bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of Herpes Simplex Virus Type 1 Infection by Cationic β-Peptides
Authors: Akkarawongsa Radeekorn , Potocky Terra B. , English Emily P. , Gellman Samuel H. , Brandt Curtis R.
Published: April 2008

Previously, it was shown that cationic α-peptides derived from the human immunodeficiency virus TAT protein transduction domain blocked herpes simplex virus type 1 (HSV-1) entry. We now show that cationic oligomers of β-amino acids (“β-peptides”) inhibit HSV-1 infection. Among three cationic β-peptides tested, the most effective inhibition was observed for the one with a strong propensity to adopt a helical conformation in which cationic and hydrophobic residues are segregated from one another (“globally amphiphilic helix”). The antiviral effect was not cell type specific. Inhibition of virus infection by the β-peptides occurred at the postattachment penetration step, with a 50% effective concentration of 3 μM for the most-effective β-peptide. The β-peptides did not inactivate virions in solution, nor did they induce resistance to infection when cells were pretreated with the β-peptides. The β-peptides showed little if any toxicity toward Vero cells. These results raise the possibility that cationic β-peptides may be useful antiviral agents for HSV-1 and demonstrate the potential of β-peptides as novel antiviral drugs.
Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from
Streptococcus pneumoniae
Authors: Yamada Mototsugu , Watanabe Takashi , Baba Nobuyoshi , Takeuchi Yasuo , Ohsawa Fukuichi , Gomi Shuichi
Published: April 2008

Biapenem is a parenteral carbapenem antibiotic that exhibits wide-ranging antibacterial activity, remarkable chemical stability, and extensive stability against human renal dehydropeptidase-I. Tebipenem is the active form of tebipenem pivoxil, a novel oral carbapenem antibiotic that has a high level of bioavailability in humans, in addition to the above-mentioned features. β-lactam antibiotics, including carbapenems, target penicillin-binding proteins (PBPs), which are membrane-associated enzymes that play essential roles in peptidoglycan biosynthesis. To envisage the binding of carbapenems to PBPs, we determined the crystal structures of the trypsin-digested forms of both PBP 2X and PBP 1A from
Streptococcus pneumoniae
strain R6, each complexed with biapenem or tebipenem. The structures of the complexes revealed that the carbapenem C-2 side chains form hydrophobic interactions with Trp374 and Thr526 of PBP 2X and with Trp411 and Thr543 of PBP 1A. The Trp and Thr residues are conserved in PBP 2B. These results suggest that interactions between the C-2 side chains of carbapenems and the conserved Trp and Thr residues in PBPs play important roles in the binding of carbapenems to PBPs.
Characterization of Fifty Putative Inclusion Membrane Proteins Encoded in theChlamydia trachomatisGenome
Authors: Li Zhongyu , Chen Chaoqun , Chen Ding , Wu Yimou , Zhong Youmin , Zhong Guangming
Published: April 2008

Although theChlamydia trachomatisgenome is predicted to encode 50 inclusion membrane proteins, only 18 have been experimentally localized in the inclusion membrane ofC. trachomatis-infected cells. Using fusion proteins and anti-fusion protein antibodies, we have systematically evaluated all 50 putative inclusion membrane proteins for their localization in the infected cells, distribution patterns, and effects on subsequent chlamydial infection when expressed ectopically, as well as their immunogenicity during chlamydial infection in humans. Twenty-two of the 50 proteins were localized in the inclusion membrane, and 7 were detected inside the inclusions, while the location of the remaining 21 was not defined. Four (CT225, CT228, CT358, and CT440) of the 22 inclusion membrane-localized proteins were visualized in the inclusion membrane ofChlamydia-infected cells for the first time in the current study. The seven intra-inclusion-localized proteins were confirmed to be chlamydial organism proteins in a Western blot assay. Further characterization of the 50 proteins revealed that neither colocalization with host cell endoplasmic reticulum nor inhibition of subsequent chlamydial infection by ectopically expressed proteins correlated with the inclusion membrane localization. Interestingly, antibodies from women withC. trachomatisurogenital infection preferentially recognized proteins localized in the inclusion membrane, and the immunodominant regions were further mapped to the region predicted to be on the cytoplasmic side of the inclusion membrane. These observations suggest that most of the inclusion membrane-localized proteins are both expressed and immunogenic duringC. trachomatisinfection in humans and that the cytoplasmic exposure may enhance the immunogenicity.
Role of the Mannose Receptor in a Murine Model ofCryptococcus neoformansInfection
Authors: Dan Jennifer M. , Kelly Ryan M. , Lee Chrono K. , Levitz Stuart M.
Published: April 2008

