bluuebunny/crossref_metadata_2025 huggingface dataset:
Modeling of Quasistatic Thermoviscoelastic Frictional Contact Problems
Authors: El-Shafei Ahmed G.
Published: March 2012

Frictional contacts of thermoviscoelastic bodies are complicated nonlinear temperature- and time-dependent problems. The introduction of friction with its irreversible character makes the problem more difficult. Additionally, the consideration of temperature, as an independent variable, destroys the convolution integral form of the viscoelasticity constitutive relations. This paper presents a computational model capable of predicting the nonlinear quasistatic response of uncoupled thermoviscoelastic frictional contact problems. The contact problem, as a variational inequality constrained model, is handled by using the Lagrange multiplier method to incorporate the inequality contact constraints. A local nonlinear friction law is adapted to model friction at the contact interface. This, in turn, eliminates difficulties that arise with the application of the classical friction laws. The temperature-dependency of viscoelasticity is modeled by applying the time-temperature superposition principle. The constitutive equations are transformed to be a function of the reduced time as the only independent variable, maintaining the convolution integral form. Two different illustrative examples are presented to demonstrate the applicability of the proposed model to analyze both nonconformal and conformal thermoviscoelastic frictional contact problems.
Investigations on
a Compression Ignition Engine Using Animal Fats and Vegetable Oil as
Fuels
Authors: Bousbaa Hamza , Sary Awad , Tazerout Mohand , Liazid Abdelkrim
Published: March 2012

Biofuels are a promising alternative to petroleum-based fuels. This paper investigates the performance, combustion, and exhaust emissions of a single cylinder diesel engine operated on baseline diesel and biofuel produced by vegetable oil and processing animal fat. The vegetable oil is called PODL20, which is a blend of palm oil and D-Limonen in proportion of 80% and 20%, respectively. The second biofuel is synthesized from the animal fat wastes (WAF) after transesterification process. Both experimental and numerical investigations are achieved in this work. The experiments are conducted at constant engine speed mode (1800 rpm) with applied loads on a wide domain. The CFD code converge is used to simulate the in-cylinder combustion for all the tested fuels. Comparative measures of brake thermal efficiency, break specific fuel consumption (bsfc), exhaust gas temperature, volumetric efficiency, and pollution (THC, CO2, CO, NO, NOx) are presented and discussed. Also, a step is achieved with in-cylinder CFD simulation of biofuel combustion. The obtained results indicate that the combustion characteristics are slightly changed when comparing neat diesel to biofuels. Some of the results obtained in this work indicate that WAF fuel decreases the total unburned fuel as well as the nitrogen oxides (NOx) emissions. The numerical results are in logic agreement with those obtained experimentally, which promotes more detailed investigations and combustion characteristics optimization in forthcoming works.
Simulation of Gas Pipelines Leakage Using Modified Characteristics Method
Authors: Nourollahi E. , Rahimi A. B. , Davarpanah E.
Published: March 2012

The process of pressure reduction and gas leakage rate (discharge characteristics) of a hole has so far been accomplished by utilizing some zero-dimensional models. In these models, the effects of complex boundaries are ignored. The major aim of this study is simulating the process of pipeline gas leakage by the aid of a modified one-dimensional characteristics model. This model, beside the possibility of modeling the impact of leakage on one-dimensional compressible flow, benefits from introducing a variety of boundary conditions to flow zone. In this approach, hole is considered as an orifice, which makes a path for gas to release in a lower pressure ambient. Also, in this study, the effects of four kinds of boundary conditions at the ends of the pipeline on gas discharge characteristics are investigated.
Second Law Assessment of a Wet Ethanol Fuelled HCCI Engine Combined With Organic Rankine Cycle
Authors: Khaliq Abdul , Trivedi Shailesh K.
Published: March 2012

In this study, first and second law analyses of a new combined power cycle based on wet ethanol fuelled homogeneous charge compression ignition (HCCI) engine and an organic Rankine cycle are presented. A computational analysis is performed to evaluate first and second law efficiencies, with the latter providing good guidance for performance improvement. The effect of changing turbocharger pressure ratio, organic Rankine cycle (ORC) evaporator pinch point temperature, turbocharger compressor efficiency, and ambient temperature have been observed on cycle’s first law efficiency, second law efficiency, and exergy destruction in each of its component. A first law efficiency of 41.5% and second law efficiency of 36.9% were obtained for the operating conditions (T0 = 300 K, rp = 3, ηT = 80%). The first law efficiency and second law efficiency of the combined power cycle significantly vary with the change in the turbocharger pressure ratio, but the change in pinch point temperature, turbocharger efficiency, and ambient temperature shows small variations in these efficiencies. Second law analysis demonstrates well how the fuel exergy is used, lost, and reused in all of the cycle components. It was found that 78.9% of the total input exergy is lost: 2.0% to the environment in the flue and 76.9% due to irreversibilities in the components. The biggest exergy loss occurs in the HCCI engine which is 68.7%, and the second largest exergy loss occurs in catalytic converter, i.e., nearly 3.13%. Results clearly show that performance evaluation based on first law analysis alone is not adequate, and hence more meaningful evaluation must include second law analysis.
Analysis of Thermo-Active Foundations With U-Tube Heat Exchangers
Authors: Rouissi Khaled , Krarti Moncef , McCartney John S.
Published: March 2012

