bluuebunny/crossref_metadata_2025 huggingface dataset:
Translational Careers
Authors: Andrews N. , Burris J. E. , Cech T. R. , Coller B. S. , Crowley W. F. , Gallin E. K. , Kelner K. L. , Kirch D. G. , Leshner A. I. , Morris C. D. , Nguyen F. T. , Oates J. , Sung N. S.
Published: May 2009

Powered by the computational muscle of bioinformatics and the broad perspective of systems biology, advances in biomedical science now have the capacity to transform medicine. Yet to fully realize the health benefits of new scientific insight, we must ensure a vibrant flow of information between the basic sciences and clinical medicine. This takes both systems and people.
The Cholera Crisis in Africa
Authors: Bhattacharya S. , Black R. , Bourgeois L. , Clemens J. , Cravioto A. , Deen J. L. , Dougan Gordon , Glass R. , Grais R. F. , Greco M. , Gust I. , Holmgren J. , Kariuki S. , Lambert P.-H. , Liu M. A. , Longini I. , Nair G. B. , Norrby R. , Nossal G. J. V. , Ogra P. , Sansonetti P. , von Seidlein L. , Songane F. , Svennerholm A.-M. , Steele D. , Walker R.
Published: May 2009

Long-lasting cholera outbreaks in Africa suggest limitations in the current strategy of disease control.
Ovulation Signals
Authors: Duggavathi Rajesha , Murphy Bruce D.
Published: May 2009

Human infertility may be associated with aberrant cell signaling events within ovarian granulosa cells.
Crossing the Line
Authors: Kidd Thomas
Published: May 2009

An axon guidance receptor generates a transcriptional response independent of its known ligand.
Two Beams Squeeze Feature Sizes in Optical Lithography
Authors: Perry Joseph W.
Published: May 2009

Competing activation and deactivation effects with shaped light beams could create in integrated circuit features much smaller than the beams' wavelengths.
Navigating Treacherous Waters
Authors: Charles Dan , Kaiser Jocelyn , Kintisch Eli , Stokstad Erik
Published: May 2009

Science lobbyists have cheered President Barack Obama's arrival at the helm of the U.S. ship of state for a host of reasons. But how long will that honeymoon last?
Science
discusses five areas that could cause friction between the new president and the research community.
Stimulus Funding Elicits a Tidal Wave of ‘Challenge Grants’
Authors: Kaiser Jocelyn
Published: May 2009

A frantic grant-writing effort that has consumed biomedical research scientists this spring came to an end last week, resulting in a huge pile of new applications—more than 10 times larger than expected—to be reviewed by the National Institutes of Health.
Texas Transplant Alfred Gilman Guides $3 Billion Cancer Project
Authors: Kaiser Jocelyn
Published: May 2009

Biochemist Alfred Gilman was named scientific director of the Cancer Prevention and Research Institute of Texas last month.
Science
interviewed Gilman recently; his comments have been edited for brevity.
Flu Researchers Train Sights On Novel Tricks of Novel H1N1
Authors: Cohen Jon
Published: May 2009

Shortly after receiving word on 23 April that the same odd strain of swine influenza had infected humans in both the United States and Mexico, researchers around the world pounced on this novel H1N1 virus.
Swine Flu Names Evolving Faster Than Swine Flu Itself
Authors: Enserink Martin
Published: May 2009

Three weeks after the world woke up to the threat of an influenza pandemic, a Babylonian confusion has arisen about what the virus—and the pandemic, if it happens—should be called.
Carbon Sheets an Atom Thick Give Rise to Graphene Dreams
Authors: Service Robert F.
Published: May 2009

Interest in a novel material with amazing properties continues to sweep through physics and chemistry labs worldwide. Will graphene's promise pay off?
Relativistic Physics in the Lab
Authors: Service Robert F.
Published: May 2009

Graphene holds enormous promise for transistors and other electronic devices (see main text). But it is already making an impact in the arcane world of high-energy physics.
Two Missions Go in Search of A Watery Lunar Bonanza
Authors: Kerr Richard A.
Published: May 2009

Frustrated by long-controversial hints of water ice on the moon, researchers-turned-miners are going to blast for the mother lode in hopes that astronauts can use water to fuel a permanent moon base.
Anti-Apical-Membrane-Antigen-1 Antibody Is More Effective than Anti-42-Kilodalton-Merozoite-Surface-Protein-1 Antibody in Inhibiting
Plasmodium falciparum
Growth, as Determined by the In Vitro Growth Inhibition Assay
Authors: Miura Kazutoyo , Zhou Hong , Diouf Ababacar , Moretz Samuel E. , Fay Michael P. , Miller Louis H. , Martin Laura B. , Pierce Mark A. , Ellis Ruth D. , Mullen Gregory E. D. , Long Carole A.
Published: May 2009