Cryptococcus neoformansis an encapsulated fungal pathogen with a predilection to infect persons with suppressed T-cell function. Cryptococcal mannoproteins (MP) are highly mannosylated antigens which elicit T-cell responses in infected mice and in convalescent patients. Key to the immunogenicity of MP is its capacity to bind to the conserved mannose receptor (MR), CD206, on dendritic cells (DCs). To test the role of the MR in the immune response toC.neoformans, wild-type and MR knockout (MR KO) mice were compared by using in vivo and ex vivo models of cryptococcosis. Following a pulmonary challenge withC.neoformans, MR KO mice died significantly faster than wild-type mice and had higher lung fungal burdens after 4 weeks of infection. Uptake of MP was similar when DCs obtained from wild-type and MR KO mice were compared. Additionally, MP did not upregulate the maturation markers major histocompatibility complex class II, CD86, and CD40 in either wild-type or MR KO DCs. However, MP stimulated lymphoproliferation in CD4+T cells obtained from the peripheral lymph nodes of infected wild-type but not MR KO mice. These studies demonstrate a nonredundant role for the MR in the development of CD4+T-cell responses to MP and protection fromC.neoformans.
Protection against Nasopharyngeal Colonization byStreptococcus pneumoniaeIs Mediated by Antigen-Specific CD4+T Cells
Authors: Trzciński Krzysztof , Thompson Claudette M. , Srivastava Amit , Basset Alan , Malley Richard , Lipsitch Marc
Published: April 2008

CD4+T-cell-dependent acquired immunity confers antibody-independent protection against pneumococcal colonization. Since this mechanism is poorly understood for extracellular bacteria, we assessed the antigen specificity of the induction and recall of this immune response by using BALB/c DO11.10Rag−/−mice, which lack mature B and T cells except for CD4+T cells specific for the OVA323-339peptide derived from ovalbumin. Serotype 6BStreptococcus pneumoniaestrain 603S and unencapsulated strain Rx1ΔlytA were modified to express OVA323-339as a fusion protein with surface protein A (PspA) (strains 603OVA1and Rx1ΔlytAOVA1) or with PspA, neuraminidase A, and pneumolysin (Rx1ΔlytAOVA3). Whole-cell vaccines (WCV) were made of ethanol-killed cells of Rx1ΔlytAplus cholera toxin (CT) adjuvant, of Rx1ΔlytAOVA1+ CT (WCV-OVA1), and of Rx1ΔlytAOVA3+ CT (WCV-OVA3). Mice intranasally immunized with WCV-OVA1, but not with WCV or CT alone, were protected against intranasal challenge with 603OVA1. There was no protection against strain 603S in mice immunized with WCV-OVA1. These results indicate antigen specificity of both immune induction and the recall response. Effector action was not restricted to antigen-bearing bacteria since colonization by 603S was reduced in animals immunized with vaccines made of OVA-expressing strains when ovalbumin or killed Rx1ΔlytAOVA3antigen was administered around the time of challenge. CD4+T-cell-mediated protection against pneumococcal colonization can be induced in an antigen-specific fashion and requires specific antigen for effective bacterial clearance, but this activity may extend beyond antigen-expressing bacteria. These results are consistent with the recruitment and/or activation of phagocytic or other nonspecific effectors by antigen-specific CD4+T cells.
Role of
Porphyromonas gingivalis
SerB in Gingival Epithelial Cell Cytoskeletal Remodeling and Cytokine Production
Authors: Hasegawa Yoshiaki , Tribble Gena D. , Baker Henry V. , Mans Jeffrey J. , Handfield Martin , Lamont Richard J.
Published: April 2008

The SerB protein of
Porphyromonas gingivalis
is a HAD family serine phosphatase that plays a critical role in entry and survival of the organism in gingival epithelial cells. SerB is secreted by
P. gingivalis
upon contact with epithelial cells. Here it is shown by microarray analysis that SerB impacts the transcriptional profile of gingival epithelial cells, with pathways involving the actin cytoskeleton and cytokine production among those significantly overpopulated with differentially regulated genes. Consistent with the transcriptional profile, a SerB mutant of
P. gingivalis
exhibited defective remodeling of actin in epithelial cells. Interaction between gingival epithelial cells and isolated SerB protein resulted in actin rearrangement and an increase in the F/G actin ratio. SerB protein was also required for
P. gingivalis
to antagonize interleukin-8 accumulation following stimulation of epithelial cells with
Fusobacterium nucleatum
. SerB is thus capable of modulating host cell signal transduction that impacts the actin cytoskeleton and cytokine production.
Acquisition of the Vacuolar ATPase Proton Pump and Phagosome Acidification Are Essential for Escape of
Francisella tularensis
into the Macrophage Cytosol
Authors: Santic Marina , Asare Rexford , Skrobonja Ivana , Jones Snake , Abu Kwaik Yousef
Published: April 2008