This paper presents a heat transfer model for thermo-active drilled-shaft foundations used for heating and cooling buildings. Specifically, this paper presents a numerical approach to evaluate the unsteady temperature distribution within the ground medium surrounding the foundation as well as indoor/outdoor heat fluxes. In particular, a 2D numerical solution was obtained using the finite difference technique with a purely implicit solution scheme. The results of the sensitivity analysis indicate that the efficiency of the thermo-active foundation can be significantly improved with a proper selection of design parameters including heat exchanger fluid flow velocity, foundation depth, and foundation materials.
Influence of Flow Coefficient and Flow Structure on Rotational Cavitation in Inducer
Authors: Tani Naoki , Yamanishi Nobuhiro , Tsujimoto Yoshinobu
Published: March 2012

Cavitation instability is a major vibration source in turbopump inducers, and its prevention is a critical design problem in rocket-engine development. As reported by Kang et al., (2009, “Cause of Cavitation Instabilities in Three Dimensional Inducer,” Int. J. Fluid Mach. Syst., 2(3), pp. 206–214), the flow coefficient plays an important role in the onset of cavitation instabilities such as rotating and asymmetric cavitation. At high flow rates, various cavitation instabilities occur; on the other hand, as the flow coefficient is reduced, these cavitation instabilities either become absent or may change in character. The purpose of the present study is to investigate the relationship between rotating cavitation and flow coefficient through numerical simulations using the Combustion Research Unstructured Navier-stokes solver with CHemistry (CRUNCH) computational fluid dynamics (CFD) code (Ahuja et al., 2001, “Simulations of Cavitating Flows Using Hybrid Unstructured Meshes,” J. Fluids Eng.Trans ASME, 123(2), pp. 331–340), and to investigate the internal flow. As a first step, the interaction between the tip vortex and inducer blade was investigated through steady-state simulations. The tip vortex was identified by a vortex detection variable, i.e., the Q-function, a second invariant of the velocity tensor, and the distance between the blade and Q-function peak was measured. For a better understanding of cavitation instabilities, unsteady simulations were also performed for two different flow coefficients. The internal flow was carefully investigated, and the relation between cavity collapse/growth and the change in angle of attack was evaluated. The tip-vortex interaction is not a primary cause of unsteady cavitation, but the negative flow divergence caused by cavity collapse has a great influence on the flow angle. Moreover, changes in flow angle also introduce backflow from the tip clearance; these two factors are primary causes of cavitation instability. When the flow coefficient is large, the backflow is weak, and the interaction with the cavity collapse is strong. In contrast, as the flow coefficient decreases, stronger backflow occurs, and the interaction between backflow, cavity collapse, and flow angle weakens.
Process effects of copper film over a step etched with a plasma-based process
Authors: Lin Chi-Chou , Kuo Yue
Published: March 2012

The additive gas effect of a new plasma-based process for etching the copper film over a dielectric step has been investigated. The addition of different gases, such as Ar, N2, and CF4, affected the copper vertical and lateral conversion rates, which are critical to the attack of the cusp region and the sidewall as well as the residue formation. This is due to changes of plasma phase chemistry and ion bombardment energy. Excessive attacks of the cusp region and the sidewall were observed when the chlorine radical concentration was high except for the short plasma exposure time or the sidewall passivation condition. When the slope angle of the dielectric step was small, the cusp structure of the copper film was barely visible; therefore, the excessive plasma attack of the cusp region was negligible. A two step etch process that minimizes excessive attacks of the cusp region and the sidewall as well as the residue formation has been developed. This new process is critical to the practical application of copper in microelectronic products.
The STING in the Tail for Cytosolic DNA–Dependent Activation of IRF3
Authors: Bowie Andrew
Published: March 2012

The adaptor STING recruits a kinase and a transcription factor to mediate the response to cytosolic DNA.
Shape-Shifting Signals
Authors: Hines Pamela J.
Published: March 2012

New leaves emerge where they are allowed.
Choosing a Path
Authors: Vinson Valda
Published: March 2012

Selective effects of different ligands provide insights into the structural plasticity of receptor signaling.
Stressed Cells Secrete Cytokine
Authors: Foley John F.
Published: March 2012

Cells subjected to nonlethal mechanical stress release the cytokine interleukin-33.
The Aminoglycoside Antibiotic Kanamycin Damages DNA Bases in Escherichia coli: Caffeine Potentiates the DNA-Damaging Effects of Kanamycin while Suppressing Cell Killing by Ciprofloxacin in Escherichia coli and Bacillus anthracis
Authors: Kang Tina Manzhu , Yuan Jessica , Nguyen Angelyn , Becket Elinne , Yang Hanjing , Miller Jeffrey H.
Published: March 2012

The distribution of mutants in the Keio collection of
Escherichia coli
gene knockout mutants that display increased sensitivity to the aminoglycosides kanamycin and neomycin indicates that damaged bases resulting from antibiotic action can lead to cell death. Strains lacking one of a number of glycosylases (e.g., AlkA, YzaB, Ogt, KsgA) or other specific repair proteins (AlkB, PhrB, SmbC) are more sensitive to these antibiotics. Mutants lacking AlkB display the strongest sensitivity among the glycosylase- or direct lesion removal-deficient strains. This perhaps suggests the involvement of ethenoadenine adducts, resulting from reactive oxygen species and lipid peroxidation, since AlkB removes this lesion. Other sensitivities displayed by mutants lacking UvrA, polymerase V (Pol V), or components of double-strand break repair indicate that kanamycin results in damaged base pairs that need to be removed or replicated past in order to avoid double-strand breaks that saturate the cellular repair capacity. Caffeine enhances the sensitivities of these repair-deficient strains to kanamycin and neomycin. The gene knockout mutants that display increased sensitivity to caffeine (
dnaQ
,
holC
,
holD
, and
priA
knockout mutants) indicate that caffeine blocks DNA replication, ultimately leading to double-strand breaks that require recombinational repair by functions encoded by
recA
,
recB
, and
recC
, among others. Additionally, caffeine partially protects cells of both
Escherichia coli
and
Bacillus anthracis
from killing by the widely used fluoroquinolone antibiotic ciprofloxacin.
Short-Term Therapy with Luliconazole, a Novel Topical Antifungal Imidazole, in Guinea Pig Models of Tinea Corporis and Tinea Pedis
Authors: Koga Hiroyasu , Nanjoh Yasuko , Kaneda Hideo , Yamaguchi Hideyo , Tsuboi Ryoji
Published: March 2012

