bluuebunny/crossref_metadata_2025 huggingface dataset:
ThecagPathogenicity Island ofHelicobacter pyloriIs Disrupted in the Majority of Patient Isolates from Different Human Populations
Authors: Kauser Farhana , Khan Aleem A. , Hussain M. Abid , Carroll Ian M. , Ahmad Naheed , Tiwari Santosh , Shouche Yogesh , Das Bimal , Alam Mahfooz , Ali S. Mahaboob , Habibullah C. M. , Sierra Rafaela , Megraud Francis , Sechi Leonardo A. , Ahmed Niyaz
Published: November 2004

Thecagpathogenicity island (cag-PAI) is one of the major virulence determinants ofHelicobacter pylori. The chromosomal integrity of this island or the lack thereof is speculated to play an important role in the progress of the gastroduodenal pathology caused byH. pylori. We determined the integrity of thecag-PAI by using specific flanking and internally anchored PCR primers to know the biogeographical distribution of strains carrying fully integralcag-PAI with proinflammatory behavior in vivo. Genotypes based on eight selected loci were studied in 335 isolates obtained from eight different geographic regions. Thecag-PAI appeared to be disrupted in the majority of patient isolates throughout the world. Conservation ofcag-PAI was highest in Japanese isolates (57.1%). However, only 18.6% of the Peruvian and 12% of the Indian isolates carried an intactcag-PAI. The integrity ofcag-PAI in European and African strains was minimal. All 10 strains from Costa Rica had rearrangements. Overall, a majority of the strains of East Asian ancestry were found to have intactcag-PAI compared to strains of other descent. We also found that thecagEandcagTgenes were less often rearranged (18%) than thecagAgene (27%). We attempted to relatecag-PAI rearrangement patterns to disease outcome. Deletion frequencies ofcagA,cagE, andcagTgenes were higher in benign cases than in isolates from severe ulcers and gastric cancer. Conversely, thecagApromoter and the left end of thecag-PAI were frequently rearranged or deleted in isolates linked to severe pathology. Analysis of thecag-PAI genotypes with a different biogeoclimatic history will contribute to our understanding of the pathogen-host interaction in health and disease.
Prevalence and Characterization of Leukotoxin-Producing
Staphylococcus intermedius
in Isolates from Dogs and Pigeons
Authors: Futagawa-Saito Keiko , Sugiyama Tsukasa , Karube Sayaka , Sakurai Naomi , Ba-Thein William , Fukuyasu Tsuguaki
Published: November 2004

Staphylococcus intermedius
isolates from dogs (
n
= 44) and pigeons (
n
= 62) were categorized into 12 types by intergenic ribosomal DNA spacer polymorphism analysis. All isolates from pigeons were
lukS
positive and all isolates from dogs were
lukS
and
lukF
positive by dot blot analysis. The mean leukotoxicity titer for dog isolates was at least 129-fold higher than that for pigeon isolates.
Complexity ofKlebsiella pneumoniaeIsolates Resistant to Both Cephamycins and Extended-Spectrum Cephalosporins at a Teaching Hospital in Taiwan
Authors: Yan Jing-Jou , Ko Wen-Chien , Wu Hsiu-Mei , Tsai Shu-Huei , Chuang Chin-Luan , Wu Jiunn-Jong
Published: November 2004

Among 99 clinicalKlebsiella pneumoniaeisolates resistant to cefoxitin and extended-spectrum cephalosporins, coexistence of AmpC (DHA-1, CMY-2, or CMY-8) and extended-spectrum β-lactamases (CTX-M and/or SHV) was detected in a total of 35. The remainder produced AmpC (n= 42), extended-spectrum β-lactamases (n= 9), metallo-β-lactamases (n= 2), or none of these enzymes (n= 11). Phenotypic characteristics of these isolates were demonstrated.
Evaluation of a Modified Gen-Probe Amplified Direct Test for Detection of
Mycobacterium tuberculosis
Complex Organisms in Cerebrospinal Fluid
Authors: Cloud Joann L. , Shutt Cheryl , Aldous Wade , Woods Gail
Published: November 2004