Apical membrane antigen 1 (AMA1) and the 42-kDa merozoite surface protein 1 (MSP1
42
) are leading malaria vaccine candidates. Several preclinical and clinical trials have been conducted, and an in vitro parasite growth inhibition assay has been used to evaluate the biological activities of the resulting antibodies. In a U.S. phase 1 trial with AMA1-C1/Alhydrogel plus CPG 7909, the vaccination elicited anti-AMA1 immunoglobulin G (IgG) which showed up to 96% inhibition. However, antibodies induced by MSP1
42
-C1/Alhydrogel plus CPG 7909 vaccine showed less than 32% inhibition in vitro. To determine whether anti-MSP1
42
IgG had less growth-inhibitory activity than anti-AMA1 IgG in vitro, the amounts of IgG that produced 50% inhibition of parasite growth (Ab
50
) were compared for rabbit and human antibodies. The Ab
50
s of rabbit and human anti-MSP1
42
IgGs were significantly higher (0.21 and 0.62 mg/ml, respectively) than those of anti-AMA1 IgGs (0.07 and 0.10 mg/ml, respectively) against 3D7 parasites. Ab
50
data against FVO parasites also demonstrated significant differences. We further investigated the Ab
50
s of mouse and monkey anti-AMA1 IgGs and showed that there were significant differences between the species (mouse, 0.28 mg/ml, and monkey, 0.14 mg/ml, against 3D7 parasites). Although it is unknown whether growth-inhibitory activity in vitro reflects protective immunity in vivo, this study showed that the Ab
50
varies with both antigen and species. Our data provide a benchmark for antibody levels for future AMA1- or MSP1
42
-based vaccine development efforts in preclinical and clinical trials.
Multiplex Strategy for Multilocus Sequence Typing,
fla
Typing, and Genetic Determination of Antimicrobial Resistance of
Campylobacter jejuni
and
Campylobacter coli
Isolates Collected in Switzerland
Authors: Korczak Bożena M. , Zurfluh Monika , Emler Stefan , Kuhn-Oertli Jacqueline , Kuhnert Peter
Published: May 2009

We present an optimized multilocus sequence typing (MLST) scheme with universal primer sets for amplifying and sequencing the seven target genes of
Campylobacter jejuni
and
Campylobacter coli
. Typing was expanded by sequence determination of the genes
flaA
and
flaB
using optimized primer sets. This approach is compatible with the MLST and
flaA
schemes used in the PubMLST database and results in an additional typing method using the
flaB
gene sequence. An identification module based on the 16S rRNA and
rpoB
genes was included, as well as the genetic determination of macrolide and quinolone resistances based on mutations in the 23S rRNA and
gyrA
genes. Experimental procedures were simplified by multiplex PCR of the 13 target genes. This comprehensive approach was evaluated with
C. jejuni
and
C. coli
isolates collected in Switzerland. MLST of 329 strains resulted in 72 sequence types (STs) among the 186
C. jejuni
strains and 39 STs for the 143
C. coli
isolates. Fourteen (19%) of the
C. jejuni
and 20 (51%) of the
C. coli
STs had not been found previously. In total, 35% of the
C. coli
strains collected in Switzerland contained mutations conferring antibiotic resistance only to quinolone, 15% contained mutations conferring resistance only to macrolides, and 6% contained mutations conferring resistance to both classes of antibiotics. In
C. jejuni
, these values were 31% and 0% for quinolone and macrolide resistance, respectively. The
rpoB
sequence allowed phylogenetic differentiation between
C. coli
and
C. jejuni
, which was not possible by 16S rRNA gene analysis. An online Integrated Database Network System (SmartGene, Zug, Switzerland)-based platform for MLST data analysis specific to
Campylobacter
was implemented. This Web-based platform allowed automated allele and ST designation, as well as epidemiological analysis of data, thus streamlining and facilitating the analysis workflow. Data networking facilitates the exchange of information between collaborating centers. The described approach simplifies and improves the genotyping of
Campylobacter
, allowing cost- and time-efficient routine monitoring.
Evaluation of an Array-Based Method for Human Papillomavirus Detection and Genotyping in Comparison with Conventional Methods Used in Cervical Cancer Screening
Authors: García-Sierra Nerea , Martró Elisa , Castellà Eva , Llatjós Mariona , Tarrats Antoni , Bascuñana Elisabet , Díaz Rosana , Carrasco María , Sirera Guillem , Matas Lurdes , Ausina Vicente
Published: May 2009

Cervical cancer is the second-most prevalent cancer in young women around the world. Infection with human papillomavirus (HPV), especially high-risk HPV types (HR-HPV), is necessary for the development of this cancer. HPV-DNA detection is increasingly being used in cervical cancer screening programs, together with the Papanicolau smear test. We evaluated the usefulness of introducing this new array-based HPV genotyping method (i.e., Clinical Arrays Papillomavirus Humano) in the cervical cancer screening algorithm in our center. The results obtained using this method were compared to those obtained by the hybrid capture II high-risk HPV DNA test (HC-II) and Papanicolau in a selected group of 408 women. The array-based assay was performed in women that were HC-II positive or presented cytological alterations. Among 246 array-positive patients, 123 (50%) presented infection with ≥2 types, and HR-HPV types were detected in 206 (83.7%), mainly HPV-16 (24.0%). Up to 132 (33.2%) specimens were classified as ASCUS (for atypical squamous cells of undetermined significance), and only 48 (36.4%) of them were HPV-DNA positive by either assay; however, 78.7% of these cases were caused by HR-HPV types. The agreement between both HPV-DNA detection techniques was fairly good (
n
= 367). Screening with Papanicolau smear and HC-II tests, followed by HPV detection and genotyping, provided an optimal identification of women at risk for the development of cervical cancer. Furthermore, with the identification of specific genotypes, either in single or multiple infections, a better prediction of disease progression was achieved. The array method also made allowed us to determine the possible contribution of the available vaccines in our setting.
Real-Time PCR-Based Pathotyping of Newcastle Disease Virus by Use of TaqMan Minor Groove Binder Probes
Authors: Farkas T. , Székely É. , Belák S. , Kiss I.
Published: May 2009