Luliconazole is a novel topical antifungal imidazole with broad-spectrum and potent antifungal activity. The drug is under clinical development in the United States for management of dermatophytosis with a short-term treatment regimen. The present study was undertaken to investigate the clinical benefit of short-term therapy with luliconazole cream in guinea pig models of tinea corporis and tinea pedis induced with
Trichophyton mentagrophytes
. The dose-dependent therapeutic efficacy of topical luliconazole cream (0.02 to 1%), measured by macroscopic improvement of skin lesions and by fungal eradication as determined by a culture assay, was demonstrated using a tinea corporis model. The improvement in skin lesions seen with luliconazole cream was observed even at a concentration of 0.02%, and its efficacy at 0.1% was equal to that of 1% bifonazole cream. The efficacy of short-term therapy with 1% luliconazole cream, which is used for clinical management, was investigated using the tinea corporis model (4- and 8-day treatment regimens) and the tinea pedis model (7- and 14-day treatment regimens). The 1% luliconazole cream completely eradicated the fungus in half or less of the treatment time required for 1% terbinafine cream and 1% bifonazole cream, as determined by a culture assay for both models. These results clearly indicate that 1% luliconazole cream is sufficiently potent for short-term treatment for dermatophytosis compared to existing drugs. Luliconazole is expected to be useful in the clinical management of dermatophytosis.
First Pharmacokinetic and Safety Study in Humans of the Novel Lipid Antiviral Conjugate CMX001, a Broad-Spectrum Oral Drug Active against Double-Stranded DNA Viruses
Authors: Painter Wendy , Robertson Alice , Trost Lawrence C. , Godkin Susan , Lampert Bernhard , Painter George
Published: March 2012

CMX001 is a novel, broad-spectrum lipid antiviral conjugate (LAC) that produces high intracellular levels of the active antiviral agent cidofovir diphosphate (CDV-PP). Study CMX001-102 was a randomized, double-blind, placebo-controlled, parallel group, dose-escalating study in healthy volunteers. The objectives of the study were to evaluate the safety and pharmacokinetic parameters of CMX001 after single and multiple doses. Single doses ranging from 0.25 to 2.0 mg/kg of body weight and multiple doses ranging from 0.1 to 1.0 mg/kg (3 total doses, administered every 6 days) were given orally. Safety was assessed using comprehensive clinical and laboratory evaluations, including enhanced monitoring for potential gastrointestinal (GI) effects using wireless capsule endoscopy (WCE). Serial plasma and pooled urine samples were collected to estimate pharmacokinetic parameters for both CMX001 and cidofovir (CDV). No adverse events occurred that prevented dose escalation. No clinically significant drug-related changes in blood chemistry, hematology, renal function, or intraocular pressure were observed. No CMX001-related gastrointestinal mucosal changes were observed by WCE. CMX001 was absorbed rapidly, with maximum plasma concentrations observed 2 to 3 h postdose. Maximum plasma drug concentration and systemic exposure of CMX001 increased approximately in proportion to dose following single and multiple doses; no significant accumulation of CMX001 or CDV was observed following multiple doses. We conclude that CMX001 is orally bioavailable and well tolerated in healthy volunteers at doses up to 2 mg/kg, approximately 140 mg in a typical adult. This is the first demonstration of the use of phospholipid conjugation technology to achieve plasma drug exposures that are expected to result in activity against multiple double-stranded DNA viruses.
In Vitro
Interactions between Aspirin and Amphotericin B against Planktonic Cells and Biofilm Cells of Candida albicans and C. parapsilosis
Authors: Zhou Yabin , Wang Ganggang , Li Yutang , Liu Yang , Song Yu , Zheng Wenshuai , Zhang Ning , Hu Xiaoyan , Yan Shikun , Jia Jihui
Published: March 2012