Laboratory evidence for tuberculous meningitis is difficult to acquire due to the low numbers of organisms present in cerebrospinal fluid (CSF) and the presence of nucleic acid amplification inhibitors. The Amplified
Mycobacterium tuberculosis
Direct Test (MTD) is sensitive and specific for the direct detection of
M. tuberculosis
complex in respiratory samples but has not been approved for CSF. We evaluated a modified version of the current MTD, optimized for use with CSF samples. Samples were prepared by spiking CSF with various numbers of
M. tuberculosis
complex organisms. The modified MTD performance was compared with results obtained using a purified RNA sample extracted using the Qiagen RNeasy Protect Bacteria Mini Kit. By use of CSF artificially spiked with
M. tuberculosis
complex, the sensitivity of the modified MTD was 100% (six of six) for CSF samples containing approximately 600 CFU/ml, 78% (seven of nine) for approximately 60 CFU/ml, 50% (three of six) for 6 CFU/ml, and 17% (one of six) for samples with <1 CFU/ml. The specificity of the modified MTD method was 100% (22 of 22). The sensitivity of the Qiagen MTD method was 100% for CSF samples containing approximately 600 CFU/ml (six of six) and approximately 60 CFU/ml (nine of nine), 50% for samples with approximately 6 CFU/ml (three of six), and 50% for samples with <1 CFU/ml (three of six). The specificity of the Qiagen MTD method was 86% (19 of 22). With the Qiagen MTD method, however, initial results were equivocal for 14 of the 27 (52%) positive samples, requiring repeat analysis, whereas with the modified MTD, only 1 of 27 (4%) was equivocal. The modified MTD for CSF samples was less time-consuming and less expensive and resulted in considerably fewer equivocal results than the Qiagen MTD method did.
Sensitive and Specific Detection of
Yersinia pseudotuberculosis
by Loop-Mediated Isothermal Amplification
Authors: Horisaka Tomoko , Fujita Kayoko , Iwata Taketoshi , Nakadai Aya , Okatani Alexandre T. , Horikita Tetsuya , Taniguchi Takahide , Honda Eiichi , Yokomizo Yuichi , Hayashidani Hideki
Published: November 2004

We developed a loop-mediated isothermal amplification method able to detect
Yersinia pseudotuberculosis
strains in 30 min by using six primers designed by targeting the
inv
gene. This method is more sensitive than PCR and might be a useful tool for detecting and identifying
Y. pseudotuberculosis
.
False-Positive
Aspergillus
Galactomannan Enzyme-Linked Immunosorbent Assay Results In Vivo during Amoxicillin-Clavulanic Acid Treatment
Authors: Mattei Daniele , Rapezzi Davide , Mordini Nicola , Cuda Federica , Lo Nigro Cristiana , Musso Maura , Arnelli Aldo , Cagnassi Sebastiano , Gallamini Andrea
Published: November 2004

Positive Platelia
Aspergillus
test results were observed in consecutive serum samples from an immunocompromised host during amoxicillin-clavulanic acid treatment, and a correlation between plasmatic amoxicillin concentration and galactomannan optical density index was observed. Amoxicillin-clavulanic acid vials tested positive for galactomannan but were negative for
Aspergillus
DNA.
Polymorphisms of the Fimbria
fim3
Gene of
Bordetella pertussis
Strains Isolated in Canada
Authors: Tsang Raymond S. W. , Lau Allan K. H. , Sill Michelle L. , Halperin Scott A. , Van Caeseele Paul , Jamieson Frances , Martin Irene E.
Published: November 2004

The
fim
genes which code for the fimbria protective antigens present in both the inactivated whole-cell and acellular vaccines were analyzed in 86 Canadian
Bordetella pertussis
isolates. At least one of the novel mutations identified was found to involve a surface epitope that has been mapped by serum antibodies from infected or vaccinated subjects.
Identification and Phylogeny of
Enterobacter sakazakii
Relative to
Enterobacter
and
Citrobacter
Species
Authors: Iversen Carol , Waddington Michael , On Stephen L. W. , Forsythe Stephen
Published: November 2004

The phylogenetic relationships of
Enterobacter sakazakii
strains were investigated using 16S ribosomal DNA (rDNA) and
hsp60
sequencing. Each analysis distributed
E. sakazakii
strains among four clusters, indicating substantial taxonomic heterogeneity. The
E. sakazakii
type strain 16S rDNA sequence was 97.8% similar to that of
Citrobacter koseri
but 97.0% similar to that of
Enterobacter cloacae
.
Prevalence of Hepatitis E Virus (HEV) Infection in Wild Boars and Deer and Genetic Identification of a Genotype 3 HEV from a Boar in Japan
Authors: Sonoda Hideto , Abe Masahiko , Sugimoto Takeshi , Sato Yukihiro , Bando Masashi , Fukui Emiko , Mizuo Hitoshi , Takahashi Masaharu , Nishizawa Tsutomu , Okamoto Hiroaki
Published: November 2004