A real-time reverse-transcription PCR was developed to detect and pathotype Newcastle disease viruses (NDV) in clinical samples. Degenerate oligonucleotide primers and TaqMan probes with nonfluorescent minor groove binder (MGB) quencher amplified and hybridized to a region in the fusion protein (F) gene that corresponds to the cleavage site of the F0 precursor, which is a key determinant of NDV pathogenicity. The application of degenerate primers and TaqMan MGB probes provided high specificity to the assay, as was shown by the successful and rapid pathotype determination of 39 NDV strains representing all the known genotypes (I to VIII) and pathotypes (lentogens/mesogens/velogens). The PCR assays specific for lentogenic and velogenic/mesogenic strains had high analytical sensitivity, detecting approximately 10 and 20 copies of the target molecule per reaction, respectively. The detection limit was also determined in terms of 50% egg infective dose (EID
50
) by using dilution series of virus stock solutions to be approximately 10
1.0
and 10
−1.3
EID
50
/ml for lentogens and velogens/mesogens, respectively. Organ, swab, and stool specimens from experimentally infected animals were tested to prove the clinical suitability of the method. The results of this study suggest that the described real-time PCR assay has the potential to be used for the rapid detection/pathotyping of NDV isolates and qualitative/quantitative measurement of the virus load.
Prevalence and Molecular Diversity of Hepatitis B Virus and Hepatitis Delta Virus in Urban and Rural Populations in Northern Gabon in Central Africa
Authors: Makuwa Maria , Mintsa-Ndong Armel , Souquière Sandrine , Nkoghé Dieudonné , Leroy Eric M. , Kazanji Mirdad
Published: May 2009

The prevalence of hepatitis B virus (HBV) surface antigen was significantly higher in urban (12.9%) than in rural (7.6%) populations (
P
= 0.003), but no difference was found in the prevalence of hepatitis delta virus (HDV), which was high in both populations. Phylogenetic analysis showed the circulation of HBV-A3 and -E genotypes and the presence of HDV-1, HDV-7, and HDV-8 clades.
Comparison of the BD Phoenix System with the Cefoxitin Disk Diffusion Test for Detection of Methicillin Resistance in
Staphylococcus aureus
and Coagulase-Negative Staphylococci
Authors: Mencacci Antonella , Montecarlo Ines , Gonfia Francesca , Moretti Amedeo , Cardaccia Angela , Farinelli Senia , Pagliochini Maria Rita , Giuliani Angela , Basileo Michela , Pasticci Maria Bruna , Bistoni Francesco
Published: May 2009

The BD Phoenix system was compared to the cefoxitin disk diffusion test for detection of methicillin (meticillin) resistance in 1,066
Staphylococcus aureus
and 1,121 coagulase-negative staphylococcus (CoNS) clinical isolates. The sensitivity for Phoenix was 100%. The specificities were 99.86% for
S. aureus
and 88.4% for CoNS.
Simulation and Prediction of the Adaptive Immune Response to Influenza A Virus Infection
Authors: Lee Ha Youn , Topham David J. , Park Sung Yong , Hollenbaugh Joseph , Treanor John , Mosmann Tim R. , Jin Xia , Ward Brian M. , Miao Hongyu , Holden-Wiltse Jeanne , Perelson Alan S. , Zand Martin , Wu Hulin
Published: May 2009

The cellular immune response to primary influenza virus infection is complex, involving multiple cell types and anatomical compartments, and is difficult to measure directly. Here we develop a two-compartment model that quantifies the interplay between viral replication and adaptive immunity. The fidelity of the model is demonstrated by accurately confirming the role of CD4 help for antibody persistence and the consequences of immune depletion experiments. The model predicts that drugs to limit viral infection and/or production must be administered within 2 days of infection, with a benefit of combination therapy when administered early, and cytotoxic CD8 T cells in the lung are as effective for viral clearance as neutralizing antibodies when present at the time of challenge. The model can be used to investigate explicit biological scenarios and generate experimentally testable hypotheses. For example, when the adaptive response depends on cellular immune cell priming, regulation of antigen presentation has greater influence on the kinetics of viral clearance than the efficiency of virus neutralization or cellular cytotoxicity. These findings suggest that the modulation of antigen presentation or the number of lung resident cytotoxic cells and the combination drug intervention are strategies to combat highly virulent influenza viruses. We further compared alternative model structures, for example, B-cell activation directly by the virus versus that through professional antigen-presenting cells or dendritic cell licensing of CD8 T cells.
Human Immunodeficiency Virus Type 1 Elite Neutralizers: Individuals with Broad and Potent Neutralizing Activity Identified by Using a High-Throughput Neutralization Assay together with an Analytical Selection Algorithm
Authors: Simek Melissa D. , Rida Wasima , Priddy Frances H. , Pung Pham , Carrow Emily , Laufer Dagna S. , Lehrman Jennifer K. , Boaz Mark , Tarragona-Fiol Tony , Miiro George , Birungi Josephine , Pozniak Anton , McPhee Dale A. , Manigart Olivier , Karita Etienne , Inwoley André , Jaoko Walter , DeHovitz Jack , Bekker Linda-Gail , Pitisuttithum Punnee , Paris Robert , Walker Laura M. , Poignard Pascal , Wrin Terri , Fast Patricia E. , Burton Dennis R. , Koff Wayne C.
Published: May 2009

The development of a rapid and efficient system to identify human immunodeficiency virus type 1 (HIV-1)-infected individuals with broad and potent HIV-1-specific neutralizing antibody responses is an important step toward the discovery of critical neutralization targets for rational AIDS vaccine design. In this study, samples from HIV-1-infected volunteers from diverse epidemiological regions were screened for neutralization responses using pseudovirus panels composed of clades A, B, C, and D and circulating recombinant forms (CRFs). Initially, 463 serum and plasma samples from Australia, Rwanda, Uganda, the United Kingdom, and Zambia were screened to explore neutralization patterns and selection ranking algorithms. Samples were identified that neutralized representative isolates from at least four clade/CRF groups with titers above prespecified thresholds and ranked based on a weighted average of their log-transformed neutralization titers. Linear regression methods selected a five-pseudovirus subset, representing clades A, B, and C and one CRF01_AE, that could identify top-ranking samples with 50% inhibitory concentration (IC50) neutralization titers of ≥100 to multiple isolates within at least four clade groups. This reduced panel was then used to screen 1,234 new samples from the Ivory Coast, Kenya, South Africa, Thailand, and the United States, and 1% were identified as elite neutralizers. Elite activity is defined as the ability to neutralize, on average, more than one pseudovirus at an IC50titer of 300 within a clade group and across at least four clade groups. These elite neutralizers provide promising starting material for the isolation of broadly neutralizing monoclonal antibodies to assist in HIV-1 vaccine design.
Requirements for the Formation of Membrane Pores by the Reovirus Myristoylated μ1N Peptide
Authors: Zhang Lan , Agosto Melina A. , Ivanovic Tijana , King David S. , Nibert Max L. , Harrison Stephen C.
Published: May 2009