The increase in drug resistance and invasion caused by biofilm formation brings enormous challenges to the management of
Candida
infection. Aspirin's antibiofilm activity
in vitro
was discovered recently. The spectrophotometric method and the XTT {2,3-
bis
(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2
H
-tetrazolium hydroxide} reduction assay used for data generation make it possible to evaluate fungal biofilm growth accurately. The combined use of the most commonly used methods, the fractional inhibitory concentration index (FICI) and a newly developed method, the Δ
E
model, which uses the concentration-effect relationship over the whole concentration range instead of using the MIC index alone, makes the interpretation of results more reliable. As an attractive tool for studying the pharmacodynamics of antimicrobial agents, time-kill curves can provide detailed information about antimicrobial efficacy as a function of both time and concentration. In the present study,
in vitro
interactions between aspirin (acetylsalicylic acid [ASA]) and amphotericin B (AMB) against planktonic cells and biofilm cells of
Candida albicans
and
C. parapsilosis
were evaluated by the checkerboard microdilution method and the time-kill test. Synergistic and indifferent effects were found for the combination of ASA and AMB against planktonic cells, while strong synergy was found against biofilm cells analyzed by FICI. The Δ
E
model gave more consistent results with FICI. The positive interactions in concentration were also confirmed by the time-kill test. Moreover, this approach also revealed the pharmacodynamics changes of ASA and synergistic action on time. Our findings suggest a potential clinical use for combination therapy with ASA and AMB to augment activity against biofilm-associated infections.
Recurrent Episodes of Candidemia Due to Candida glabrata with a Mutation in Hot Spot 1 of the
FKS2
Gene Developed after Prolonged Therapy with Caspofungin
Authors: Durán-Valle María Teresa , Gago Sara , Gómez-López Alicia , Cuenca-Estrella Manuel , Jiménez Díez-Canseco Leticia , Gómez-Garcés José Luis , Zaragoza Oscar
Published: March 2012

We report two episodes of recurrent candidemia caused by echinocandin-resistant
Candida glabrata
in a 69-year-old patient who underwent repeated abdominal surgery. In the first episode of candidemia, an echinocandin-susceptible
Candida glabrata
strain was isolated, and the patient was treated with caspofungin. The isolates from the later episodes showed resistance to echinocandins. Analysis of the HS1 region of the
FKS2
gene showed the amino acid substitution S663P. Microsatellite analysis demonstrated a strong genetic relationship between the isolates.
Cryptococcus neoformans-Cryptococcus gattii Species Complex: an International Study of Wild-Type Susceptibility Endpoint Distributions and Epidemiological Cutoff Values for Amphotericin B and Flucytosine
Authors: Espinel-Ingroff A. , Chowdhary A. , Cuenca-Estrella M. , Fothergill A. , Fuller J. , Hagen F. , Govender N. , Guarro J. , Johnson E. , Lass-Flörl C. , Lockhart S. R. , Martins M. A. , Meis J. F. , Melhem M. S. C. , Ostrosky-Zeichner L. , Pelaez T. , Pfaller M. A. , Schell W. A. , Trilles L. , Kidd S. , Turnidge J.
Published: March 2012

Clinical breakpoints (CBPs) are not available for theCryptococcus neoformans-Cryptococcus gattiispecies complex. MIC distributions were constructed for the wild type (WT) to establish epidemiologic cutoff values (ECVs) forC. neoformansandC. gattiiversus amphotericin B and flucytosine. A total of 3,590 amphotericin B and 3,045 flucytosine CLSI MICs forC. neoformans(including 1,002 VNI isolates and 8 to 39 VNII, VNIII, and VNIV isolates) and 985 and 853 MICs forC. gattii, respectively (including 42 to 259 VGI, VGII, VGIII, and VGIV isolates), were gathered in 9 to 16 (amphotericin B) and 8 to 13 (flucytosine) laboratories (Europe, United States, Australia, Brazil, Canada, India, and South Africa) and aggregated for the analyses. Additionally, 442 amphotericin B and 313 flucytosine MICs measured by using CLSI-YNB medium instead of CLSI-RPMI medium and 237 Etest amphotericin B MICs forC. neoformanswere evaluated. CLSI-RPMI ECVs for distributions originating in ≥3 laboratories (with the percentages of isolates for which MICs were less than or equal to ECVs given in parentheses) were as follows: for amphotericin B, 0.5 μg/ml forC. neoformansVNI (97.2%) andC. gattiiVGI and VGIIa (99.2 and 97.5%, respectively) and 1 μg/ml forC. neoformans(98.5%) andC. gattiinontyped (100%) and VGII (99.2%) isolates; for flucytosine, 4 μg/ml forC. gattiinontyped (96.4%) and VGI (95.7%) isolates, 8 μg/ml for VNI (96.6%) isolates, and 16 μg/ml forC. neoformansnontyped (98.6%) andC. gattiiVGII (97.1%) isolates. Other molecular types had apparent variations in MIC distributions, but the number of laboratories contributing data was too low to allow us to ascertain that the differences were due to factors other than assay variation. ECVs may aid in the detection of isolates with acquired resistance mechanisms.
Strand Length-Dependent Antimicrobial Activity and Membrane-Active Mechanism of Arginine- and Valine-Rich β-Hairpin-Like Antimicrobial Peptides
Authors: Dong Na , Ma Qingquan , Shan Anshan , Lv Yinfeng , Hu Wanning , Gu Yao , Li Yuzhi
Published: March 2012

Antimicrobial peptides with amphipathic β-hairpin-like structures have potent antimicrobial properties and low cytotoxicity. The effect of VR or RV motifs on β-hairpin-like antimicrobial peptides has not been investigated. In this study, a series of β-hairpin-like peptides, Ac-C(VR)

n

D
PG (RV)

n

C-NH
2
(
n
= 1, 2, 3, 4, or 5), were synthesized, and the effect of chain length on antimicrobial activity was evaluated. The antimicrobial activity of the peptides initially increased and then decreased with chain length. Longer peptides stimulated the toxicity to mammalian cells. VR3, a 16-mer peptide with seven amino acids in the strand, displayed the highest therapeutic index and represents the optimal chain length. VR3 reduced bacterial counts in the mouse peritoneum and increased the survival rate of mice at 7 days after
Salmonella enterica
serovar Typhimurium infection
in vivo
. The circular dichroism (CD) spectra demonstrated that the secondary structure of the peptides was a β-hairpin or β-sheet in the presence of an aqueous and membrane-mimicking environment. VR3 had the same degree of penetration into the outer and inner membranes as melittin. Experiments simulating the membrane environment showed that Trp-containing VRW3 (a VR3 analog) tends to interact preferentially with negatively charged vesicles in comparison to zwitterionic vesicles, which supports the biological activity data. Additionally, VR3 resulted in greater membrane damage than melittin as determined using a flow cytometry-based membrane integrity assay. Collectively, the data for synthetic lipid vesicles and whole bacteria demonstrated that the VR3 peptide killed bacteria via targeting the cell membrane. This assay could be an effective pathway to screen novel candidates for antibiotic development.
Emerging Role of Ubiquitination in Antiviral RIG-I Signaling
Authors: Maelfait Jonathan , Beyaert Rudi
Published: March 2012