Zoonotic transmission of hepatitis E virus (HEV) from captured wild deer or boars to humans has been suggested. Antibody to HEV was detected in 9% of 35 wild boars and 2% of 117 wild deer tested, and a presumably indigenous HEV of genotype 3 was isolated from a boar in Japan.
Stochastic Transmission of Multiple Genotypically Distinct
Anaplasma marginale
Strains in a Herd with High Prevalence of
Anaplasma
Infection
Authors: Palmer Guy H. , Knowles Donald P. , Rodriguez Jose-Luis , Gnad David P. , Hollis Larry C. , Marston Twig , Brayton Kelly A.
Published: November 2004

Multiple genotypically unique strains of the tick-borne pathogen
Anaplasma marginale
occur and are transmitted within regions where the organism is endemic. In this study, we tested the hypothesis that specific
A. marginale
strains are preferentially transmitted. The study herd of cattle (
n
= 261) had an infection prevalence of 29% as determined by competitive inhibition enzyme-linked immunosorbent assay and PCR, with complete concordance between results of the two assays. Genotyping revealed the presence of 11 unique strains within the herd. Although the majority of the individuals (70 of 75) were infected with only a single
A. marginale
strain, five animals each carried two strains with markedly distinct genotypes, indicating that superinfection does occur with distinct
A. marginale
strains, as has been reported with
A. marginale
and
A. marginale
subsp.
centrale
strains. Identification of strains in animals born into and infected within the herd during the period from 1998 to 2003 revealed no significant difference from the overall strain prevalence in the herd, results that do not support the occurrence of preferential strain transmission within a population of persistently infected animals and are most consistent with pathogen strain transmission being stochastic.
Effect of Transport Time, Temperature, and Concentration on the Survival of Group B Streptococci in Amies Transport Medium
Authors: Stoner K. A. , Rabe L. K. , Hillier S. L.
Published: November 2004

The impact of transport time and temperature on survival of group B streptococci (GBS) in Amies transport medium was evaluated. Viability of 10 or more CFU of GBS was maintained for 4 days at 24 or 3°C. However, there was a significant decrease in viability for GBS held at 30°C for 4 days.
Spoligotyping Profile Change Caused by Deletion of a Direct Variable Repeat in a
Mycobacterium tuberculosis
Isogenic Laboratory Strain
Authors: Aranaz Alicia , Romero Beatriz , Montero Natalia , Álvarez Julio , Bezos Javier , de Juan Lucía , Mateos Ana , Domínguez Lucas
Published: November 2004

Spoligotyping is a major tool for molecular typing of
Mycobacterium tuberculosis
complex organisms. For epidemiological purposes, strains are considered clonal only when their spoligotyping patterns are identical. We report a change in the spoligotyping profiles of truly isogenic strains (a clinical isolate and a subculture derived in the laboratory) caused by deletion of a direct variable repeat. Without the information about the relationship between them, a link between these strains would have gone unnoticed. Evolutionary events should be taken into account in the interpretation of spoligotyping results and in the design of databases.
Comparison of the Sensitivities and Viral Load Values of the AMPLICOR HIV-1 MONITOR Version 1.0 and 1.5 Tests
Authors: Caliendo Angela M. , Ingersoll Jessica , Green Alicia M. , Nolte Frederick S. , Easley Kirk A.
Published: November 2004

This study compared the sensitivity and viral load values of the AMPLICOR HIV-1 MONITOR microwell version 1.0, microwell version 1.5, and COBAS version 1.5 tests. Based on the percentage of positive replicates, the microwell version 1.5 and COBAS version 1.5 tests are more sensitive than the microwell version 1.0 test. Viral load values obtained with the COBAS version 1.5 test are lower than those obtained with either the microwell version 1.0 or microwell version 1.5 test.
Association between a High BK Virus Load in Urine Samples of Patients with Graft-Versus-Host Disease and Development of Hemorrhagic Cystitis after Hematopoietic Stem Cell Transplantation
Authors: Bogdanovic G. , Priftakis P. , Giraud G. , Kuzniar M. , Ferraldeschi R. , Kokhaei P. , Mellstedt H. , Remberger M. , Ljungman P. , Winiarski J. , Dalianis T.
Published: November 2004