The outer capsid of the nonenveloped mammalian reovirus contains 200 trimers of the μ1 protein, each complexed with three copies of the protector protein σ3. Conformational changes in μ1 following the proteolytic removal of σ3 lead to release of the myristoylated N-terminal cleavage fragment μ1N and ultimately to membrane penetration. The μ1N fragment forms pores in red blood cell (RBC) membranes. In this report, we describe the interaction of recombinant μ1 trimers and synthetic μ1N peptides with both RBCs and liposomes. The μ1 trimer mediates hemolysis and liposome disruption under conditions that promote the μ1 conformational change, and mutations that inhibit μ1 conformational change in the context of intact virus particles also prevent liposome disruption by particle-free μ1 trimer. Autolytic cleavage to form μ1N is required for hemolysis but not for liposome disruption. Pretreatment of RBCs with proteases rescues hemolysis activity, suggesting that μ1N cleavage is not required when steric barriers are removed. Synthetic myristoylated μ1N peptide forms size-selective pores in liposomes, as measured by fluorescence dequenching of labeled dextrans of different sizes. Addition of a C-terminal solubility tag to the peptide does not affect activity, but sequence substitution V13N or L36D reduces liposome disruption. These substitutions are in regions of alternating hydrophobic residues. Their locations, the presence of an N-terminal myristoyl group, and the full activity of a C-terminally extended peptide, along with circular dichroism data that indicate prevalence of β-strand secondary structure, suggest a model in which μ1N β-hairpins assemble in the membrane to form a β-barrel pore.
Mumps Virus Matrix, Fusion, and Nucleocapsid Proteins Cooperate for Efficient Production of Virus-Like Particles
Authors: Li Ming , Schmitt Phuong Tieu , Li Zhuo , McCrory Thomas S. , He Biao , Schmitt Anthony P.
Published: May 2009

Paramyxovirus particles, like other enveloped virus particles, are formed by budding from membranes of infected cells. To define mumps virus (MuV) proteins important for this process, viral proteins were expressed either singly or in combination in mammalian cells to produce virus-like particles (VLPs). Only the MuV matrix (M) protein when expressed by itself was capable of inducing particle release, but the quantity of these M-alone particles was very small. Efficient production of mumps VLPs occurred only when the M protein was coexpressed together with other viral proteins, with maximum production achieved upon coexpression of the viral M, nucleocapsid (NP), and fusion (F) proteins together. Electron microscopy analysis confirmed that VLPs were morphologically similar to MuV virions. The two MuV glycoproteins were not equal contributors to particle formation. The F protein was a major contributor to VLP production, while the hemagglutinin-neuraminidase protein made a smaller contribution. Evidence for the involvement of class E protein machinery in VLP budding was obtained, with mumps VLP production inhibited upon expression of dominant-negative versions of the class E proteins Vps4A and Chmp4b. Disruption of the sequence 24-FPVI-27 within the MuV M protein led to poor VLP production, consistent with findings of earlier studies of a related sequence, FPIV, important for the budding of parainfluenza virus 5. Together, these results demonstrate that different MuV structural proteins cooperate together for efficient particle production and that particle budding likely involves host class E protein machinery.
Nef-Induced CD4 Endocytosis in Human Immunodeficiency Virus Type 1 Host Cells: Role of p56lckKinase
Authors: Laguette Nadine , Brégnard Christelle , Bouchet Jérôme , Benmerah Alexandre , Benichou Serge , Basmaciogullari Stéphane
Published: May 2009

Human immunodeficiency virus type 1 (HIV-1) Nef interferes with the endocytic machinery to modulate the cell surface expression of CD4. However, the basal trafficking of CD4 is governed by different rules in the target cells of HIV-1: whereas CD4 is rapidly internalized from the cell surface in myeloid cells, CD4 is stabilized at the plasma membrane through its interaction with the p56lckkinase in lymphoid cells. In this study, we showed that Nef was able to downregulate CD4 in both lymphoid and myeloid cell lines but that an increase in the internalization rate of CD4 could be observed only in lymphoid cells. Expression of p56lckin nonlymphoid CD4-expressing cells restores the ability of Nef in order to increase the internalization rate of CD4. Concurrent with this observation, the expression of a p56lck-binding-deficient mutant of CD4 in lymphoid cells abrogates the Nef-induced acceleration of CD4 internalization. We also show that the expression of Nef causes a decrease in the association of p56lckwith cell surface-expressed CD4. Regardless of the presence of p56lck, the downregulation of CD4 by Nef was followed by CD4 degradation. Our results imply that Nef uses distinct mechanisms to downregulate the cell surface expression levels of CD4 in either lymphoid or myeloid target cells of HIV-1.
A Computer Technique for Estimating the Size of Sexual Maturity in Crabs
Authors: Somerton D. A.
Published: May 2009