Detection of viruses by the innate immune system involves the action of specialized pattern recognition receptors. Intracellular RIG-I receptors sense the presence of viral nucleic acids in infected cells and trigger signaling pathways that lead to the production of proinflammatory and antiviral proteins. Over the past few years, posttranslational modification of RIG-I and downstream signaling proteins by different types of ubiquitination has been found to be a key event in the regulation of RIG-I-induced NF-κB and interferon regulatory factor 3 (IRF3) activation. Multiple ubiquitin ligases, deubiquitinases, and ubiquitin binding scaffold proteins contribute to both positive and negative regulation of the RIG-I-induced antiviral immune response. A better understanding of the function and activity of these proteins might eventually lead to the development of novel therapeutic approaches for management of viral diseases.
Landscape characteristics and coho salmon (Oncorhynchus kisutch) distributions: explaining abundance versus occupancy
Authors: Steel E.A. , Jensen D.W. , Burnett K.M. , Christiansen K. , Firman J.C. , Feist B.E. , Anlauf K.J. , Larsen D.P.
Published: March 2012

Distribution of fishes, both occupancy and abundance, is often correlated with landscape-scale characteristics (e.g., geology, climate, and human disturbance). Understanding these relationships is essential for effective conservation of depressed populations. We used landscape characteristics to explain the distribution of coho salmon ( Oncorhynchus kisutch ) in the Oregon Plan data set, one of the first long-term, probabilistic salmon monitoring data sets covering the full range of potential habitats. First we compared data structure and model performance between the Oregon Plan data set and two published data sets on coho salmon distribution. Most of the variation in spawner abundance occurred between reaches but much also occurred between years, limiting potential model performance. Similar suites of landscape predictors are correlated with coho salmon distribution across regions and data sets. We then modeled coho salmon spawner distribution using the Oregon Plan data set and determined that landscape characteristics could not explain presence vs. absence of spawners but that the percentage of agriculture, winter temperature range, and the intrinsic potential of the stream could explain some variation in abundance (weighted average R2= 0.30) where spawners were present. We conclude that the previous use of nonrandom monitoring data sets may have obscured understanding of species distribution, and we suggest minor modifications to large-scale monitoring programs.
Asphyxiation and entombment mechanisms in fines rich spawning substrates: experimental evidence with brook trout (Salvelinus fontinalis) embryos
Authors: Franssen Jan , Blais Catherine , Lapointe Michel , Bérubé Francis , Bergeron Normand , Magnan Pierre
Published: March 2012

We investigated the distinct physical controls causing entombment and asphyxiation, the key mechanisms influencing salmonid egg-to-emergence (EtE) survival. Entombment occurs when sediment blocks the interstitial pathways (macropores) that larvae use to emerge from the streambed, while asphyxiation is related to low oxygen flux, which is a function of interstitial flow velocity. EtE survival has been related to substrate composition and flow velocity. However, in streambed sediments these variables are correlated, and few studies have examined the sensitivity of EtE survival to changes in velocity and oxygen flux at fixed substrate composition. EtE survival has not yet been directly related to the size and density of macropores. We incubated brook trout ( Salvelinus fontinalis ) embryos in artificial redds with different sediment compositions and hydraulic gradients to examine independently the effects of substrate composition, macropore geometry, and flow velocity on EtE survival, emergence timing, and fry condition. In situ measurements of macropore size were obtained using a computed tomography scanner. Despite high oxygen concentrations, we observed that entombment or blockage effects caused high embryo mortality in fines-rich substrates with few large macropores, and triggered early emergence of rare survivors. These outcomes could not be mitigated by increased flow velocity and oxygen flux to the egg pocket.
Life history schedule and periodic recruitment of female snow crab (Chionoecetes opilio) in the eastern Bering Sea
Authors: Ernst Billy , Armstrong David A. , Burgos Julián , Orensanz J.M. (Lobo)
Published: March 2012

Snow crab ( Chionoecetes opilio ) populations have fluctuated cyclically in eastern Canada and the eastern Bering Sea, where recruitment to the mature female pool has occurred over a period of three decades (1978–2007) in pulses with a mean period of 7 years. It has been hypothesized that this was the result of a parent–offspring relation between sequentially linked strong cohorts of mature primiparous females, which requires that periodicity matches the time lapsed between egg extrusion by the maternal broodstock and the offspring reaching maturity. We show that female age at maturity (post-settlement) varies between 4.5 and 7.5 years, with most females maturing at 5.5–6.5 years (7–8 years after egg extrusion). Pulses of female recruitment to the mature population do not show a latitudinal trend, consistent with uniformity in age-at-maturity. Results of tracking crab abundance and size–frequency distributions in cod stomach and trawl samples between successive pulses of the cycle are consistent with the hypothesis of serial linkage among pulses. Periodicity is reflected in trends of clutch fullness and average shell condition and in the negative correlation between the strength of primiparous female cohorts and the mean size of their members.
High-resolution melting analysis of common and recombinant genotypes of the Atlantic cod (Gadus morhua) hemoglobin β1 gene in transatlantic populations
Authors: Wetten Ola Frang , Wilson Robert C. , Andersen Øivind
Published: March 2012