BK virus (BKV) load in urine alone or in combination with acute graft-versus-host disease (GVHD) was correlated to development of hemorrhagic cystitis (HC). BKV load in combination with acute GVHD discriminated the best, while BKV and viral load alone, but not GVHD, still showed predictive ability for HC.
Demonstration of Two Distinct Hemotropic Mycoplasmas in French Dogs
Authors: Kenny Martin J. , Shaw Susan E. , Beugnet Fréderic , Tasker Séverine
Published: November 2004

In North America it has been shown that distinct hemotropic mycoplasmas exist in dogs. Blood samples from 460 French dogs were analyzed by PCR to evaluate hemoplasma infection status. Seventy-one dogs (15.4%) were positive; of these, 44 (9.6%) were infected with an organism closely related to “CandidatusMycoplasma haemoparvum” only, 15 (3.3%) were infected withMycoplasma haemocanisonly, and 12 dogs (2.6%) were dually infected with both organisms.
Differentiation of
Rhizomucor
Species on the Basis of Their Different Sensitivities to Lovastatin
Authors: Lukács Gyöngyi , Papp Tamás , Nyilasi Ildikó , Nagy Erzsébet , Vágvölgyi Csaba
Published: November 2004

The opportunistic pathogens
Rhizomucor pusillus
and
Rhizomucor miehei
may be agents of frequently fatal mycotic diseases. In the present study, the susceptibilities of 27 clinical and environmental isolates of
R. miehei
and
R. pusillus
to lovastatin under different culturing conditions were investigated. Most of the
R. miehei
strains grew at lovastatin concentrations as high as 64 to 128 μg/ml. In contrast, the inhibitory effect of lovastatin on all of the
R. pusillus
strains was evident at lovastatin concentrations as low as 1 to 2 μg/ml. A simple and reliable method for species-level differentiation, based on the significantly higher sensitivity of
R. pusillus
to lovastatin than that of
R. miehei
, was elaborated. According this, on malt extract agar containing 6 μg of lovastatin/ml,
R. pusillus
is not able to produce colonies, while
R. miehei
will form compact colonies.
An Unexpected Experimental Pitfall in the Molecular Diagnosis of Bacterial Endophthalmitis
Authors: Ugahary Luana , van de Sande Wendy , van Meurs Jan C. , van Belkum Alex
Published: November 2004

General primer-mediated ribosomal DNA amplification during endophthalmitis may improve the quality of diagnostic microbiology. However, extreme care needs to be taken not to introduce contaminating bacterial DNA during surgery procedures. The use of decontaminating iodine solutions can lead to such contamination due to the presence of DNA from
Pseudomonas
-like organisms.
Natural
Clostridium botulinum
Type C Toxicosis in a Group of Cats
Authors: Elad D. , Yas-Natan E. , Aroch I. , Shamir M. H. , Kleinbart S. , Hadash D. , Chaffer M. , Greenberg K. , Shlosberg A.
Published: November 2004

Clinical signs of botulism were observed in a group of eight cats, four of which died, after being fed pelican carrion.
Clostridium botulinum
type C was isolated from one cat. The microorganism and its toxin were found in the pelican. This is apparently the first report of natural botulism in cats.
Laboratory-Confirmed Transmission of Vaccinia Virus Infection through Sexual Contact with a Military Vaccinee
Authors: Egan Christina , Kelly Cassandra D. , Rush-Wilson Kim , Davis Stephen W. , Samsonoff William A. , Pfeiffer Heidi , Miller Jim , Taylor Jill , Cirino Nick M.
Published: November 2004

A laboratory-confirmed, inadvertent transmission of vaccinia virus from an unusual source highlights the importance of epidemiologic tracing, proper biosafety practices in the clinical diagnostic laboratories, and educating clinicians and laboratorians to potential bioterrorism-initiated outbreaks as well as look-alike disease discrimination.
Disseminated
Beauveria bassiana
Infection in a Patient with Acute Lymphoblastic Leukemia
Authors: Tucker D. L. , Beresford C. H. , Sigler L. , Rogers K.
Published: November 2004

We describe a case of disseminated
Beauveria bassiana
infection in a patient with acute lymphoblastic leukemia. Her infection was successfully treated with amphotericin B and itraconazole.
B. bassiana
is rarely reported as a human pathogen. It is commonly found in soil and because of its pathogenicity to many insect species is incorporated into several pesticides.
Genetic Confirmation of Quinine-Resistant
Plasmodium falciparum
Malaria Followed by Postmalaria Neurological Syndrome in a Traveler from Mozambique
Authors: Palmieri Fabrizio , Petrosillo Nicola , Paglia Maria Grazia , Conte Aristide , Goletti Delia , Pucillo Leopoldo Paolo , Menegon Michela , Sannella Anna , Severini Carlo , Majori Giancarlo
Published: November 2004