The
Francisella tularensis
-containing phagosome (FCP) matures to a late-endosome-like phagosome prior to bacterial escape into the cytosols of macrophages, where bacterial proliferation occurs. Our data show that within the first 15 min after infection of primary human monocyte-derived macrophages (hMDMs), ∼90% of the FCPs acquire the proton vacuolar ATPase (vATPase) pump and the lysomotropic dye LysoTracker, which concentrates in acidic compartments, similar to phagosomes harboring the
Listeria monocytogenes
control. The acquired proton vATPase pump and lysomotropic dye are gradually lost by 30 to 60 min postinfection, which coincides with bacterial escape into the cytosols of hMDMs. Colocalization of phagosomes harboring the
iglD
mutant with the vATPase pump and the LysoTracker dye was also transient, and the loss of colocalization was faster than that observed for the wild-type strain, which is consistent with the faster escape of the
iglD
mutant into the macrophage cytosol. In contrast, colocalization of both makers with phagosomes harboring the
iglC
mutant was persistent, which is consistent with fusion to the lysosomes and failure of the
iglC
mutant to escape into the macrophage cytosol. We have utilized a fluorescence microscopy-based phagosome integrity assay for differential labeling of vacuolar versus cytosolic bacteria, using antibacterial antibodies loaded into the cytosols of live hMDMs. We show that specific inhibition of the proton vATPase pump by bafilomycin A1 (BFA) blocks rapid bacterial escape into the cytosols of hMDMs, but 30% to 50% of the bacteria escape into the cytosol by 6 to 12 h after BFA treatment. The effect of BFA on the blocking of bacterial escape into the cytosol is completely reversible, as the bacteria escape after removal of BFA. We also show that the limited fusion of the FCP to lysosomes is not due to failure to recruit the late-endosomal fusion regulator Rab7. Therefore, within few minutes of its biogenesis, the FCP transiently acquires the proton vATPase pump to acidify the phagosome, and this transient acidification is essential for subsequent bacterial escape into the macrophage cytosol.
Identification of
Streptococcus sanguinis
Genes Required for Biofilm Formation and Examination of Their Role in Endocarditis Virulence
Authors: Ge Xiuchun , Kitten Todd , Chen Zhenming , Lee Sehmi P. , Munro Cindy L. , Xu Ping
Published: April 2008

Streptococcus sanguinis
is one of the pioneers in the bacterial colonization of teeth and is one of the most abundant species in the oral biofilm called dental plaque.
S. sanguinis
is also the most common viridans group streptococcal species implicated in infective endocarditis. To investigate the association of biofilm and endocarditis, we established a biofilm assay and examined biofilm formation with a signature-tagged mutagenesis library of
S. sanguinis
. Four genes that have not previously been associated with biofilm formation in any other bacterium,
purB, purL, thrB
, and
pyrE
, were putatively identified as contributing to in vitro biofilm formation in
S. sanguinis
. By examining 800 mutants for attenuation in the rabbit endocarditis model and for reduction in biofilm formation in vitro, we found some mutants that were both biofilm defective and attenuated for endocarditis. However, we also identified mutants with only reduced biofilm formation or with only attenuation in the endocarditis model. This result indicates that the ability to form biofilms in vitro is not associated with endocarditis virulence in vivo in
S. sanguinis
.
Inheritance of Immune Polarization Patterns Is Linked to Resistance versus Susceptibility toCryptococcus neoformansin a Mouse Model
Authors: Chen Gwo-hsiao , McNamara David A. , Hernandez Yadira , Huffnagle Gary B. , Toews Galen B. , Olszewski Michal A.
Published: April 2008

Genetic background variation between inbred strains accounts for different levels of susceptibility toCryptococcus neoformansin the mouse infection model. To elucidate the inheritance of immunophenotypic traits and their associations with clearance outcomes during cryptococcal infection, we compared C57BL/6, BALB/c, and their first-generation hybrid, CB6F1 (F1), mice. Mice from each group were infected withC. neoformans(104CFU) and analyzed at weekly intervals over a 6-week period. BALB/c mice progressively cleared the cryptococcal infection in the lungs and showed a Th1-skewed immune response: a Th1-shifted cytokine profile, modest lung pathology, and no significant elevation in the systemic immunoglobulin E (IgE) level. In contrast, C57BL/6 mice developed a chronic infection with a Th2-skewed immune response: a Th2-shifted cytokine profile, pulmonary eosinophilia, severe lung pathology, elevated serum IgE, fungemia, and cryptococcal dissemination in the central nervous system. F1 mice demonstrated intermediate resistance toC. neoformans, with a stronger resemblance to the immunophenotype of the resistant (BALB/c) mice. F1 mice also demonstrated enhanced pulmonary recruitment of lymphocytes, especially CD8+T cells, in comparison to both parental strains, suggesting positive heterosis. We conclude that the inheritance of traits responsible for early cytokine induction in the infected lungs and dendritic-cell maturation/activation status in draining nodes is responsible for the intermediate immune response polarization and clearance outcome observed initially in the lungs of F1 mice. The enhanced pulmonary lymphocyte recruitment could be responsible for a gradual shutdown of the undesirable Th2 arm of the immune response and subsequently improved anticryptococcal resistance in F1 mice.
Immune Recognition ofStreptococcus pyogenesby Dendritic Cells
Authors: Loof Torsten G. , Goldmann Oliver , Medina Eva
Published: April 2008

