% particle volume fraction). The low particle concentration ensures that nanoparticles do not significantly alter the flow characteristics of nanofluids inside the solar collector. The results obtained from this study will facilitate the development of highly efficient solar thermal collectors using plasmonic nanofluids.
A Novel Lens-Walled Compound Parabolic Concentrator for Photovoltaic Applications
Authors: Su Yuehong , Pei Gang , Riffat Saffa B. , Huang Hulin
Published: March 2012

A compound parabolic concentrator (CPC) is a nonimaging concentrator that can concentrate solar radiation coming within its acceptance angle. A low concentration CPC photovoltaic system has the advantages of reduced Photovoltaics (PVs) cell size, increased efficiency and stationary operation. The acceptance angle of a CPC is associated with its geometrical concentration ratio, by which the size of PV cell could be reduced. Truncation is a way to increase the actual acceptance angle of a mirror CPC, but it also reduces the geometrical concentration ratio. On the other hand, a solid dielectric CPC can have a much larger acceptance angle, but it has a larger weight. To overcome these drawbacks, this study presents a novel lens-walled CPC that has a thin lens attached to the inside of a common mirror CPC or has the lens to be mirror coated on its outside surface. The shape of the lens is formed by rotating the parabolic curves of a CPC by a small degree internally around the top end points of the curves. The refraction of the lens allows the lens-walled CPC to concentrate light from wider incidence angle. The commercial optical analysis software PHOTOPIA is used to verify the principle of the presented lens-walled CPC and examine its optical performance against the common CPCs. As an example, the simulation is aimed to evaluate whether a lens-walled CPC with a geometrical concentration ratio of 4 has any advantage over a common CPC with a geometrical concentration ratio of 2.5 in terms of actual acceptance angle, optical efficiency and optical concentration ratio.
An Improved Coefficient Calculator for the California Energy Commission 6 Parameter Photovoltaic Module Model
Authors: Dobos Aron P.
Published: March 2012

This paper describes an improved algorithm for calculating the six parameters required by the California Energy Commission (CEC) photovoltaic (PV) Calculator module model. Rebate applications in California require results from the CEC PV model, and thus depend on an up-to-date database of module characteristics. Currently, adding new modules to the database requires calculating operational coefficients using a general purpose equation solver—a cumbersome process for the 300+ modules added on average every month. The combination of empirical regressions and heuristic methods presented herein achieve automated convergence for 99.87% of the 5487 modules in the CEC database and greatly enhance the accuracy and efficiency by which new modules can be characterized and approved for use. The added robustness also permits general purpose use of the CEC/6 parameter module model by modelers and system analysts when standard module specifications are known, even if the module does not exist in a preprocessed database.
An Aerodynamic Investigation of an Isolated Stationary Formula 1 Wheel Assembly
Authors: Axerio-Cilies John , Issakhanian Emin , Jimenez Juan , Iaccarino Gianluca
Published: March 2012

The flowfield around a 60% scale stationary Formula 1 tire in contact with the ground in a closed wind tunnel at a Reynolds number of 500,000 was computationally examined in order to assess the accuracy of different turbulence modeling techniques and confirm the existence of large scale flow features. A simplified and replica tire model that includes all brake components was tested to determine the sensitivity of the wake to cross flow within the tire hub along with the flow blockage caused by the brake assembly. The results of steady and unsteady Reynolds averaged Navier-Stokes (URANS) equations and a large eddy simulation (LES) were compared with the experimental data. The LES closure and the RANS closure that accounted for unsteadiness with low eddy viscosity (unsteady kω-SST) matched closest to the experimental data both in point wise velocity comparisons along with location and intensity of the strong counter-rotating vortex pair dominating the far wake of the tire.
Mixed Elastohydrodynamic Lubrication in Finite Roller Contacts Involving Realistic Geometry and Surface Roughness
Authors: Zhu Dong , Wang Jiaxu , Ren Ning , Wang Q. Jane
Published: March 2012

Concentrated (or counterformal) contacts are found in many mechanical components that transmit significant power. Traditionally, concentrated contacts can be roughly categorized to point and line contacts. In point contacts, the contact area is small in both principal directions, while in line contacts, it is small in one direction but assumed to be infinitely long in the other direction. However, these two types of geometry are results of simplification that does not precisely cover all the contact conditions in engineering practice. Actually most line contact components are purposely designed to have a crown in the contact length direction in order to accommodate possible non-uniform load distribution and misalignment. Moreover, the contact length is always finite, and at two ends of the contact there usually exist round corners or chamfers to reduce stress concentration. In the present work, the deterministic mixed EHL model developed previously has been modified to take into account the realistic geometry. Sample cases have been analyzed to investigate the effects of contact length, crowning, and end corners (or chamfers) on the EHL film thickness and the stress concentration, and also to demonstrate the entire transition from full-film and mixed EHL down to a practically dry contact under severe operating conditions with real machined roughness. It appears that this modified model can be used as an engineering tool for roller design optimization through in-depth mixed EHL performance evaluation.
Application of GaInNAs for the gain medium of a photonic crystal microcavity
Authors: Nagatomo H. , Kukita K. , Goto H. , Nakao R. , Nakano K. , Ishikawa F. , Morifuji M. , Kondow M.
Published: March 2012