A case of quinine-resistant
Plasmodium falciparum
malaria, followed by a postmalaria neurological syndrome and a recurrence episode, is described. Genetic characterization of the
P. falciparum
isolate obtained by analysis of
msp1
and
msp2
amplicons revealed the coexistence of two genotypes causing the first malaria episode and the presence of a unique isolate responsible for the recurrence.
Predicting benefits of spawning-habitat rehabilitation to salmonid (Oncorhynchusspp.) fry production in a regulated California river
Authors: Merz Joseph E , Setka Jose D , Pasternack Gregory B , Wheaton Joseph M
Published: November 2004

We tested the hypothesis that spawning-bed enhancement increases survival and growth of chinook salmon (Oncorhynchus tshawytscha) embryos in a regulated California stream with a gravel deficit. We also examined how 12 physical parameters correlated within spawning sites and how well they predicted survival and growth of chinook salmon and steelhead (Oncorhynchus mykiss) embryos. Salmon embryos planted in enhanced gravels had higher rates of survival to the swim-up stage than embryos planted in unenhanced spawning gravels. No significant increase in growth was observed. Intergravel temperature and substrate size were strongly correlated with distance downstream from the lowest nonpassable dam. Intergravel turbidity and total suspended and volatile solids were also strongly correlated. Multiple-regression models were built with a combination of physical measurements to predict survival and length of salmon and steelhead embryos. Survival models accounted for 87% of the variation around the mean for salmon and 82% for steelhead. Growth models accounted for 95% of the variation around the mean for salmon and 89% for steelhead. These findings suggest that spawning-bed enhancement can improve embryo survival in degraded habitat. Additionally, measurements of a suite of physical parameters before and after spawning-bed manipulation can accurately predict benefits to target species.
Availability to Steller sea lions (Eumetopias jubatus) of a seasonal prey resource: a prespawning aggregation of eulachon (Thaleichthys pacificus)
Authors: Sigler Michael F , Womble Jamie N , Vollenweider Johanna J
Published: November 2004

The availability of seasonally abundant energy-rich prey can be a significant factor for the survival and reproductive success of predator populations. Large numbers of Steller sea lions (Eumetopias jubatus) were attracted to a prespawning aggregation of eulachon (Thaleichthys pacificus) in Berners Bay in southeast Alaska during AprilMay in 2002 and 2003. Sea lion abundance increased as eulachon gathered in Berners Bay, peaked as eulachon abundance peaked, and decreased as the eulachon moved up-river. As sea lion abundance increased in Berners Bay, sea lion abundance decreased at Benjamin Island, a sea lion haulout located 22 km away. The eulachon provided an abundant, energy-rich, predictable prey source for the Steller sea lions: (i) eulachon energy density was 9.70 ± 0.24 kJ·g1, much higher than that of any forage species reported in the North Pacific Ocean except northern lampfish (Stenobrachius leucopsarus); (ii) a large surplus of prey was available per sea lion while the eulachon aggregation was present; and (iii) the spawning run usually begins between late April and early May. The eulachon pulse may be critical to Steller sea lions during a period of high energetic demands.
Importance of landscape variables and morphology on nutrients in Missouri reservoirs
Authors: Jones J R , Knowlton M F , Obrecht D V , Cook E A
Published: November 2004

The proportion of cropland cover in the catchments of Missouri reservoirs, a surrogate for non-point-source nutrient loss from agricultural watersheds, accounts for some 60%70% of the cross-system variance in long-term averages of total phosphorus and total nitrogen (n = 126, ln transformation for nutrients and logit for cropland). The addition of dam height and an index of flushing rate improved r2values to ~77% for both nutrients. Even among reservoir catchments with >80% grass and forest cover, cropland accounted for most of the variation in nutrients. Reservoir nutrients showed a strong negative relation to forest cover. Relations between grass cover and nutrients were positive but weak, and grass had no significant statistical effect once cropland was taken into account. Residual analysis suggests that urban reservoirs would have about twice the nutrient level of reservoirs in non-cropland basins (forest and grass). The increase in nutrients with the proportion of cropland and the decrease with forest cover have previously been documented in Missouri streams.
Hydrogen peroxide distribution, production, and decay in boreal lakes
Authors: Häkkinen Petri J , Anesio Alexandre M , Granéli Wilhelm
Published: November 2004