High-resolution melting (HRM) analysis was applied to haplotype the Met55Val–Lys62Ala mutations of the Atlantic cod ( Gadus morhua ) Hb-β1 gene responsible for the important hemoglobin polymorphisms. The Val55–Ala62 haplotype predominated in cod populations throughout the Northwest Atlantic Ocean and the northern Norwegian and Baltic seas, while the Met55–Lys62 variant was mostly found in the North Sea, Kattegat, and along the southern part of the Norwegian coast. Whereas the distribution of the two main haplotypes show a temperature-related north–south gradient in Northeast Atlantic populations, this study provided no evidence for such a cline on the western side of the North Atlantic Ocean. Coupling and repulsion double heterozygotes were readily distinguished by the HRM assay, but no repulsion heterozygote specimens were found on either side of the Atlantic Ocean. The recombinant haplotype Val55–Lys62 was detected in variable numbers in both Northwest and Northeast Atlantic populations, with the highest frequencies in the Canadian populations. The reciprocal Met55–Ala62 recombination was almost absent in the populations examined and probably represents a disadvantage, particularly at elevated temperatures. Our HRM assay affords low-cost, precise, and efficient Hb-β1 polymorphism haplotyping in large numbers of DNA samples in small, moderately equipped laboratories.
Biocomplexity in a demersal exploited fish, white hake (Urophycis tenuis): depth-related structure and inadequacy of current management approaches
Authors: Roy Denis , Hurlbut Thomas R. , Ruzzante Daniel E.
Published: March 2012

Understanding the factors generating patterns of genetic diversity is critical to implementing robust conservation and management strategies for exploited marine species. Yet, often too little is known about population structure to properly tailor management schemes. Here we report evidence of substantial population structure in white hake ( Urophycis tenuis ) in the Northwest Atlantic, perhaps among the highest levels of population structure exhibited by a highly exploited, widely dispersed, long-lived marine fish. We show that depth plays a role in this extensive and temporally stable structure, which does not conform to previously established fisheries management units. Three genetically distinguishable populations were identified, where all straddle several management divisions and two (Southern Gulf of St. Lawrence and Scotian Shelf) overlap in their range, coexisting within a single division. The most highly exploited population in the Southern Gulf of St. Lawrence was also the most isolated and likely the smallest (genetically effective). This work shows that conservation and management priorities must include population structure and stability in establishing effective species recovery strategies.
Three-dimensional kernel utilization distributions improve estimates of space use in aquatic animals
Authors: Simpfendorfer Colin A. , Olsen Esben M. , Heupel Michelle R. , Moland Even
Published: March 2012

Tracking data have previously been used to define animal movement patterns through two-dimensional (2D) kernel utilization distributions and separate analysis of vertical locations. Here we describe the use of three-dimensional (3D) kernel utilization distributions to estimate the volumetric space use of individuals based on tracking data and to estimate the overlap in activity space between individuals. Data from European eels ( Anguilla anguilla ) from Norwegian coastal waters were used to compare the information conveyed by 2D and 3D activity space estimates and the utility of this approach for aquatic species. The use of 3D kernels produced detailed representations of space use in A. anguilla that permitted examination of depth use in a geographic context. Comparison of 2D and 3D home ranges showed that 2D analyses overestimated the amount of overlap between individuals by 13%–20%, because individuals sometimes occurred in the same location but used different depths. Hence, the 3D approach provided more comprehensive representations of animal movement in three dimensions while producing a metric that can be used for testing hypotheses relating to scientific descriptions of activity space, habitat use, and movement parameters.
Microstructural study of cetyltrimethylammonium bromide / 1-butanol / salt / water system — SANS and 2D-NOESY analysis
Authors: Kuperkar K. , Patriati A. , Putra E.G.R. , Singh K. , Marangoni D.G. , Bahadur P.
Published: March 2012

Interaction of 1-butanol (BuOH) with a cationic surfactant, cetyltrimethylammonium bromide (CTAB) aggregate, in water and salt solution has been studied by viscometry, small-angle neutron scattering (SANS), and 2D-NMR techniques. The experimental results are interpreted in terms of a possible micellar growth occurring in the presence of added alcohol and salt. It was observed that the addition of BuOH strongly influences the viscosity of the CTAB/salt micellar system, reaching a peak viscosity at about 0.5% w/v of BuOH over a range of salt concentrations. Scattering measurements support the idea of a structural transformation by the observation of a spectral shift (broadening) as the total concentration of surfactant varies, indicating a decrease in the intermicellar distance and narrow size distribution. The chemical shift from 1H NMR measurements gave complementary data on the solubilization of BuOH in CTAB micelles, whereas the expected locus (site) of the additive added to the surfactant including the dynamics of the molecules in micellar aggregates were successfully correlated by significant and positive cross peaks obtained from two-dimensional nuclear Overhauser effect spectroscopy (2D-NOESY).
Stereodynamics study of the O+ + D2 (υ = 0, j = 0–2) → OD+ + D reaction
Authors: Chen Jiawu , Liu Xinguo , Zhang Qinggang
Published: March 2012