The authors demonstrated the functionality of a circularly arranged submicron scale optical cavity with a GaInNAs gain medium and an AlOx cladding layer within a two-dimensional photonic crystal slab. The GaInNAs gain has negligible optical degradations due to process damage, probably stemming from the suppressed diffusion carriers and the small surface recombination velocity of the material. The calculated spectrum when using a finite different time domain simulation provides a cavity mode containing a whispering gallery mode at a wavelength close to 1.3 μm. An observation of the tuned spectral peaks related to the cavity mode shows this cavity has promise for future device applications.
Structural and magnetic characterization of superparamagnetic iron platinum nanoparticle contrast agents for magnetic resonance imaging
Authors: Taylor Robert M. , Huber Dale L. , Monson Todd C. , Esch Victor , Sillerud Laurel O.
Published: March 2012

The authors report the synthesis, from simple salts, and the physical characterization of superparamagnetic iron platinum nanoparticles (SIPPs) suitable for use as contrast agents in magnetic resonance imaging. The properties of these particles were determined by means of transmission electron microscopy (TEM), thermogravimetric analysis, inductively coupled plasma-optical emission spectroscopy (ICP-OES), superconducting quantum interference device (SQUID) magnetometry, and nuclear magnetic resonance relaxivity at 4.7 T. TEM showed that the diameters of the particles ranged from 9.3 to 10 nm, depending on the mole ratio of iron to platinum precursors, and on the concentration of octadecylamine (ODA) used in their preparation. The iron to platinum stoichiometry determined by ICP-OES varied from 1.4:1 to 3.7:1 and was similarly dependent on the initial mole ratios of iron and platinum salts, as well as on the concentration of ODA in the reaction. SQUID magnetometry showed that the SIPPs were superparamagnetic and had magnetic moments that increased with increasing iron content from 62 to 72 A·m2/kg Fe. The measured relaxivities of the SIPPs at 4.7 T were higher than commercially available superparamagnetic iron oxide nanoparticles, suggesting that these particles may be superior contrast agents in T2-weighted magnetic resonance imaging.
L-Selectin and P-Selectin Are Novel Biomarkers of Cervicovaginal Inflammation for Preclinical Mucosal Safety Assessment of Anti-HIV-1 Microbicide
Authors: Zhong Maohua , He Benxia , Yang Jingyi , Bao Rong , Zhang Yan , Zhou Dihan , Chen Yaoqing , Li Liangzhu , Han Chen , Yang Yi , Sun Ying , Cao Yuan , Li Yaoming , Shi Wei , Jiang Shibo , Zhang Xiaoyan , Yan Huimin
Published: March 2012

A major obstacle thwarting preclinical development of microbicides is the lack of a validated biomarker of cervicovaginal inflammation. Therefore, the present study aims to identify novel noninvasive soluble markers in a murine model for assessment of microbicide mucosal safety. By performing cytokine antibody array analysis, we identified two adhesion molecules, L-selectin and P-selectin, which significantly increased when mucosal inflammation was triggered by nonoxynol-9 (N9), an anti-HIV-1 microbicide candidate that failed clinical trials, in a refined murine model of agent-induced cervicovaginal inflammation. We found that patterns of detection of L-selectin and P-selectin were obviously different from those of the two previously defined biomarkers of cervicovaginal inflammation, monocyte chemotactic protein 1 (MCP-1) and interleukin 6 (IL-6). The levels of these two soluble selectins correlated better than those of MCP-1 and IL-6 with the duration and severity of mucosal inflammation triggered by N9 and two approved proinflammatory compounds, benzalkonium chloride (BZK) and sodium dodecyl sulfate (SDS), but not by two nonproinflammatory compounds, carboxymethyl celluose (CMC; microbicide excipients) and tenofovir (TFV; microbicide candidate). These data indicated that L-selectin and P-selectin can serve as additional novel cervicovaginal inflammation biomarkers for preclinical mucosal safety evaluation of candidate microbicides for the prevention of infection with HIV and other sexually transmitted pathogens.
Prevalence of
qnr
,
aac(6
′
)-Ib-cr
,
qepA
, and
oqxAB
in Escherichia coli Isolates from Humans, Animals, and the Environment
Authors: Chen Xiang , Zhang Weiqiu , Pan Weijuan , Yin Jiajun , Pan Zhiming , Gao Song , Jiao Xinan
Published: March 2012