A new computer technique for estimating the size of 50% sexual maturity from crab morphometric data is described. Using nonhierarchical cluster analysis, crabs are assigned to either of two maturity groups based on the size of one body dimension relative to another. The size of 50% maturity is then estimated by using nonlinear regression to fit a logistic function to percent maturity and size estimates. The size of 50% maturity in the eastern Bering Sea was estimated to be 102.8 and 101.9 mm (carapace length) for male and female Paralithodes camtschatica and 114.7 mm (carapace width) for male Chionoecetes bairdi. These estimates are similar to estimates for these species obtained previously by other techniques.Key words: crabs, growth, sexual maturity, Paralithodes, Chionoecetes
Daily Growth Rings in the Otoliths of Juvenile Sockeye Salmon (Oncorhynchus nerka)
Authors: Wilson K. H. , Larkin P. A.
Published: May 2009

Sockeye salmon fry were collected from the Fulton River spawning channel at Babine Lake, British Columbia, in May 1978. The fish were reared for 26 d in enclosures in the spawning channel and were sampled every 7 to 10 d. The sagittae were removed from 25 fish from each sample, and the growth rings in one otolith from each fish were counted. A regression of the number of rings on the number of days since capture showed that these rings are, on average, formed daily, beginning at the time of emergence. A number of possible technical and biological causes of variation in ring counts within and between samples are considered.Key words: otolith, sagittae, daily growth rings, sockeye salmon fry
Bacteria Associated with Fin Rot Disease in Hatchery-Reared Atlantic Salmon (Salmo salar)
Authors: Schneider Robert , Nicholson Bruce L.
Published: May 2009

Fin rot is a progressive necrotic disease of many fish species. Several bacteria have been implicated in the etiology of the disease. To determine the bacteria associated with the disease in Atlantic salmon, fish were randomly sampled at weekly intervals at two hatcheries from August 1977 to April 1978. The degree of fin rot was scored numerically by a standard method and bacteria were enumerated by plate count on several media. Representative colonies were isolated for identification. The extent and severity of fin rot increased as the water temperature decreased. The average total colony counts from healthy fins of fish at both hatcheries were low (2.5 × 103/g) and included a variety of bacteria. The average total colony counts from fins with severe rot were high (2.0 × 105/g) with one or more Flexibacter species and Aeromonas salmonicida accounting for 50–90% of the total. Statistical analysis showed a highly significant positive correlation of fin rot with Aeromonas salmonicida colony counts at hatchery I, whereas the disease was correlated only with Flexibacter colony counts at hatchery II. High colony counts of both Flexibacter sp. and A. salmonicida were correlated with low water temperatures at the respective hatcheries. Electron microscopical examination of fins with advanced lesions revealed evidence of tissue necrosis surrounding bacteria. Thus, while no relationship was observed between bacteria and the onset of fin rot disease, evidence was obtained implicating at least two species of bacteria as probable etiological agents of the progressive disease.Key words: bacteria, fin rot disease, Atlantic salmon
Enhancement of the Survival of Rainbow Trout (Salmo gairdneri) Eggs and Fry in an Acid Lake through Incubation in Limestone
Authors: Gunn J. M. , Keller W.
Published: May 2009

Incubation of eyed rainbow trout (Salmo gairdneri) eggs within boxes (60 × 60 × 30 cm) of crushed limestone enhanced hatching success and sac fry surival in acidic (pH ~5.3) George Lake. Hatching (egg–sac fry) success in limestone (86.9%) along a sheltered shoreline (interstitial pH 6.2–7.6) approached results in Fairbank, a near-neutral control lake (93.7–97.9%). Eggs incubated in limestone along a windswept shoreline and subjected to periodic depression of interstitial water pH (minimum recorded 5.6) due to wave action exhibited poor hatching success (57.4%) comparable to results (11.2–57.1%) for eggs exposed within substrates of mixed, noncalcareous gravel (minimum pH 5.2–5.4). Sac fry survival (sac fry alevins) was high in sheltered limestone substrates (70.9%), low in wind-exposed limestone substrates (23.2%), and very poor (0.2–0.4%) in noncalcareous gravel.Exposure to emergent alevins hatched within limestone to ambient, acidic lake water resulted in 65.2–78.8% mortality during a 5-d holding period. Mortality decreased greatly among alevins held at pH 5.6–5.9 (48.0%) and pH 6.1–6.3 (2.0%)Incubation of eggs within limestone substrates holds promise for use as a tool in the maintenance of salmonid populations in acidic lakes. Key words : rainbow trout, pH, limestone, acidic lake
Hypolimnion Oxygen Consumption in Lakes: Discussion of Productivity and Morphometry Effects
Authors: Charlton M. N.
Published: May 2009

Until recently, hypolimnion oxygen consumption was thought to be a way of comparing the productivity of lakes. This study shows that hypolimnion oxygen represents hypolimnion thickness and temperature as well as productivity. A relationship based on the multiplicative effects of chlorophyll (productivity), thickness, and temperature closely fits the observed oxygen depletion in the Laurentian Great Lakes and in many small lakes. Applied to Lake Erie, the relationship suggests that although a 50% decrease in productivity may result in higher oxygen concentrations, significant oxygen depletion would still occur. The use of oxygen concentrations, depletion rates, or areal deficits to compare the productivity of lakes is not justified without reference to hypolimnion thickness and temperature.Key words: lake, hypolimnion, oxygen, productivity, Lake Erie
Thermal Habitat Partitioning by Fishes in Lake Michigan
Authors: Brandt Stephen B. , Magnuson John J. , Crowder Larry B.
Published: May 2009