Streptococcus pyogenesis one of the most frequent human pathogens. Recent studies have identified dendritic cells (DCs) as important contributors to host defense againstS. pyogenes. The objective of this study was to identify the receptors involved in immune recognition ofS. pyogenesby DCs. To determine whether Toll-like receptors (TLRs) were involved in DC sensing ofS. pyogenes, we evaluated the response of bone marrow-derived DCs obtained from mice deficient in MyD88, an adapter molecule used by almost all TLRs, followingS. pyogenesstimulation. Despite the fact that MyD88−/−DCs did not differ from wild-type DCs in the ability to internalize and killS. pyogenes, the up-regulation of maturation markers, such as CD40, CD80, and CD86, and the production of inflammatory cytokines, such as interleukin-12 (IL-12), IL-6, and tumor necrosis factor alpha, were dramatically impaired inS. pyogenes-stimulated MyD88−/−DCs. These results suggest that signaling through TLRs is the principal pathway by which DCs senseS. pyogenesand become activated. Surprisingly, DCs deficient in signaling through each of the TLRs reported as potential receptors for gram-positive cell components, such as TLR1, TLR2, TLR4, TLR9, and TLR2/6, were not impaired in the secretion of proinflammatory cytokines and the up-regulation of costimulatory molecules afterS. pyogenesstimulation. In conclusion, our results exclude a major involvement of a single TLR or the heterodimer TLR2/6 inS. pyogenessensing by DCs and argue for a multimodal recognition in which a combination of several different TLR-mediated signals is essential for a rapid and effective response to the pathogen.
Injury surveillance in multi-sport events: the International Olympic Committee approach
Authors: Junge A , Engebretsen L , Alonso J M , Renström P , Mountjoy M , Aubry M , Dvorak J
Published: April 2008

Background:

The protection of athletes’ health by preventing injuries is an important task for international sports federations. Standardised injury surveillance provides not only important epidemiological information, but also directions for injury prevention, and the opportunity for monitoring long-term changes in the frequency and circumstances of injury. Numerous studies have evaluated sports injuries during the season, but few have focused on injuries during major sport events such as World Championships, World Cups or the Olympic Games.

Objectives:

To provide an injury surveillance system for multi-sports tournaments, using the 2008 Olympic Games in Beijing as an example.

Methods:

A group of experienced researchers reviewed existing injury report systems and developed a scientific sound and concise injury surveillance system for large multi-sport events.

Results:

The injury report system for multi-sport events is based on an established system for team sports tournaments and has proved feasible for individual sports during the International Association of Athletics Federations World Championships in Athletics 2007. The most important principles and advantages of the system are comprehensive definition of injury, injury report by the physician responsible for the athlete, a single-page report of all injuries, and daily report irrespective of whether or not an injury occurred. Implementation of the injury surveillance system, all definitions, the report form, and the analysis of data are described in detail to enable other researchers to implement the injury surveillance system in any sports tournament.

Conclusion:

The injury surveillance system has been accepted by experienced team physicians and shown to be feasible for single-sport and multi-sport events. It can be modified depending on the specific objectives of a certain sport or research question; however, a standardised use of injury definition, report forms and methodology will ensure the comparability of results.
Use of field-based tests to identify risk factors for injury to fast bowlers in cricket
Authors: Dennis R J , Finch C F , McIntosh A S , Elliott B C
Published: April 2008

Objective:

To identify risk factors for injury to cricket fast bowlers using field-based tests.

Design:

Prospective cohort study.

Setting:

High performance Australian cricket.

Participants:

Ninety-one male adolescent and adult fast bowlers (aged 12–33 years).

Assessment of risk factors:

A field-based pre-participation screening, consisting of musculoskeletal, fitness and anthropometric assessments and analysis of bowling technique was undertaken. Bowlers were prospectively monitored over the 2003–4 season and bowling workload and injuries were recorded. Logistic regression was used to identify injury risk factors.

Main outcome measurement:

Repetitive microtrauma injury to the trunk, back or lower limb associated with fast bowling.

Results:

Two variables were identified as independent predictors of injury in the multivariate logistic regression analysis. Bowlers with hip internal rotation of ⩽30° on the leg ipsilateral to the bowling arm were at a significantly reduced risk of injury (OR 0.20, 95% CI 0.06 to 0.73) compared with bowlers with >40° of rotation. Bowlers with an ankle dorsiflexion lunge of 12.1–14.0 cm on the leg contralateral to the bowling arm were at a significantly increased risk (OR 4.03, 95% CI 1.07 to 15.21) than bowlers with a lunge of >14 cm. Bowlers with a lunge of ⩽12 cm were also at an increased risk, but not significantly so (OR 1.38, 95% CI 0.40 to 4.84).

Conclusions:

Biomechanical research is needed to investigate how these two intrinsic risk factors increase injury risk so that appropriate interventions can be developed.
Interim evaluation of the effect of a new scrum law on neck and back injuries in rugby union
Authors: Gianotti S , Hume P A , Hopkins W G , Harawira J , Truman R
Published: April 2008

Background:

In January 2007 the International Rugby Board implemented a new law for scrum engagement aimed at improving player welfare by reducing impact force and scrum collapses. In New Zealand the new law was included in RugbySmart, an annual compulsory workshop for coaches and referees.

Objective:

To determine the effect of the new law on scrum-related moderate to serious neck and back injury claims in 2007.

Methods:

Claims filed with the Accident Compensation Corporation (the provider of no-fault injury compensation and rehabilitation in New Zealand) were combined with numbers of registered players to estimate moderate to serious scrum-related claims for players who take part in scrums (forwards). Poisson linear regression was used to compare the observed claims per 100 000 forwards for 2007 with the rate predicted from data for 2002–6.

Results:

The observed and predicted claims per 100 000 forwards were 52 and 76, respectively (rate ratio 0.69; 90% CI 0.42 to 1.12). The likelihoods of substantial benefit (rate ratio <0.90) and harm (rate ratio >1.1) attributable to the scrum law were 82% and 5%, respectively.