qnr
,
aac(6
′
)-Ib-cr
,
qepA
, and
oqxAB
genes were detected in 5.7%, 4.9%, 2.6%, and 20.2% of 1,022
Escherichia coli
isolates from humans, animals, and the environment, respectively, collected between 1993 and 2010 in China. The prevalence of
oqxAB
in porcine isolates (51.0%) was significantly higher than that in other isolates. This is the first report of
oqxAB
-positive isolates from ducks and geese and as early as 1994 from chickens.
Targeting Persisters for Tuberculosis Control
Authors: Zhang Ying , Yew Wing Wai , Barer Michael R.
Published: March 2012

Mycobacterial persisters, the survivors from antibiotic exposure, necessitate the lengthy treatment of tuberculosis (TB) and pose a significant challenge for our control of the disease. We suggest that persisters in TB are heterogeneous in nature and comprise various proportions of the population depending on the circumstances; the mechanisms of their formation are complex and may be related to those required for persistence in chronic infection. Results from recent studies implicate multiple pathways for persister formation, including energy production, the stringent response, global regulators, the
trans
-translation pathway, proteasomal protein degradation, toxin-antitoxin modules, and transporter or efflux mechanisms. A combination of specifically persister-targeted approaches, such as catching them when active and susceptible either by stimulating them to “wake up” or by intermittent drug dosing, the development of new drugs, the use of appropriate drug combinations, and combined chemotherapy and immunotherapy, may be needed for more effective elimination of persisters and better treatment of TB. Variations in levels of persister formation and in host genetics can play a role in the outcome of clinical treatment, and thus, these may entail personalized treatment regimens.
Neutrophils Mediate Maturation and Efflux of Lung Dendritic Cells in Response to Aspergillus fumigatus Germ Tubes
Authors: Park Stacy J. , Burdick Marie D. , Mehrad Borna
Published: March 2012

Invasive aspergillosis is a life-threatening complication of neutrophil deficiency or dysfunction. Neutropenia has previously been associated with enhanced influx of CD11b-expressing conventional dendritic cells to the lungs in response toAspergillusspecies, but whether neutrophils directly modulate the function of dendritic cells in this infection is not known. We hypothesized that, in the setting of intrapulmonary challenge withAspergillus, neutrophils promote the maturation and traffic of lung conventional dendritic cells to draining mediastinal lymph nodes. We report that neutropenia results in a marked accumulation of dendritic cells in the lungs of mice challenged withAspergillusbut greatly diminishes their egress to mediastinal lymph nodes independent of neutrophil microbicidal functions. Furthermore, the phenotype of lung dendritic cells was more immature in neutropenic animals than in nonneutropenic mice exposed to the microorganism. Consistent with this, coincubation with neutrophils greatly enhanced the upregulation of costimulatory molecules on dendritic cells exposed toAspergillus in vitro, a process that was dependent on cell contact and the dendritic cell receptor DC-SIGN. Taken together, our data support an immunomodulatory cross talk between neutrophils and dendritic cells in the context of host response toAspergillusthat promotes the maturation and efflux of lung dendritic cells.
Susceptibility of Inbred Mice to Rickettsia parkeri
Authors: Grasperge Britton J. , Reif Kathryn E. , Morgan Timothy D. , Sunyakumthorn Piyanate , Bynog Joseph , Paddock Christopher D. , Macaluso Kevin R.
Published: March 2012

Rickettsia parkeri, a member of the spotted fever groupRickettsia, is the causative agent of American boutonneuse fever in humans. Despite the increased recognition of human cases, limited information is available regarding the infection of invertebrate and vertebrate hosts for this emerging tick-borne disease. Toward the development of a viable transmission model and to further characterize the pathology associated withR. parkeriinfection, inbred mouse strains (A/J, BALB/c, C3H/HeJ, and C3H/HeN) were intravenously and intradermally inoculated with 105low-passage-numberR. parkeri(Portsmouth strain), and infection, gross pathology, and histopathology were scored. Additionally, a quantitative real-time PCR (qPCR) was performed to estimate rickettsial load in heart, lung, spleen, and liver tissues of infected mice at 19 days postinoculation. Of the A/J, BALB/c, and C3H/HeN mice, none displayed universal pathology consistent with sustained infection. Compared to age-matched control mice, the intravenously inoculated C3H/HeJ mice exhibited marked facial edema and marked splenomegaly upon gross examination, while the intradermally inoculated mice developed characteristic eschar-like lesions. The C3H/HeJ mice also exhibited the greatest concentrations of rickettsial DNA from heart, lung, liver, and spleen samples when examined by qPCR. The similarity of the pathology of human disease and sustained infection suggests that the C3H/HeJ strain of mice is a promising candidate for subsequent experiments to examine the tick transmission, dissemination, and pathology ofR. parkeririckettsiosis.
Surface Proteome of “Mycobacterium avium subsp. hominissuis” during the Early Stages of Macrophage Infection
Authors: McNamara Michael , Tzeng Shin-Cheng , Maier Claudia , Zhang Li , Bermudez Luiz E.
Published: March 2012