The vector correlations between products and reagents for the ion–molecule reaction O+ + D2 → OD+ + D with different rotational quantum numbers (j = 0, 1, or 2) were explored theoretically using the quasi-classical trajectory method (QCT) on a Martìnez–Millán–González (MMG) surface. The three angular distributions P(θr), P([Formula: see text]), and P(θr,[Formula: see text]), as well as four polarization-dependent differential cross sections (PDDCSs) were calculated. The results indicate that a reagent’s rotational excitation greatly influences both the vector correlations of k–k′, k–j′, and k–k′–j′ and the PDDCSs of the title reaction, which means the reactivity is very sensitive to the rotational quantum number.
Ionic-liquid-supported 1,5,7-triazabicyclo[4.4.0]dec-5-ene — An efficient and recyclable organocatalyst for Michael addition to α,β-unsaturated ketones
Authors: Muthyala Manoj Kumar , Chhikara Bhupender S , Parang Keykavous , Kumar Anil
Published: March 2012

A novel ionic-liquid-supported 1,5,7-triazabicyclo[4.4.0]dec-5-ene (IL–TBD) was synthesized and investigated for its ability to act as an active organocatalyst in the Michael addition of active methylene compounds and thiophenols to chalcones under solvent-free conditions. The IL–TBD afforded Michael addition products in excellent yields (82%–94%) at room temperature, and it was simply recycled and reused at least five times without significant loss of catalytic activity.
Cathodoluminescence, X-ray excited optical luminescence, and X-ray absorption near-edge structure studies of ZnO nanostructures
Authors: Lobacheva Olga , Corcoran Patricia L. , Murphy Michael W. , Ko Jun Young Peter , Sham Tsun-Kong
Published: March 2012

ZnO nanostructures of various morphologies and crystallinities were fabricated by thermal evaporation from Zn powder in a tube furnace in the presence of oxygen. It was found that the morphology of ZnO nanostructures was affected by synthesis parameters, such as growth temperature, carrier gas flow, and the presence of catalyst on the surface of the substrate. Representative ZnO nanostructures were studied by X-ray excited optical luminescence (XEOL) and cathodoluminescence (CL) methods. The luminescence from these samples exhibits a morphology dependence of the branching ratio of the near band gap (NBG) emission in the UV and defect emission in the green (GE). The appearance of the optical emission also depends on the excitation method. X-ray absorption near-edge structures (XANES) at the O K-edge and Zn L-edge are also presented and their implications discussed.
Assessing the utility of three TaqMan probes for the diagnosis of tuberculosis and resistance to rifampin and isoniazid in Veracruz, México
Authors: Zenteno-Cuevas Roberto , Cuevas-Cordoba Betzaida , Enciso Antonio , Enciso Leonor , Cuellar Aremy
Published: March 2012

Mutations at codons 526 and 531 in the rpoB gene and at 315 in the katG gene are considered diagnostic markers for resistance to rifampin and isoniazid in tuberculosis. The aim of this study was to design and evaluate three TaqMan probes for the identification of these mutations in 138 respiratory samples positive for acid-fast bacilli, and 32 clinical isolates from a region with considerable levels of drug resistance. The specificities of the probes for the diagnosis of resistance to both drugs were 100%; however, the sensitivities were calculated to be 50% for isoniazid and 56% for rifampin. DNA sequencing of rpoB and katG; and the spoligotyping assay of the clinical isolates, confirmed the diversity of the mutations and the presence of 11 spoligotypes with a shared international type and eight unique spoligotypes. Analysis of the respiratory samples identified 22 (16%) as drug-resistant and 4 (3%) as multidrug-resistant tuberculosis. The diagnostic value of the TaqMan probes was compromised by the diversity of mutations found in the clinical isolates. This highlights the need for better understanding of the molecular mechanisms responsible for drug resistance prior to the use of molecular probes, especially in regions with significant levels of drug-resistant tuberculosis.
Identification of envelope protein ORF10 of channel catfish herpesvirus
Authors: Liu Yulin , Yuan Junfa , Wang Weimin , Chen Xiaoxuan , Tang Rong , Wang Min , Li Lijuan
Published: March 2012

Channel catfish virus (CCV) is a viral pathogen of fry and fingerling channel catfish and can cause significant commercial loss. Previous studies have shown that the CCV virion contains at least 25 predicted structural proteins, including viral protein 10, which is encoded by the orf10 gene of the CCV. In this paper, the orf10 gene was expressed in Escherichia coli and used to produce a specific antibody. Western blot analysis confirmed that open reading frame 10 is an envelope protein. A viral neutralization assay demonstrated that open reading frame 10 antiserum was able to inhibit CCV infection of channel catfish ovary cells, suggesting that viral protein 10 is likely to play an important role in the CCV infection of channel catfish ovary cells.
Disruption of genes for the enhanced biosynthesis of α-ketoglutarate in Corynebacterium glutamicum
Authors: Jo Jae-Hyung , Seol Hye-Young , Lee Yun-Bom , Kim Min-Hong , Hyun Hyung-Hwan , Lee Hyune-Hwan
Published: March 2012