Conclusion:

The decline in scrum-related injury claims is consistent with a beneficial effect of the new scrum law in the first year of its implementation. Another year of monitoring should provide more evidence for the efficacy of the new law.
Electrophoretic Identification of Sebastes and Helicolenus in the Northwestern Atlantic
Authors: McGlade J. M. , Annand M. C. , Kenchington T. J.
Published: April 2008

An electrophoretic survey of 16 enzymes was conducted on representatives of the genera Helicolenus sp. and Sebastes spp. The survey was designed to develop an identification scheme for the commercially exploited species, because in the absence of any detailed description of their geographic distribution in the Scotian Shelf, they are currently managed as a single unit. Twelve enzymes were diagnostic for H. dactylopterus, three were diagnostic for S. fasciatus, while on the basis of the mobility of the most common allele none of the enzymes examined could distinguish between S. mentella and S. marinus. A protocol for the identification of S. fasciatus is thus presented, which incorporates the results of this survey. It is also suitable to describe the geographic distribution of commercially important species. The electrophoretic identification of the Sebastes species allowed fish with intermediate meristic characters, such as the number of anal fin rays, to be unequivocally identified. It was concluded that generic separation of Helicolenus and Sebastes is warranted, that S. fasciatus is distinct from S. marinus and S. mentella, but that individuals of S. marinus and S. mentella cannot be differentiated electrophoretically.
Decline of Mysis relicta During the Acidification of Lake 223
Authors: Nero R. W. , Schindler D. W.
Published: April 2008

The population size of Mysis relicta in Lake 223 of the Experimental Lakes Area, northwestern Ontario, decreased from 6 700 000 ± 1 330 000 (± 95% confidence limits) during August of 1978, to 270 000 ± 75 000 during August of 1979, a 96% decrease. Because Mysis, a cold stenotherm, is restricted to the metalimnion and hypolimnion of lakes during summer, the pH range encountered by the population was 5.51 to 6.32 in 1978 and 5.23 to 6.10 in 1979, even though mean pH values in epilimnion waters for the 2 yr were 5.84 and 5.60. A decrease in pH of its habitat from 6.2 to 5.6 during fall overturn in 1979 caused the elimination of the remaining 4% of the population. Comparisons with four control lakes suggested that the decline and disappearance were not normal occurrences in unstressed lakes. Concentrations of Zn, Al, Mn, Fe, Cd, Cu, Ni, and Hg in Lake 223 water were low, and concentrations in Mysis were less than or equal to those in animals from five control lakes, suggesting that the decline in this species was not due to the toxic effects of metals. All size classes were affected, so that direct toxicity of hydrogen ion may be responsible for this abrupt population collapse. These results suggest that Mysis may be a useful early indicator of acidification damage to Precambrian Shield lakes.
Age and Growth of the Shortfin Mako, Isurus oxyrinchus, Using Four Methods
Authors: Pratt Jr. Harold L. , Casey John G.
Published: April 2008

Age and growth rate of shortfin mako, Isurus oxyrinchus, captured by hook and line between 1961 and 1981 were determined using four methods: (1) temporal analysis of length–month information, (2) results of tagging data, (3) length–frequency analysis, and (4) ring counts on vertebrae. A temporal analysis of length–month information relating size to age for individuals less than 150 cm fork length (FL) was used to determine size (60–70 cm FL), time of birth (late spring), and early growth rate (50 cm/yr for ages 0–I, 32 cm/yr for ages I–II). This growth rate was used as a basis for interpreting the accuracy of other methods. Annual growth rates were calculated from 32 tag–recaptured mako sharks and resolved graphically into a growth curve. Length–frequency modes extended age estimates to intermediate-sized makos. Counts of growth rings on vertebral centra stained with silver nitrate were employed to back-calculate lengths at ages for the full range (69–328 cm). Our interpretation was based on the hypothesis that two rings are formed on the centrum each year; these age estimates agreed well with results from other methods. Males and females had a similar growth rate even though females grow much larger than males. The oldest female in the sample was 11.5 yr at 328 cm. The oldest male was 4.5 yr at 225 cm. The von Bertalanffy asymptotic growth function adequately described shortfin mako growth: male L∞ = 302 cm, K = 0.266, t0 = −1; female L∞ = 345 cm, K = 0.203, t0 = −1.
Reproductive Potential of Three American Lobster (Homarus americanus) Stocks in the Canadian Maritimes
Authors: Campbell A. , Robinson D. G.
Published: April 2008

New information on female size at maturity, fecundity, and relative egg production per recruit is presented for American lobsters (Homarus americanus) from three areas in the Canadian Maritimes. Based on pleopod examination, sizes at 50% maturity for females were estimated at 108.1 mm carapace length (CL) from the Fundy area (Bay of Fundy and southwestern Nova Scotia), at 92.5 mm CL from eastern Nova Scotia, and at 78.5 mm CL from Northumberland Strait. There was a curvilinear relationship between the number of eggs per female and CL. An egg-per-recruit model predicted that in all three areas the second and third molt groups beyond the legal minimum recruit size contribute the most to egg production under current exploitation rates. Lobsters in Northumberland Strait and eastern Nova Scotia produce up to 30–50% of their eggs at sizes smaller than those at which females from the Bay of Fundy start to produce eggs. Although the stock–recruitment relationships for H. americanus are unknown, the egg-per-recruit assessment suggests that all three areas would benefit in egg production increases by increasing minimum legal recruit size by one molt increment.
Mysid Life History and Seasonal Variation in Predation Pressure on Zooplankton
Authors: Murtaugh Paul A.
Published: April 2008