“
Mycobacterium avium
subsp.
hominissuis
” is a robust and pervasive environmental bacterium that can cause opportunistic infections in humans. The bacterium overcomes the host immune response and is capable of surviving and replicating within host macrophages. Little is known about the bacterial mechanisms that facilitate these processes, but it can be expected that surface-exposed proteins play an important role. In this study, the selective biotinylation of surface-exposed proteins, streptavidin affinity purification, and shotgun mass spectrometry were used to characterize the surface-exposed proteome of
M. avium
subsp.
hominissuis
. This analysis detected more than 100 proteins exposed at the bacterial surface of
M. avium
subsp.
hominissuis
. Comparisons of surface-exposed proteins between conditions simulating early infection identified several groups of proteins whose presence on the bacterial surface was either constitutive or appeared to be unique to specific culture conditions. This proteomic profile facilitates an improved understanding of
M. avium
subsp.
hominissuis
and how it establishes infection. Additionally, surface-exposed proteins are excellent targets for the host adaptive immune system, and their identification can inform the development of novel treatments, diagnostic tools, and vaccines for mycobacterial disease.
Quorum-Sensing and BvrR/BvrS Regulation, the Type IV Secretion System, Cyclic Glucans, and BacA in the Virulence of Brucella ovis: Similarities to and Differences from Smooth Brucellae
Authors: Martín-Martín Ana I. , Sancho Pilar , de Miguel María Jesús , Fernández-Lago Luis , Vizcaíno Nieves
Published: March 2012

Brucella ovis
is a rough bacterium—lacking O-polysaccharide chains in the lipopolysaccharide—that is virulent in its natural host and whose virulence mechanisms remain almost unexplored. In a search for additional traits that distinguish
B. ovis
from smooth
Brucella
, which require O-polysaccharide chains for virulence, we have analyzed the significance in
B. ovis
of the main virulence factors described for smooth
Brucella
. Attempts to obtain strains of virulent
B. ovis
strain PA that are mutated in the BvrR/BvrS two-component regulatory system were unsuccessful, suggesting the requirement of that system for
in vitro
survival, while the inactivation of
bacA
—in contrast to the results seen with smooth
Brucella
—did not affect splenic colonization in mice or behavior in J774.A1 murine macrophages. Defects in the synthesis of cyclic ß-1,2 glucans reduced the uptake of
B. ovis
PA in macrophages and, although the intracellular multiplication rate was unaffected, led to attenuation in mice. Growth of strains with mutations in the type IV secretion system (encoded by the
virB
operon) and the quorum-sensing-related regulator VjbR was severely attenuated in the mouse model, and although the mutant strains internalized like the parental strain in J774.A1 murine macrophages, they were impaired for intracellular replication. As described for
B. melitensis
, VjbR regulates the transcription of the
virB
operon positively, and the
N
-dodecanoyl-
dl
-homoserine lactone (C
12
-HSL) autoinducer abrogates this effect. In contrast, no apparent VjbR-mediated regulation of the
fliF
flagellar gene was observed in
B. ovis
, probably due to the two deletions detected upstream of
fliF
. These results, together with others reported in the text, point to similarities between rough virulent
B. ovis
and smooth
Brucella
species as regards virulence but also reveal distinctive traits that could be related to the particular pathogenicity and host tropism characteristics of
B. ovis
.
The Multiple Signaling Systems Regulating Virulence in Pseudomonas aeruginosa
Authors: Nadal Jimenez Pol , Koch Gudrun , Thompson Jessica A. , Xavier Karina B. , Cool Robbert H. , Quax Wim J.
Published: March 2012

Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacteriumPseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e.,N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.
Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria
Authors: Gao Beile , Gupta Radhey S.
Published: March 2012

The phylumActinobacteriaharbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups ofActinobacteriaas well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either allActinobacteriaor their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylumActinobacteria(excludingCoriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders ofActinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups ofActinobacteriain diverse environments. Genetic and biochemical studies on theseActinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups ofActinobacteria.
Quantitative risk measures applied to Alaskan commercial fisheries
Authors: Sethi Suresh Andrew , Dalton Michael , Hilborn Ray
Published: March 2012