The distribution, production, and decay of hydrogen peroxide (H2O2) were studied in 10 boreal lakes of differing physicalchemical characteristics. Diurnal and vertical fluctuations in H2O2concentration were followed in the lakes by sampling at six depths three times per day. In addition, incubations of water filtered through 0.2-µ mesh were made under artificial irradiation to study the abiotic production and decay of H2O2. H2O2concentrations after 8 h of artificial irradiation were significantly correlated with neither absorption coefficients at 320 nm nor with dissolved organic carbon (DOC) concentrations. However, H2O2concentration increased rapidly with DOC concentration among lakes with DOC concentrations below 10 mg·L1. The H2O2concentration after exposure to ultraviolet radiation was positively related to the half-life of H2O2, which in turn was negatively correlated with iron and manganese concentrations (r2 = 0.68 and 0.70, respectively). In situ H2O2concentrations at the surface of the water column ranged between 30 and 1041 nmol·L1and were largely determined by the decay rates of H2O2and the mixing depth of the water column.
Biological reference points in the management of North American sea urchin fisheries
Authors: Botsford Louis W , Campbell Alan , Miller Robert
Published: November 2004

The precautionary approach calls for both target and limit reference points (TRPs and LRPs, respectively) and notes the vulnerability of developing fisheries to excess effort. LRPs should reflect a population's ability to continue to persist, which depends on lifetime egg production (LEP) and current abundance. The unique characteristics of sea urchin fisheries, such as (i) tight ecological coupling, (ii) their being roe fisheries, (iii) protection of juveniles under adult spine canopies, and (iv) broadcast spawning, can influence their management. Most North American sea urchin fisheries developed rapidly. Their reference points include (i) several LRPs and TRPs based on the logistic or surplus production model, (ii) a unique TRP involving direct monitoring of the bathymetric position of their macro phyte food, and (iii) an LRP based on the fraction of natural, unfished LEP. The dominant effect of fishing down and serial depletion on catch and effort data from developing sea urchin fisheries adversely affects fits to the logistic model. Reference points based on tight ecological coupling will be useful only where food webs are simple and one-dimensional. Sea urchin fisheries developed in the future should consider the fraction of natural LEP as an LRP and attempt to limit early excess fishing capacity.
Current usage of fisheries indicators and reference points, and their potential application to management of fisheries for marine invertebrates
Authors: Caddy J F
Published: November 2004

The use of indicators in management of invertebrate resources is placed in the context provided by more extensive applications in finfish fisheries. Indicators proposed for the Convention on International Trade in Endangered Species based on extent-of-decline and trend analysis are appropriate should full assessments be unavailable. Measuring reproductive performance frequently builds on egg-per-recruit considerations, given that age structure and stock–recruit relationships are rarely available. Reference points derived from models are compared with direct use of data series, and a broad-brush approach providing a redundancy of indicators is recommended. Indicators may measure productivity as well as biomass and exploitation rate, but ecosystem, spatial, habitat, environmental characteristics, and socio economic considerations also require monitoring. There is a need to integrate multiple indicators and limit reference points into harvest rules and other decisional infrastructures. The various driving force – pressure – state – impact – response classifications of indicators in use for environmental assessment are now being proposed for marine resources and offer one context for combining multiple indicators. Another is provided by the traffic light approach already used for invertebrate fisheries. The use of indicators and reference points in stock rebuilding is described.
Biological reference points for sea scallops (Placopecten magellanicus): the benefits and costs of being nearly sessile
Authors: Smith Stephen J , Rago Paul
Published: November 2004

In this paper, we concentrate on spatial aspects of growth and reproduction for sea scallops (Placopecten magellanicus) to advance the general theory for development of reference points for sessile animals and to illustrate the general points with several specific examples. Nonlinear mixed effects models can be used to define the spatial distribution of growth rates and their implications for the definition of growth overfishing. We develop a basin model to illustrate that the typical "boom and bust" effects, often attributed to environmental factors, are explained equally well by spatial variations in habitat quality, spatial concentration of fisheries, and dispersal of larvae among areas. Results suggest that incentives to concentrate fishing effort in lower productivity areas may be an effective tool for reducing recruitment variation and improving yields. Reductions in fishing mortality might be possible with closed areas as they can be used to reduce the concentration of effort on high scallop densities. Further, rotational area management strategies can offer the promise of balancing demands for increased yield, prevention of recruitment overfishing, maintaining spawning reserves, and reducing habitat damage and bycatch.
Comparison of reference points estimated using a size-based method for two high-latitude crab species in the United States and Canada
Authors: Siddeek M SM , Sainte-Marie Bernard , Boutillier Jim , Bishop Gretchen
Published: November 2004