The bivoltine life history of Neomysis mercedis in Lake Washington, Seattle, results in seasonal variation in population size structure that influences the amount and quality of predation suffered by its zooplankton prey. Population densities and size–frequency data for Neomysis are combined with information on the influence of body size on feeding rate and composition of the diet to predict relative predation intensity on five size classes of Daphnia over a 27-mo period. An imperfect relationship between mysid numbers and expected predation intensity and seasonal fluctuations in the relative vulnerability of different-sized prey are two consequences of the mysid's pattern of life history.
Use of the Size–Frequency (Hynes) Method to Estimate Annual Production of a Stream Fish Population
Authors: Garman Greg C. , Waters Thomas F.
Published: April 2008

Previously developed and accepted methods of fish production estimation, such as instantaneous growth (G method), require aging of sampled individuals. Hynes' size–frequency method, however, does not require cohort separation. Annual production and approximate 95% confidence intervals are presented and compared for populations of brook, brown, and rainbow trout (Salvelinus fontinalis, Salmo trutta, and Salmo gairdneri) in Valley Creek, Minnesota, 1977–78, using the size–frequency and G methods. No significant difference was found between production values calculated by the two methods. It is proposed that the size–frequency method provides a reliable determination of annual production of fish populations and will be especially useful where accurate aging of individuals is not possible or where aging represents excessive labor.
Increased Survival in Salmonid Hybrids by Induced Triploidy
Authors: Scheerer Paul D. , Thorgaard Gary H.
Published: April 2008

All possible hybrid crosses between brook (Salvelinus fontinalis), brown (Salmo trutta), and rainbow (Salmo gairdneri) trout were made and a portion of the fertilized eggs from each mating were heat shocked to induce triploidy. Within a species, triploids generally showed poorer survival to the initiation of feeding than diploids. In most crosses, however, triploid hybrids showed much better survival than diploid hybrids. The triploid tiger trout (brown × brook) hybrid showed the most potential of the hybrids tested. Induced triploidy could be a useful general method for increasing survival in interspecific fish hybrids.
Epigenetic Mechanisms: Reflections on Evolutionary Processes
Authors: Balon Eugene K.
Published: April 2008

Evolutionary trends leading to certain patterns call for reflection on possible processes which maintain the stability of these patterns and facilitate their changes. Epigenetic processes (like heterochrony) operate mainly in early ontogeny and trigger a chain reaction of changes in induction, regulation and control of the formation of vital structures and functions. Genetic variation maintained by reproduction via supernumerous despecialized zygotes is enhanced by epigenesis. The tendency to optimize, especially in stable and competitive environments, is resisted by a barrier against easy inheritance of selected phenotypic characters, and by juvenilization. If optimization would be allowed to succeed, any new unpredictable perturbation would cause extinction; therefore variations must constantly oscillate around two steady states needed to address any survival goal. This oscillatory process is explained, and named, the Chen principle. The generalist's homeostatic state can be termed altricial and the specialist's precocial. Consequently, "altricial [Formula: see text] precocial dynamic states" form a dichotomy reflected in most evolutionary patterns. Both theories explain the processes we came to perceive as a result of partly closed thermodynamic systems within the open-ended system of nonequilibrium thermodynamics.
INFORMATION, INCENTIVES AND PRACTICE PATTERNS: THE CASE OF TB DOTS SERVICES AND PRIVATE PHYSICIANS IN THE PHILIPPINES
Authors: KRAFT ALELI D. , CAPUNO JOSEPH J. , QUIMBO STELLA A. , TAN CARLOS ANTONIO R.
Published: April 2008

To explain divergent physician practices, studies focus on either differences in education and training or in financial incentives. The policy challenge is to identify the most cost-effective interventions to encourage adherence to practice guidelines. Utilizing private physician data in major cities in the Philippines, we show the effects of training and financial incentives in physician adoption of the TB DOTS protocol. Training seems to be more important when the new protocol is a significant departure from the old know-how, while financial incentives seem to work better on those who are already clinically competent. These imply that uniform application of information-based and incentive-based interventions may not be cost-effective.
PARALLEL IMPORTS, INNOVATIONS AND NATIONAL WELFARE: THE ROLE OF THE SIZES OF INCOME CLASSES AND NATIONAL MARKETS FOR HEALTH CARE
Authors: ACHARYYA RAJAT , GARCÍA-ALONSO MARÍA D.C.
Published: April 2008