Thermal distribution of Lake Michigan fishes were determined by aimed bottom trawling (n = 68) along temperature isotherms (3–20 °C) in a region where the thermocline intersected the bottom off Grand Haven, Michigan, during September. Alewife (Alosa pseudoharengus), rainbow smelt (Osmerus mordax), spottail shiner (Notropis hudsonius), and trout-perch (Percopsis omiscomaycus) comprised 94% of the catch by numbers. Species segregated along temperature gradients. Patterns of thermal habitat partitioning were maintained despite rapid oscillations in thermocline location. Alewife, rainbow trout, and yellow perch (Perca flavescens) showed intraspecific differences in thermal distribution of size-classes. Thermal niche shifts of some fishes on the bottom apparently occur at dawn and dusk. Patterns of thermal resource use are considered in relation to competition, predation, and thermal ecology of the more common species.Key words: competition, fishes, habitat partitioning, Lake Michigan, predation, temperature
Diurnal Variation in the Feeding Intensity and Catchability of Silver Hake (Merluccius bilinearis)
Authors: Bowman Ray E. , Bowman Edgar W.
Published: May 2009

Feeding intensity and catchability of silver hake (Merluccius bilinearis) during periods of daylight and darkness were examined. Silver hake feed at night from just after dark until predawn, but mostly between dusk and midnight. After ~15 h in the stomach, partly digested food passes into the intestine where it continues to be digested for another 9 h before being evacuated. A variety of free-swimming crustaceans (i.e. Crangon septemspinosa, Dichelopandalus leptocerus, and Monoculodes intermedius) make up the largest part of the diet. Silver hake are located on or immediately above the bottom during the day and off bottom at night. Pelagic trawls, off-bottom trawls, and bottom trawls with roller gear tend to pass over silver hake during the day, while bottom trawls with chain-disc sweeps and cable sweeps catch large quantities. A high opening trawl combined with a chain-disc sweep would substantially increase the mean yield per tow by a vessel operating on a 24-h basis.Key words: silver hake, Merluccius bilinearis; feeding, food, diurnal variation, catchability, availability
ESTIMATION OF THERMAL CONDUCTIVITY OF POROUS MATERIAL WITH FEM AND FRACTAL GEOMETRY
Authors: LI SHOUJU , WANG YUEFANG , LIU YINGXI , SUN WEI
Published: May 2009

The relationship between thermal conductivity of porous material and fractal dimension is numerically simulated by using the finite element method. The solid matrix and pore space are generated randomly according to material porosity. Material parameters and element properties are changed by using ANSYS parameter design language. The effective thermal conductivity is derived according to thermal flux through some sections computed by FEM and Fourier heat transform law. The investigation shows that the effective thermal conductivity decreases with increasing porosity. The effective thermal conductivity will decrease exponentially with increasing fractal dimension of porosity space and increase exponentially with increasing fractal dimension of solid matrix.
SCHEME FOR REMOTELY PREPARING THREE-PARTICLE GHZ-CLASS STATES
Authors: PAN GUI-XIA , LIU YI-MIN , ZHANG WEN , ZHANG ZHAN-JUN
Published: May 2009

A scheme is proposed for remotely preparing a class of three-particle GHZ states by using a Bell state and a three-qubit GHZ state as the quantum channel. In the scheme, a two-qubit collective state measurement is performed and the necessary classical communication cost is 0.25 cbit on average. In general, the target state can be successfully prepared with the probability 1/4. However, if the state belongs to some special classes, the preparation success probability can reach 0.5 or even 1 after consuming a little additional classical resource. Comparing with the recent scheme [Opt. Commun.281, 871 (2008)], the present scheme has some advantages, e.g., the simpler quantum joint measurement and the less classical resource consumption.
THE PERFORMANCE OF GENETIC ALGORITHM WITH ADJUSTMENT OF A SEARCH SPACE
Authors: AMIRJANOV ADIL
Published: May 2009

This paper investigates the effect of a linear adjustment of a search space size in genetic algorithm (GA) on the macroscopic statistical properties of population (such as the average fitness and the variance fitness of population). The equations of motion were derived for one-max problem that expressed the macroscopic statistical properties of population after the adjustment of a search space size. Analysis of a performance of GA that includes a computational cost and a quality of the optimal solution was made for linear and power laws of search space adjustment.
ANTICIPATED FUNCTION SYNCHRONIZATION WITH UNKNOWN PARAMETERS OF DISCRETE-TIME CHAOTIC SYSTEMS
Authors: LI YIN , LI BIAO , CHEN YONG
Published: May 2009

In this paper, firstly, the control problem for the chaos synchronization of discrete-time chaotic (hyperchaotic) systems with unknown parameters are considered. Next, backstepping control law is derived to make the error signals between drive 2D discrete-time chaotic system and response 2D discrete-time chaotic system with two uncertain parameters asymptotically synchronized. Finally, the approach is extended to the synchronization problem for 3D discrete-time chaotic system with two unknown parameters. Numerical simulations are presented to show the effectiveness of the proposed chaos synchronization scheme.
STABILITY AND ACCURACY OF LATTICE BOLTZMANN SCHEMES FOR ANISOTROPIC ADVECTION-DIFFUSION EQUATIONS
Authors: SUGA SHINSUKE
Published: May 2009

The stability of the numerical schemes for anisotropic advection-diffusion equations derived from the lattice Boltzmann equation with the D2Q4 particle velocity model is analyzed through eigenvalue analysis of the amplification matrices of the scheme. Accuracy of the schemes is investigated by solving benchmark problems, and the LBM scheme is compared with traditional implicit schemes. Numerical experiments demonstrate that the LBM scheme produces stable numerical solutions close to the analytical solutions when the values of the relaxation parameters in x and y directions are greater than 1.9 and the Courant numbers satisfy the stability condition. Furthermore, the numerical solutions produced by the LBM scheme are more accurate than those of the Crank–Nicolson finite difference scheme for the case where the Courant numbers are set to be values close to the upper bound of the stability region of the scheme.
IMPERFECT COORDINATION IN OPTIMIZATION
Authors: BARRIOS ELENA RAMÍREZ , OCHOA JUAN G. DÍAZ
Published: May 2009