We briefly reviewed the decision rules currently used for managing two major high-latitude crab stocks, snow crab (Chionoecetes opilio) and Dungeness crab (Cancer magister), in the United States and Canada and compared them with model-based reference points, harvest rate, and biomass proportion relative to virgin biomass, developed using species- and area-specific parameters. The model followed a size-based approach, which incorporated BevertonHolt and Ricker stockrecruitment models and estimated mean and median reference points. The recruitment was also perturbed to generate distributions of reference points. The BevertonHolt stockrecruitment model provided a lower harvest rate than that of the Ricker model. Harvest rates were lower for combined sexes spawning biomass than for female-only spawning biomass. Increasing the minimum size at first capture and decreasing the handling mortality resulted in increased harvest rates. Changes in fishery duration and timing of fishery open date did not change the harvest rate appreciably. The harvest rates for the Canadian snow and Dungeness crabs were mostly higher than those estimated for the Bering Sea and Southeast Alaska stocks. Reliable estimates of a number of life history parameters are lacking for both species, and hence, the results of this exercise need to be treated in a precautionary manner.
Altering molecular weight distributions: Benzylphosphinimide titanium complexes as ethylene polymerization catalysts
Authors: Hollink Emily , Wei Pingrong , Stephan Douglas W
Published: November 2004

The phosphines and corresponding phosphinimines R2BnPNSiMe3 (R = t-Bu, Cy), p-C6H4(CH2PR2)2 (R = t-Bu (1), Cy (2)), and p-C6H4(CH2PR2NSiMe3)2 (R = t-Bu (3), Cy (4)) were prepared in high yields. Subsequent reaction with Ti precursors afforded (R2BnPN)TiCp*Cl2 (Cp* = η-C5Me5; R = t-Bu (5), Cy (6)), (R2BnPN)TiCpCl2 (Cp = η-C5H5; R = t-Bu (7), Cy (8)), p-C6H4(CH2PR2NTiCp*Cl2)2 (R = t-Bu (9), Cy (10)), and p-C6H4(CH2PR2NTiCpCl2)2 (R = t-Bu (11), Cy (12)). Methylation of the above complexes gave (R2BnPN)TiCp*Me2 (R = t-Bu (13), Cy (14)), (R2BnPN)TiCpMe2 (R = t-Bu (15), Cy (16)), p-C6H4(CH2PR2NTiCp*Me2)2 (R = t-Bu (17), Cy (18)), and p-C6H4(CH2PR2NTiCpMe2)2 (R = t-Bu (19), Cy (20)). The activity of these species as catalyst precursors in ethylene polymerization catalysis was evaluated using Schlenk line and Buchi reactor techniques using activation by methylaluminoxane (MAO) or [Ph3C][B(C6F5)4]. All these catalysts showed good activities and yield polymers with relatively broad molecular weight distributions. The bimodal polymers derived from catalysts generated using MAO are proposed to result from additional active species, possibly as a result of reaction of MAO with the benzylic fragments. X-ray data are reported for 1, 48, 10, 1214, 16, and 1820.Key words: phosphinimides, polymerization, catalysis, polyethylene, titanium, polymer molecular weight distributions.
A simple synthesis of benzimidazole N-oxides from 2-nitroaniline derivatives  Scope and limitations
Authors: Buján Elba I , Salum María Laura
Published: November 2004

Several benzimidazole N-oxide derivatives were synthesized in very good yield by heating at reflux the corresponding N-alkyl-2-nitroaniline derivative with NaOH in 60% 1,4-dioxanewater. The effect of substituents on the aromatic ring and amino group on the reaction is discussed.Key words: synthesis, benzimidazole N-oxides.
Gaussian basis sets for low-lying excited states of neutral atoms with 2 ≤ Z ≤ 36
Authors: Barreto M T , Neto A Canal , Jorge F E
Published: November 2004