This paper shows that regardless of any intra-country income differences, parallel imports result in a lower level of health-care innovation but, contrary to popular as well as conventional theoretical wisdom, a lower price in the Third World compared to market-based discrimination. Despite such a lower price, however, parallel imports unambiguously make all buyers in the Third World worse off when intra-country income disparity exists. On the other hand, even discarding the MNC's profit, there will be cases in which the richer country prefers price discrimination as well. That is, in those cases, no countries will have any incentive under the welfare criterion to undo price discrimination, contrary to Richardson (2002).
COMBINATION ENTROPY AND COMBINATION GRANULATION IN ROUGH SET THEORY
Authors: QIAN YUHUA , LIANG JIYE
Published: April 2008

Based on the intuitionistic knowledge content nature of information gain, the concepts of combination entropy and combination granulation are introduced in rough set theory. The conditional combination entropy and the mutual information are defined and their several useful properties are derived. Furthermore, the relationship between the combination entropy and the combination granulation is established, which can be expressed as CE(R) + CG(R) = 1. All properties of the above concepts are all special instances of those of the concepts in incomplete information systems. These results have a wide variety of applications, such as measuring knowledge content, measuring the significance of an attribute, constructing decision trees and building a heuristic function in a heuristic reduct algorithm in rough set theory.
SIMPLIFIED FUZZY INFERENCE RULE-BASED GENETICALLY OPTIMIZED HYBRID FUZZY NEURAL NETWORKS
Authors: PARK BYOUNG-JUN , PEDRYCZ WITOLD , OH SUNG-KWUN
Published: April 2008

In this study, we introduce an advanced architecture of genetically optimized Hybrid Fuzzy Neural Networks (gHFNN) and develop a comprehensive design methodology supporting their construction. A series of numeric experiments is included to illustrate the performance of the networks. The construction of gHFNN exploits fundamental technologies of Computational Intelligence (CI), namely fuzzy sets, neural networks, and genetic algorithms (GAs). The architecture of the gHFNNs results from a synergistic usage of the genetic optimization-driven hybrid system generated by combining Fuzzy Neural Networks (FNN) with Polynomial Neural Networks (PNN). In this tandem, a FNN supports the formation of the condition part of the rule-based structure of the gHFNN. The conclusion part of the gHFNN is designed using PNNs. We distinguish between two types of the simplified fuzzy inference rule-based FNN structures showing how this taxonomy depends upon the type of a fuzzy partition of input variables. As to the conclusion part of the gHFNN, the development of the PNN dwells on two general optimization mechanisms: the structural optimization is realized via GAs whereas in case of the parametric optimization we proceed with a standard least square method-based learning. To evaluate the performance of the gHFNN, we experimented with three representative numerical examples. A comparative analysis demonstrates that the proposed gHFNN come with higher accuracy as well as superb predictive capabilities when compared with other neurofuzzy models.
INTERVAL METHODS IN KNOWLEDGE REPRESENTATION
Authors: Kreinovich V.
Published: April 2008

This section is maintained by Vladik Kreinovich. Please send your abstracts (or copies of papers that you want to see reviewed here) to vladik@utep.edu, or by regular mail to: V. Kreinovich, Department of Computer Science, University of Texas, El Paso, TX 79968, USA.
HÖLDER-TYPE INEQUALITIES FOR THE POLYGAMMA FUNCTIONS
Authors: ALZER HORST
Published: April 2008

The nth polygamma function is defined by ψ(n) = (Γ′/Γ)(n), where Γ denotes Euler's gamma function. We prove: let n ≥ 1 be an integer and let p, q be non-zero real numbers.

(i) The inequality [Formula: see text] holds for all positive numbers x, y if and only if p > 0, q > 0, 1/p + 1/q ≥ 1.

(ii) The inequality [Formula: see text] holds for all positive numbers x, y if and only if either p < 0, q < 0 or pq < 0, 1/p + 1/q ≤ 1.
AN ANALYTICAL APPROACH TO MERTON'S RATIONAL OPTION PRICING THEORY
Authors: ELIZONDO ROCIO , PADILLA PABLO
Published: April 2008

In the early seventies, Merton developed a theory based on economical arguments to study the properties of option and warrant prices. The main tool in the proofs is the portfolio dominance principle. In the context where the price of a contingent claim satisfies a partial differential equation, we provide analytical proofs of Merton's rational option pricing theory. We use several versions of the maximum principle as well as the sliding and the moving planes methods to prove our results. Our approach enables us to extend the theory to nonlinear models.
High-level interconnect model for the quantum logic array architecture
Authors: Metodi Tzvetan S. , Thaker Darshan D. , Cross Andrew W. , Chuang Isaac L. , Chong Frederic T.
Published: April 2008

We summarize the main characteristics of the quantum logic array (QLA) architecture with a careful look at the key issues not described in the original conference publications: primarily, the teleportation-based logical interconnect. The design goal of the the quantum logic array architecture is to illustrate a model for a large-scale quantum architecture that solves the primary challenges of system-level reliability and data distribution over large distances. The QLA's logical interconnect design, which employs the quantum repeater protocol, is in principle capable of supporting the communication requirements for applications as large as the factoring of a 2048-bit number using Shor's quantum factoring algorithm. Our physical-level assumptions and architectural component validations are based on the trapped ion technology for implementing quantum computing.
Synopsis diffusion for robust aggregation in sensor networks
Authors: Nath Suman , Gibbons Phillip B. , Seshan Srinivasan , Anderson Zachary
Published: April 2008