We present a novel optimization method for an Ising like system suspended in a lattice with nonstatic defects. Depending on the size of the experimental probe the system spontaneously defines a defect free lattice where the control function can be optimized using conventional methods as Metropolis heuristics. We illustrate this method in a lattice with variable defects and show how the magnetization of the system depends on the spontaneous definition of the defect-free lattice. This approximation should be useful as a basis for the definition of systems of agents with imperfect coordination.
APPROXIMATE ℓ-STATE SOLUTIONS OF A SPIN-0 PARTICLE FOR WOODS–SAXON POTENTIAL
Authors: ARDA ALTUĞ , SEVER RAMAZAN
Published: May 2009

The radial part of Klein–Gordon equation is solved for the Woods–Saxon potential within the framework of an approximation to the centrifugal barrier. The bound states and the corresponding normalized eigenfunctions of the Woods–Saxon potential are computed by using the Nikiforov–Uvarov method. The results are consistent with the ones obtained in the case of generalized Woods–Saxon potential. The solutions of the Schrödinger equation by using the same approximation are also studied as a special case, and obtained the consistent results with the ones obtained before.
PARALLEL TEMPERING FOR THE TRAVELING SALESMAN PROBLEM
Authors: WANG CHIAMING , HYMAN JEFFREY D. , PERCUS ALLON , CAFLISCH RUSSEL
Published: May 2009

We explore the potential of parallel tempering as a combinatorial optimization method, applying it to the traveling salesman problem. We compare simulation results of parallel tempering with a benchmark implementation of simulated annealing, and study how different choices of parameters affect the relative performance of the two methods. We find that a straightforward implementation of parallel tempering can outperform simulated annealing in several crucial respects. When parameters are chosen appropriately, both methods yield close approximation to the actual minimum distance for an instance with 200 nodes. However, parallel tempering yields more consistently accurate results when a series of independent simulations are performed. Our results suggest that parallel tempering might offer a simple but powerful alternative to simulated annealing for combinatorial optimization problems.
Endothelial cell traction and ECM density influence both capillary morphogenesis and maintenance in 3-D
Authors: Kniazeva Ekaterina , Putnam Andrew J.
Published: May 2009

Identifying the mechanisms regulating angiogenesis in pathological conditions such as cancer and heart disease is crucial to develop successful therapies. The dependence of angiogenesis on characteristic properties of these conditions, such as alterations in tissue stiffness due to changes in the composition of the extracellular matrix (ECM), may shed light on potential therapeutic strategies. Prior studies have suggested that ECM compliance regulates capillary morphogenesis, but the mechanisms remain unclear. In this study, we hypothesized that ECM density, which influences substrate mechanics, may regulate angiogenesis via a mechanism involving actin-mediated cell-generated forces. To investigate this hypothesis, we utilized an in vitro model of angiogenesis in which endothelial cells coated on microcarrier beads are distributed within a three-dimensional (3-D) fibrin ECM. A monolayer of fibroblasts, which provides pro-angiogenic factors, is cultured on top of the gel. Variations in fibrin gel density, along with a library of pharmacological agents that inhibit forces generated by the actin cytoskeleton, were used to prove the necessity of cell-generated tractional forces in blood vessel formation. Our data demonstrate that cell-generated forces not only play a crucial role in the early sprouting stages of capillary morphogenesis but are also required in the later maintenance stages, and thereby suggest a broader interdependence among tissue stiffness, cell contractile forces, and angiogenesis.
Identification of the large-conductance background K+ channel in mouse B cells as TREK-2
Authors: Zheng Haifeng , Nam Joo Hyun , Pang Bo , Shin Dong Hoon , Kim Ji Seon , Chun Yang-Sook , Park Jong-Wan , Bang Hyowon , Kim Woo Kyung , Earm Yung E. , Kim Sung Joon
Published: May 2009

Mouse B cells and their cell line (WEHI-231) express large-conductance background K+ channels (LKbg) that are activated by arachidonic acids, characteristics similar to TREK-2. However, there is no evidence to identify the molecular nature of LKbg; some properties of LKbg were partly different from the reported results of TREK type channels. In this study, we compared the properties of cloned TREK-2 and LKbg in terms of their sensitivities to ATP, phosphatidylinositol 4,5-bisphosphate (PIP2), intracellular pH (pHi), and membrane stretch. Similar to the previous findings of LKbg, TREK-2 showed spontaneous activation after membrane excision (i-o patch) and were inhibited by MgATP or by PIP2. The inhibition by MgATP was prevented by wortmannin, suggesting membrane-delimited regulation of TREKs by phosphoinositide (PI) kinase. The same was observed with the property of LKbg; the activation of TREK-2 by membrane stretch was suppressed by U73122 (PLC inhibitor). As with the known properties of TREK-2, LKbg were activated by acidic pHi and inhibited by PKC activator. Finally, we confirmed the expression of TREK-2 in WEHI-231 by using RT-PCR and immunoblot analyses. The amplitude of background K+ current and the TREK-2 expression in WEHI-231 were commonly decreased by genetic knockdown of TREK-2 using small interfering RNA. The downregulation of TREK-2 attenuated Ca2+-influx induced by arachidonic acid in WEHI-231. As a whole, these results strongly indicate that TREK-2 encodes LKbg in mouse B cells. We also newly suggest that the low activity of TREK-2 in intact cells is due to the inhibition by intrinsic PIP2.
The role of PGC-1α on mitochondrial function and apoptotic susceptibility in muscle
Authors: Adhihetty Peter J. , Uguccioni Giulia , Leick Lotte , Hidalgo Juan , Pilegaard Henriette , Hood David A.
Published: May 2009