The development of microbial strains for the enhanced production of α-ketoglutarate (α-KG) was investigated using a strain of Corynebacterium glutamicum that overproduces of l-glutamate, by disrupting three genes involved in the α-KG biosynthetic pathway. The pathways competing with the biosynthesis of α-KG were blocked by knocking out aceA (encoding isocitrate lyase, ICL), gdh (encoding glutamate dehydrogenase, l-gluDH), and gltB (encoding glutamate synthase or glutamate-2-oxoglutarate aminotransferase, GOGAT). The strain with aceA, gltB, and gdh disrupted showed reduced ICL activity and no GOGAT and l-gluDH activities, resulting in up to 16-fold more α-KG production than the control strain in flask culture. These results suggest that l-gluDH is the key enzyme in the conversion of α-KG to l-glutamate; therefore, prevention of this step could promote α-KG accumulation. The inactivation of ICL leads the carbon flow to α-KG by blocking the glyoxylate pathway. However, the disruption of gltB did not affect the biosynthesis of α-KG. Our results can be applied in the industrial production of α-KG by using C. glutamicum as producer.
LOCAL COMMUNITY IDENTIFICATION IN SOCIAL NETWORKS
Authors: NGONMANG BLAISE , TCHUENTE MAURICE , VIENNET EMMANUEL
Published: March 2012

In social networks, the detection of communities has gained considerable interest because it can be used for instance for visualization, recommendation in business applications or the analysis of the spread of infectious diseases. Many methods proposed in the literature for the solution of this problem, assume that the structure of the entire network is known, which is not realistic for very large and dynamic networks. For this reason, approaches have been introduced recently to find the local community of a node. Most of these methods often fail when the starting node is at the boundary of a community. In addition, they are not able to detect overlapping communities. In this work, we propose new methods to find local communities that don't have these drawbacks. Experiences on real and computer generated social networks such as Netscience, Amazon 2006 and Lancichinetti et al.'s benchmark show that these methods perform better than the solutions with which the comparisons were performed.
DESIGNING A FUSION-DRIVEN SENSOR NETWORK TO SELECTIVELY TRACK MOBILE TARGETS
Authors: PHOHA SHASHI , MALLAPRAGADA GOUTHAM , WEN YICHENG , BEIN DOINA , RAY ASOK
Published: March 2012

Sensor networks that can support time-critical operations pose challenging problems for tracking events of interest. We propose an architecture for a sensor network that autonomously adapts in real-time to data fusion requirements so as not to miss events of interest and provides accurate real-time mobile target tracking. In the proposed architecture, the sensed data is processed in an abstract space called Information Space and the communication between nodes is modeled as an abstract space called Network Design Space. The two abstract spaces are connected through an interaction interface called InfoNet, that seamlessly translates the messages between the two. The proposed architecture is validated experimentally on a laboratory testbed for multiple scenarios.
RELIABLE INTERNET-BASED MASTER-WORKER COMPUTING IN THE PRESENCE OF MALICIOUS WORKERS
Authors: ANTA ANTONIO FERNÁNDEZ , GEORGIOU CHRYSSIS , LÓPEZ LUIS , SANTOS AGUSTÍN
Published: March 2012

We consider a Master-Worker distributed system where a master processor assigns, over the Internet, tasks to a collection of n workers, which are untrusted and might act maliciously. In addition, a worker may not reply to the master, or its reply may not reach the master, due to unavailabilities or failures of the worker or the network. Each task returns a value, and the goal is for the master to accept only correct values with high probability. Furthermore, we assume that the service provided by the workers is not free; for each task that a worker is assigned, the master is charged with a work-unit. Therefore, considering a single task assigned to several workers, our objective is to have the master processor to accept the correct value of the task with high probability, with the smallest possible amount of work (number of workers the master assigns the task). We probabilistically bound the number of faulty processors by assuming a known probability p < 1/2 of any processor to be faulty.

Our work demonstrates that it is possible to obtain, with provable analytical guarantees, high probability of correct acceptance with low work. In particular, we first show lower bounds on the minimum amount of (expected) work required, so that any algorithm accepts the correct value with probability of success 1 - ε, where ε ≪ 1 (e.g., 1/n). Then we develop and analyze two algorithms, each using a different decision strategy, and show that both algorithms obtain the same probability of success 1 - ε, and in doing so, they require similar upper bounds on the (expected) work. Furthermore, under certain conditions, these upper bounds are asymptotically optimal with respect to our lower bounds.
ON THE COMPUTATIONAL COMPLEXITY OF ROUTING IN FAULTY K-ARY N-CUBES AND HYPERCUBES
Authors: STEWART IAIN A.
Published: March 2012

We equate a routing algorithm in a (faulty) interconnection network whose underlying graph is a k-ary n-cube or a hypercube, that attempts to route a packet from a fixed source node to a fixed destination node, with the sub-digraph of (healthy) links potentially usable by this routing algorithm as it attempts to route the packet. This gives rise to a naturally defined problem, parameterized by this routing algorithm, relating to whether a packet can be routed from a given source node to a given destination node in one of our interconnection networks in which there are (possibly exponentially many) faulty links. We show that there exist such problems that are PSPACE-complete (all are solvable in PSPACE) but that there are (existing and popular) routing algorithms for which the computational complexity of the corresponding problem is significantly easier (yet still computationally intractable).
CLASSIFICATION OF MULTILINEAR REAL QUADRATIC PARTIAL DIFFERENCE EQUATIONS LINEARIZABLE BY POINT AND HOPF–COLE TRANSFORMATIONS
Authors: LEVI DECIO , SCIMITERNA CHRISTIAN
Published: March 2012

We use the conditions of linearizability by point and by Hopf–Cole transformations, introduced recently by the authors, to classify all real multilinear equations on a square lattice with at most quadratic nonlinearity. We find that, up to a linear transformation of the dependent variable and an exchange of the independent variables, only two equations in this class are linearizable by point transformations and none by Hopf–Cole transformations.