Risk measures can summarize the complex variability inherent in fisheries management into simple metrics. We use quantitative risk measures from investment theory to analyze catch and revenue risks for 90 commercial fisheries in Alaska, USA, nearly a complete census. We estimate the relationship between fishery characteristics and catch risk using nonparametric random forest regression to identify attributes associated with high or low risks. Catch and revenue risks for individual Alaskan fisheries are substantial and are higher than risks for farmed food alternatives. Revenue risks are greater than catch risks for most fisheries, indicating that price variability is an additional source of risk to fishermen. Regression results indicate that higher productivity species tend to be higher risk, and there is an increasing gradient of risk moving north and west across Alaskan waters, with the remote western Bering Sea fisheries tending to have the highest risks. Low risk fisheries generally have large catches and support larger fleets. Finally, fisheries with greater catch history under some form of dedicated access privileges tend to have lower catch risks.
Impact of the Deepwater Horizon well blowout on the economics of US Gulf fisheries
Authors: Sumaila U. Rashid , Cisneros-Montemayor Andrés M. , Dyck Andrew , Huang Ling , Cheung William , Jacquet Jennifer , Kleisner Kristin , Lam Vicky , McCrea-Strub Ashley , Swartz Wilf , Watson Reg , Zeller Dirk , Pauly Daniel
Published: March 2012

Marine oil spills usually harm organisms at two interfaces: near the water surface and on shore. However, because of the depth of the April 2010 Deepwater Horizon well blowout, deeper parts of the Gulf of Mexico are likely impacted. We estimate the potential negative economic effects of this blowout and oil spill on commercial and recreational fishing, as well as mariculture (marine aquaculture) in the US Gulf area, by computing potential losses throughout the fish value chain. We find that the spill could, in the next 7 years, result in (midpoint) present value losses of total revenues, total profits, wages, and economic impact of US$3.7, US$1.9, US$1.2, and US$8.7 billion, respectively. Commercial and recreational fisheries would likely suffer the most losses, with a respective estimated US$1.6 and US$1.9 billion of total revenue losses, US$0.8 and US$1.1 billion in total profit losses, and US$4.9 and US$3.5 billion of total economic losses.
Low-cost estimates of mortality rate from single tag recoveries: addressing short-term trap-happy and trap-shy bias
Authors: McGarvey Richard , Matthews Janet M.
Published: March 2012

Conventional single tag-recovery data are widely available for stock assessments, notably of invertebrate fisheries, worldwide. Though not commonly used for this purpose, the times-at-large in single tag-recovery data provide (relatively) direct information about average mortality rate as a sample of survival times. Mortality rate is estimated using simple formulas given as functions of the mean time-at-large of tagged and recaptured animals. Here we extend an earlier time-at-large mortality estimator to address a potentially common source of bias: trap-happy or trap-shy behavior shortly following tag release. A maximum likelihood solution is derived, yielding an unbiased estimate of instantaneous mortality rate where the interval of usable times-at-large for observed recaptures may be truncated on both sides to any biologist-chosen experimental (recapture) time frame. In tests of the new doubly-truncated mortality estimator using simulated tag-recovery times-at-large, omitting the first 8 weeks of recaptures from the mortality estimate largely eliminated the bias introduced by simulated short-term trap-happy and trap-shy behavior. Bias in the mortality estimate declined by an order of magnitude more than the observed increase in standard error.
Spatial and seasonal variability in the diet of round goby (Neogobius melanostomus): stable isotopes indicate that stomach contents overestimate the importance of dreissenids
Authors: Brush Jaclyn M. , Fisk Aaron T. , Hussey Nigel E. , Johnson Timothy B.
Published: March 2012

Our results provide new information that diet, carbon source and trophic position of an invasive fish species, round goby ( Neogobius melanostomus ), varies seasonally, spatially and with body size in littoral habitats of Lake Ontario. Based on stomach contents and stable isotopes, round goby fed at a higher trophic position in the cooler, less productive Kingston Basin relative to the Bay of Quinte. Bay of Quinte round goby were more reliant on terrestrial carbon, whereas littoral carbon dominated in the Kingston Basin. Although stomach contents suggested dreissenids were the dominant prey item of round goby, stable isotope mixing models estimated that dreissenids were never >39% and 11% of the diet in Bay of Quinte and Kingston Basin, respectively. Stable isotopes indicated amphipods, chironomids and cladocerans were the most important prey, and were at times common items in stomach contents, but this varied with site, season and year. Given their high abundance, the impact of round gobies on the benthic biodiversity of the Great Lakes may be more significant than indicated by stomach content analysis alone.
Oxidative transformation of N-substituted 2-aminophenols to 2-substituted benzoxazoles catalyzed by polymer-incarcerated and carbon-stabilized platinum nanoclusters
Authors: Yoo Woo-Jin , Yuan Hao , Miyamura Hiroyuki , Kobayashi Shū
Published: March 2012