Mitochondria are critical for cellular bioenergetics, and they mediate apoptosis within cells. We used whole body peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α) knockout (KO) animals to investigate its role on organelle function, apoptotic signaling, and cytochrome- c oxidase activity, an indicator of mitochondrial content, in muscle and other tissues (brain, liver, and pancreas). Lack of PGC-1α reduced mitochondrial content in all muscles (17–44%; P < 0.05) but had no effect in brain, liver, and pancreas. However, the tissue expression of proteins involved in mitochondrial DNA maintenance [transcription factor A (Tfam)], import (Tim23), and remodeling [mitofusin 2 (Mfn2) and dynamin-related protein 1 (Drp1)] did not parallel the decrease in mitochondrial content in PGC-1α KO animals. These proteins remained unchanged or were upregulated ( P < 0.05) in the highly oxidative heart, indicating a change in mitochondrial composition. A change in muscle organelle composition was also evident from the alterations in subsarcolemmal and intermyofibrillar mitochondrial respiration, which was impaired in the absence of PGC-1α. However, endurance-trained KO animals did not exhibit reduced mitochondrial respiration. Mitochondrial reactive oxygen species (ROS) production was not affected by the lack of PGC-1α, but subsarcolemmal mitochondria from PGC-1α KO animals released a greater amount of cytochrome c than in WT animals following exogenous ROS treatment. Our results indicate that the lack of PGC-1α results in 1) a muscle type-specific suppression of mitochondrial content that depends on basal oxidative capacity, 2) an alteration in mitochondrial composition, 3) impaired mitochondrial respiratory function that can be improved by training, and 4) a greater basal protein release from subsarcolemmal mitochondria, indicating an enhanced mitochondrial apoptotic susceptibility.
Differences in the quantal release of catecholamines in chromaffin cells of rat embryos and their mothers
Authors: Fernández-Morales José C. , Cortés-Gil Lorena , García Antonio G. , de Diego Antonio M. G.
Published: May 2009

Studies on the bulk catecholamine release from fetal and neonatal rat adrenals, adrenal slices, or isolated chromaffin cells stimulated with high K+, hypoxia, hypercapnia, or acidosis are available. However, a study analyzing the kinetics of quantal secretion is lacking. We report here such a study in which we compare the quantal release of catecholamines from immature rat embryo chromaffin cells (ECCs) and their mothers' (MCCs). Cell challenging with a strong depolarizing stimulus (75 mM K+) caused spike bursts having the following characteristics. ECCs released more multispike events and wave envelopes than MCCs. This, together with narrower single-spike events, a faster decay, and a threefold smaller quantal size suggest a faster secretory machinery in ECCs. Furthermore, with a milder stimulus (25 mM K+) enhanced Ca2+entry by L-type Ca2+channel activator BAY K 8644 did not change the kinetic parameters of single spikes in ECCs; in contrast, augmentation of Ca2+entry increased spike amplitude and width, quantal size, and decay time in MCCs. This suggests that in mature MCCs, the last exocytotic steps are more tightly regulated than in immature ECCs. Finally, we found that quantal secretion was fully controlled by L-type voltage-dependent Ca2+channels (VDCCs) in ECCs, whereas both L- and non-L VDCCs (N and PQ) contributed equally to secretion control in MCCs. Our results have the following physiological, pharmacological, and clinical relevance: 1) they may help to better understand the regulation of adrenal catecholamine release in response to stress during fetal life and delivery; 2) if clinically used, L-type Ca2+channel blockers may augment the incidence of sudden infant death syndrome (SIDS); and 3) so-called Ca2+promotors or activators of Ca2+entry through L-type VDCCs may be useful to secure a healthy catecholamine surge upon violent stress during fetal life, at birth, or to prevent the SIDS in neonates at risk.
Ischemia-reperfusion reduces cystathionine-β-synthase-mediated hydrogen sulfide generation in the kidney
Authors: Xu Zhibin , Prathapasinghe Gamika , Wu Nan , Hwang Sun-Young , Siow Yaw L. , O Karmin
Published: May 2009

Cystathionine-β-synthase (CBS) catalyzes the rate-limiting step in the transsulfuration pathway for the metabolism of homocysteine (Hcy) in the kidney. Our recent study demonstrates that ischemia-reperfusion reduces the activity of CBS leading to Hcy accumulation in the kidney, which in turn contributes to renal injury. CBS is also capable of catalyzing the reaction of cysteine with Hcy to produce hydrogen sulfide (H2S), a gaseous molecule that plays an important role in many physiological and pathological processes. The aim of the present study was to examine the effect of ischemia-reperfusion on CBS-mediated H2S production in the kidney and to determine whether changes in the endogenous H2S generation had any impact on renal ischemia-reperfusion injury. The left kidney of Sprague-Dawley rat was subjected to 45-min ischemia followed by 6-h reperfusion. The ischemia-reperfusion caused lipid peroxidation and cell death in the kidney. The CBS-mediated H2S production was decreased, leading to a significant reduction in the renal H2S level. The activity of cystathionine-γ-lyase, another enzyme responsible for endogenous H2S generation, was not significantly altered in the kidney upon ischemia-reperfusion. Partial restoration of CBS activity by intraperitoneal injection of the nitric oxide scavenger, 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide not only increased renal H2S levels but also alleviated ischemia-reperfusion-induced lipid peroxidation and reduced cell damage in the kidney tissue. Furthermore, administration of an exogenous H2S donor, NaHS (100 μg/kg), improved renal function. Taken together, these results suggest that maintenance of tissue H2S level may offer a renal protective effect against ischemia-reperfusion injury.