Previous approaches for computing duplicate-sensitive aggregates in wireless sensor networks have used a tree topology, in order to conserve energy and to avoid double-counting sensor readings. However, a tree topology is not robust against node and communication failures, which are common in sensor networks. In this article, we present
synopsis diffusion
, a general framework for achieving significantly more accurate and reliable answers by combining energy-efficient multipath routing schemes with techniques that avoid double-counting. Synopsis diffusion avoids double-counting through the use of
order- and duplicate-insensitive (ODI) synopses
that compactly summarize intermediate results during in-network aggregation. We provide a surprisingly simple test that makes it easy to check the correctness of an ODI synopsis. We show that the properties of ODI synopses and synopsis diffusion create
implicit
acknowledgments of packet delivery. Such acknowledgments enable energy-efficient adaptation of message routes to dynamic message loss conditions, even in the presence of asymmetric links. Finally, we illustrate using extensive simulations the significant robustness, accuracy, and energy-efficiency improvements of synopsis diffusion over previous approaches.
Programming models for sensor networks
Authors: Sugihara Ryo , Gupta Rajesh K.
Published: April 2008

Sensor networks have a significant potential in diverse applications some of which are already beginning to be deployed in areas such as environmental monitoring. As the application logic becomes more complex, programming difficulties are becoming a barrier to adoption of these networks. The difficulty in programming sensor networks is not only due to their inherently distributed nature but also the need for mechanisms to address their harsh operating conditions such as unreliable communications, faulty nodes, and extremely constrained resources. Researchers have proposed different programming models to overcome these difficulties with the ultimate goal of making programming easy while making full use of available resources. In this article, we first explore the requirements for programming models for sensor networks. Then we present a taxonomy of the programming models, classified according to the level of abstractions they provide. We present an evaluation of various programming models for their responsiveness to the requirements. Our results point to promising efforts in the area and a discussion of the future directions of research in this area.
Aggregation methods for large-scale sensor networks
Authors: Chitnis Laukik , Dobra Alin , Ranka Sanjay
Published: April 2008

The ability to efficiently aggregate information—for example compute the average temperature—in large networks is crucial for the successful employment of sensor networks. This article addresses the problem of designing
truly scalable
protocols for computing aggregates in the presence of faults, protocols that can enable million node sensor networks to work efficiently. More precisely, we make four distinct contributions. First, we introduce a simple fault model and analyze the behavior of two existing protocols under the fault model:
tree aggregation
and
gossip aggregation
. Second, since the behavior of the two protocols depends on the size of the network and probability of failure, we introduce a hybrid approach that can leverage the strengths of the two protocols and minimize the weaknesses; the new protocol is analyzed under the same fault model. Third, we propose methodology for determining the
optimal
mix between the two basic protocols; the methodology consists in formulating an optimization problem, using models of the protocol behavior, and solving it. Fourth, we perform extensive experiments to evaluate the performance of the hybrid protocol and show that it usually performs better, sometimes orders of magnitude better, than both the tree and gossip aggregation.
Compositional mining of multirelational biological datasets
Authors: Jin Ying , Murali T. M. , Ramakrishnan Naren
Published: April 2008

High-throughput biological screens are yielding ever-growing streams of information about multiple aspects of cellular activity. As more and more categories of datasets come online, there is a corresponding multitude of ways in which inferences can be chained across them, motivating the need for compositional data mining algorithms. In this article, we argue that such compositional data mining can be effectively realized by functionally cascading redescription mining and biclustering algorithms as primitives. Both these primitives mirror shifts of vocabulary that can be composed in arbitrary ways to create rich chains of inferences. Given a relational database and its schema, we show how the schema can be automatically compiled into a compositional data mining program, and how different domains in the schema can be related through logical sequences of biclustering and redescription invocations. This feature allows us to rapidly prototype new data mining applications, yielding greater understanding of scientific datasets. We describe two applications of compositional data mining: (i) matching terms across categories of the Gene Ontology and (ii) understanding the molecular mechanisms underlying stress response in human cells.
A new efficient probabilistic model for mining labeled ordered trees applied to glycobiology
Authors: Hashimoto Kosuke , Aoki-Kinoshita Kiyoko Flora , Ueda Nobuhisa , Kanehisa Minoru , Mamitsuka Hiroshi
Published: April 2008

Mining frequent patterns from large datasets is an important issue in data mining. Recently, complex and unstructured (or semi-structured) datasets have appeared as targets for major data mining applications, including text mining, web mining and bioinformatics. Our work focuses on labeled ordered trees, which are typically semi-structured datasets. In bioinformatics, carbohydrate sugar chains, or glycans, can be modeled as labeled ordered trees. Glycans are the third major class of biomolecules, having important roles in signaling and recognition. For mining labeled ordered trees, we propose a new probabilistic model and its efficient learning scheme which significantly improves the time and space complexity of an existing probabilistic model for labeled ordered trees. We evaluated the performance of the proposed model, comparing it with those of other probabilistic models, using synthetic as well as real datasets from glycobiology. Experimental results showed that the proposed model drastically reduced the computation time of the competing model, keeping the predictive power and avoiding overfitting to the training data. Finally, we assessed our results on real data from a variety of biological viewpoints, verifying known facts in glycobiology.