The preparation of 2-substituted benzoxazoles was achieved through a sequential aerobic oxidation – enolization – oxidative cyclization reaction of N-substituted 2-aminophenols catalyzed by platinum nanoclusters supported on a polymer / carbon black composite material.
Diversity of bacteria and mycobacteria in biofilms of two urban drinking water distribution systems
Authors: Liu Ruyin , Yu Zhisheng , Zhang Hongxun , Yang Min , Shi Baoyou , Liu Xinchun
Published: March 2012

In this study, to give insight into the bacterial diversity of biofilms from full-scale drinking water distribution systems (DWDSs), the bacterial community compositions of biofilms from two urban DWDSs (Guangzhou and Beijing, China) were determined using a 16S rRNA gene library technique. Meanwhile, the occurrence and diversity of mycobacteria were also analyzed by a Mycobacterium -specific hsp gene assay. The biofilms from the full-scale DWDSs have complex bacterial populations. Proteobacteria was the common and predominant group in all biofilm samples, in agreement with previous reports. The community structures of bacteria at the three sites in Guangzhou DWDS were significantly different, despite the similar physicochemical properties of portable water. Some abundant and peculiar bacterial phylotypes were noteworthy, including Methylophilus , Massilia , and Planomicrobium , members of which are rarely found in DWDSs and their roles in DWDS biofilms are still unclear. The diversity of Mycobacterium species in biofilm samples was rather low. Mycobacterium arupense and Mycobacterium gordonae were the primary Mycobacterium species in Guangzhou and Beijing biofilms, respectively, indicating that M. arupense may be more resistant to chloride than M. gordonae.
Characterizing the structural diversity of a bacterial community associated with filter materials in recirculating aquaculture systems of Scortum barcoo
Authors: Zhu Peng , Ye Yangfang , Pei Fangfang , Lu Kaihong
Published: March 2012

The bacterial community structure associated with filter materials in the recirculating aquaculture system of Scortum barcoo was investigated using the 16S rRNA gene clone library method. Preliminary results showed that the clone library constructed from the initial operation condition was characterized by 31 taxa of bacteria belonging to eight phyla including Proteobacteria, Acidobacteria, Firmicutes, Fusobacteria, Sphingobacteria, Bacteroidetes, Verrucomicrobiae, and Actinobacteria. There were 14 taxa of bacteria belonging to four phyla including Proteobacteria, Acidobacteria, Planctomycetacia, and Nitrospirae from the stable operation condition where the water quality was well maintained. Nitrospirae was only found under the stable operation condition in this study. Our results further indicated that Nitrospira was dominated by members of the Nitrospira sp. lineages, with a minor fraction related to Nitrospira moscoviensis and an unknown Nitrospira cluster. These great differences of both diversity and composition between two operation conditions suggested that the composition of the microbial community varied with the degree of water quality in the recirculating aquaculture system of S. barcoo.
Change in antimicrobial susceptibility of Escherichia coli urinary tract isolates at a single institution over a period of 10 years
Authors: Walkty A. , Lagacé-Wiens P.R.S. , Karlowsky J.A. , Hoban D.J. , Manickam K. , Adam H. , Pieroni P. , Alfa M.
Published: March 2012

Urinary tract infections are common. Few published studies have demonstrated the change in Escherichia coli urinary isolate antimicrobial susceptibility over time within a given area and (or) population. The purpose of this study was to evaluate the change in susceptibility of E. coli clinical isolates obtained from urine specimens at a single institution over a period of 10 years. The microbiology laboratory information system at St. Boniface Hospital (Winnipeg, Manitoba, Canada) was searched retrospectively from 1 January 2000 to 31 December 2009, for all E. coli isolates from either a midstream or catheter urine source that had susceptibility testing performed. Only one isolate per patient was included during the entire study period. Antimicrobial susceptibility testing was carried out with either a Microscan instrument (pre-April 2004) or a Vitek instrument (May 2004 onwards). In total, 7353 E. coli urinary isolates were included for evaluation. Ciprofloxacin susceptibility declined significantly, from 99% in 2000 to 85% in 2009 (p < 0.0001). A small but statistically significant decline in susceptibility was also observed for ampicillin, cefazolin, trimethoprim–sulfamethoxazole, gentamicin, and nitrofurantoin. These data suggest that certain antimicrobials recommended for the treatment of urinary tract infections (ciprofloxacin, trimethoprim–sulfamethoxazole) may no longer be optimal.
PARALLEL CLUSTERING WITH CFINDER
Authors: POLLNER PETER , PALLA GERGELY , VICSEK TAMAS
Published: March 2012

The amount of available data about complex systems is increasing every year, measurements of larger and larger systems are collected and recorded. A natural representation of such data is given by networks, whose size is following the size of the original system. The current trend of multiple cores in computing infrastructures call for a parallel reimplementation of earlier methods. Here we present the grid version of CFinder, which can locate overlapping communities in directed, weighted or undirected networks based on the clique percolation method (CPM). We show that the computation of the communities can be distributed among several CPU-s or computers. Although switching to the parallel version not necessarily leads to gain in computing time, it definitely makes the community structure of extremely large networks accessible.
DIFFUSION CASCADES: SPREADING PHENOMENA IN BLOG NETWORK COMMUNITIES
Authors: BRAHIM ABDELHAMID SALAH , LE GRAND BÉNÉDICTE , LATAPY MATTHIEU
Published: March 2012

A diffusion cascade occurs when information spreads from one node to the rest of the network through a succession of diffusion events. So far diffusion phenomena have been mostly considered at a macroscopic scale i.e. by studying all nodes of the network. We give a complementary way to analyse network interactions by considering the problem at different scales. To that purpose, we use the community structure of the network to characterize diffusion between nodes (and between communities) and to identify interactions behaviour patterns.
LOCATING COMMUNITIES ON REAL DATASET GRAPHS USING SYNTHETIC COORDINATES
Authors: PAPADAKIS HARRIS , PANAGIOTAKIS COSTAS , FRAGOPOULOU PARASKEVI
Published: March 2012

One of the fundamental problems in social networking with a lot of potential applications is to detect effectively the communities that are created by the users' interaction. Other applications, such as finding web communities, uncovering the structure of social networks, or even analyzing a graph's structure to uncover Internet attacks are equally as important. All these problems converge to a common goal, the development of flexible and efficient local community detection algorithms. In this paper, we demonstrate the performance of an algorithm that uncovers the entire community structure of a network, based solely on local interactions between neighboring nodes and a distributed clustering algorithm. The proposed algorithm, named VCD, is based on the distributed computation of a synthetic coordinates for each graph node. Experimental results and comparisons with another method from the literature (Lancichinetti et al.) are presented. The algorithm is also tested on two real dataset graphs from the SNAP: Stanford Large Network Dataset Collection. In all cases the experimental results demonstrate the high performance of our algorithm in terms of accuracy to detect communities, and its computational efficiency.
ANVAYA: A WORKFLOWS ENVIRONMENT FOR AUTOMATED GENOME ANALYSIS
Authors: LIMAYE BHAKTI , BANERJEE RUMA , DATTA AVIK , INAMDAR HARSHAL , VATS PANKAJ , DAHALE SONAL , BHANDARI ALOK , RAMAKRISHNAN E. P. , TUPAKULA RAJNIKANTH , MALVIYA SANDEEP , BAYASKAR AVINASH , GADHARI RENU , JAIN SANKALP , GAVANE VIVEK , MAHAJAN RASHMI , SUNITHA K , JOSHI RAJENDRA
Published: March 2012

Anvaya is a workflow environment for automated genome analysis that provides an interface for several bioinformatics tools and databases, loosely coupled together in a coordinated system, enabling the execution of a set of analyses tools in series or in parallel. It is a client-server workflow environment that has an advantage over existing software as it enables extensive pre & post processing of biological data in an efficient manner. "Anvaya" offers the user, novel functionalities to carry out exhaustive comparative analysis via "custom tools," which are tools with new functionality not available in standard tools, and "built-in PERL parsers," which automate data-flow between tools that hitherto, required manual intervention. It also provides a set of 11 pre-defined workflows for frequently used pipelines in genome annotation and comparative genomics ranging from EST assembly and annotation to phylogenetic reconstruction and microarray analysis. It provides a platform that serves as a single-stop solution for biologists to carry out hassle-free and comprehensive analysis, without being bothered about the nuances involved in tool installation, command line parameters, format conversions required to connect tools and manage/process multiple data sets at a single instance.
GENERALIZED β-CONFORMAL CHANGE AND SPECIAL FINSLER SPACES
Authors: YOUSSEF NABIL L. , ABED S. H. , ELGENDI S. G.
Published: March 2012

This work is a continuation of the paper [Generalized beta-conformal change of Finsler metrics, Int. J. Geom. Meth. Mod. Phys. 7(4) (2010) 565–582]. In the present paper, we investigate the change of Finsler metrics [Formula: see text] which we refer to as a generalized β-conformal change. Under this change, we study some special Finsler spaces, namely, quasi-C-reducible, semi-C-reducible, C-reducible, C2-like, S3-like and S4-like Finsler spaces. We obtain some characterizations of the energy β-change, the Randers change and the Kropina change. We also obtain the transformation of the T-tensor under this change and study some interesting special cases. We then impose a certain condition on the generalized β-conformal change, which we call the b-condition, and investigate the geometric consequences of such a condition. Finally, we give the conditions under which a generalized β-conformal change is projective and generalize some known results in the literature.
FLUIDS IN WEYL GEOMETRIES
Authors: FATIBENE L. , FRANCAVIGLIA M.
Published: March 2012

We shall investigate the consequences of non-trivial Weyl geometries on conservation laws of a fluid. In particular we shall obtain a set of properties which allow to obtain in this generalized setting the standard relation between conservation of the energy-momentum tensor and number of particles.
GEOMETRIC HAMILTON–JACOBI FIELD THEORY
Authors: VITAGLIANO LUCA
Published: March 2012

I review my proposal about how to extend the geometric Hamilton–Jacobi theory to higher derivative field theories on fiber bundles.
Using probabilistic shale smear modelling to relate SGR predictions of column height to fault-zone heterogeneity
Authors: Yielding Graham
Published: March 2012

Fault-seal analysis in hydrocarbon exploration often involves prediction of the sealing capacity of fault rock at reservoir–reservoir juxtapositions on subsurface faults. A proxy property, such as Shale Gouge Ratio (SGR), is mapped on to the fault surface, and then SGR is either (a) calibrated by observations of known sealing faults, to define its sealing capacity (empirical approach), or (b) assumed to be equal to the composition of the fault rock, for which a database of capillary threshold pressures is available from cores (deterministic approach). The deterministic approach implicitly assumes that capillary pressures measured on centimetre-scale samples are representative of seismically mappable faults, for example that faults of intermediate SGR are equivalent to phyllosilicate framework fault rocks.

This contribution builds on earlier outcrop and modelling work to suggest an alternative explanation for the observed progressive increase in sealing capacity on faults of increasing SGR. Stochastic models of disrupted shale smears display the same pattern of increasing sealing capacity as SGR increases. These models have a bimodal ‘fault rock’ composed only of sealing shale smears and non-sealing matrix and, yet, at intermediate SGR the predicted column heights are similar to those normally ascribed to intermediate composition fault rocks. The resulting ‘fault-seal envelope’ in the models is a statistical estimate of the maximum trappable column height, dependent on the random occurrence of a gap in the smeared fault surface.
A relational database for the digitization of fluvial architecture
Authors: Colombera Luca , Mountney Nigel P. , McCaffrey William D.
Published: March 2012

Depositional (facies) models of fluvial architecture permit straightforward categorization of deposits, but are necessarily simplistic. Here we describe a complementary database methodology which is designed to encapsulate the inherent complexity of fluvial systems and their preserved deposits. The database is implemented as a series of tables (characterizing qualitative and quantitative architectural and geomorphological properties and system attributes) populated with data derived from peer-reviewed studies of both modern rivers and ancient fluvial successions, and from other reliable sources. Architectural properties (geometries, internal organization, spatial distribution and reciprocal relationships of lithosomes) are assigned to three different orders of genetic bodies organized in a hierarchical framework, ultimately belonging to stratigraphic volumes that are homogeneous in terms of their controlling factors and internal parameters. Interrogation of the database generates a varied suite of quantitative information, whose principal applications include: (i) the quantitative comparison of fluvial architecture to evaluate the relative importance of intrinsic and extrinsic controls; (ii) development of quantitatively justified fluvial depositional models through the integration of data from multiple sources; (iii) development of better constraints on the workflows used to infer borehole correlations and to condition stochastic models of subsurface architecture; (iv) identification of appropriate modern and ancient analogues for hydrocarbon reservoirs.
A survey on automated dynamic malware-analysis techniques and tools
Authors: Egele Manuel , Scholte Theodoor , Kirda Engin , Kruegel Christopher
Published: March 2012

Anti-virus vendors are confronted with a multitude of potentially malicious samples today. Receiving thousands of new samples every day is not uncommon. The signatures that detect confirmed malicious threats are mainly still created manually, so it is important to discriminate between samples that pose a new unknown threat and those that are mere variants of known malware.

This survey article provides an overview of techniques based on dynamic analysis that are used to analyze potentially malicious samples. It also covers analysis programs that leverage these It also covers analysis programs that employ these techniques to assist human analysts in assessing, in a timely and appropriate manner, whether a given sample deserves closer manual inspection due to its unknown malicious behavior.