The improved generator coordinate HartreeFock method is used to generate Gaussian basis sets for low-lying excited states of neutral atoms from He (Z = 2) to Kr (Z = 36). Then, excitation energies and orbital energies of the outermost orbitals of each symmetry are calculated and compared with the corresponding values obtained with numerical HartreeFock calculations. Besides this, the basis sets for Be (3P) and F (2P) are contracted by a standard procedure and, then, enriched with polarization functions. From these basis sets, total energies, dissociation energy, and bond length for BeF are calculated and compared with results obtained with other basis sets and with experimental values. The sets for HeKr are useful in constructing basis sets for molecular calculations. Key words: improved generator coordinate HartreeFock method, Gaussian basis sets, low-lying excited states, neutral atoms.
A new efficient synthesis of α-methyl-β-ketoesters through an Eschenmoser sulfide reaction
Authors: Bellec Christian , Gaurat Olivier
Published: November 2004

Various α-methyl-β-ketoesters were readily synthesized through Eschenmoser condensation of thioamides with a commercially available bromoester. β-Enaminoesters were easily prepared through this sulfide contraction reaction and were hydrolysed to afford the corresponding β-ketoesters in moderate to good yields.Key words: α-alkylated-β-ketoesters, Eschenmoser, β-enaminoesters.
Synthesis of the tetranitro derivative of thiacalix[4]arene and its acidbase properties
Authors: Hu Xiaojun , Zhu Zhongliang , Shen Tianxiang , Shi Xianfa , Ren Jie , Sun Qiuhong
Published: November 2004

The tetranitro derivative 3 of thiacalix[4]arene was synthesized and characterized. Its acidbase properties in water solution were studied by UV spectroscopy. The four pKa values of 3 were determined by target testing factor analysis (TTFA). The pure UV absorption curves and pH distribution curves of five forms of 3 presented in aqueous solution were also calculated by TTFA.Key words: thiacalixarene, nitro derivative, acidbase properties.
Study of acid hydrolysis of bromazepam
Authors: Damjanović Tatjana , Popović Gordana , Verbić Srđan , Pfendt Lidija
Published: November 2004

Quantitative study of an acid hydrolysis of bromazepam, which in acidic solution simultaneously undergoes reversible 4,5-azomethine bond cleavage and protolytic reactions, was performed (t = 25 °C). When an equilibrium is established, four species are simultaneously present in solution. Two approaches, both based on theoretically derived dependence between the absorbance (A) and the solution acidity ([H3O+]), were used to determine appropriate equilibrium constants. In the first, the least-squares method was used to fit experimentally obtained (A, [H3O+]) value pairs to a derived function. With values obtained as fitting parameters, the probability distribution for equilibrium constants was calculated with the virtual experiments performed using Monte Carlo simulations. In the second one, spectrophotometric analysis indicated an existence of two distinct pH intervals, both with three dominant species involved. Spectral data were used to calculate equilibrium constants by a linear curve fitting analysis. Values obtained for equilibrium constants from the numerical and the experimental approaches are in good accordance and were used to calculate distribution of all the species as a function of pcH. Key words: bromazepam, acid hydrolysis, equilibrium constants.
Difluorocarbene induced facile synthesis of chlorohydrins from glycidyl ethers
Authors: Singh Sapna , Bhadury Pinaki S , Sharma Mamta , Palit Meehir , Jaiswal Devendra K
Published: November 2004

A novel and unusual approach based on a ClCF2COONaDMF system has been developed for the synthesis of chlorohydrins via an unexpected mechanism. In a first ever report for the synthesis of chlorohydrins from glycidyl ethers, e.g., CH2=CH-CH2-O-Z, CH3CH2-O-Z, C6H5-O-Z, C6H4(o-CH3)-O-Z, CH2=C(CH3)C(=O)-O-Z, etc., (where Z = glycidyl), difluorocarbene-induced facile regioselective ring opening of epoxides has generated the compound in high yield (70%83%). [Formula: see text] Key words: difluorocarbene, sodium chlorodifluoroacetate, chlorohydrins.
Spectroscopic and photophysical properties of carbazole-based triads
Authors: Belletête Michel , Bédard Mélanie , Bouchard Jimmy , Leclerc Mario , Durocher Gilles
Published: November 2004

A study of the spectroscopy and photophysics of four carbazole-based triads, namely, 1,4-bis(N-octylcarbazol-2-yl)phenylene (CPC), 2,5-bis(N-octylcarbazol-2-yl)thiophene (CTC), 2,7-bis(N-octylcarbazol-2-yl)-9,9-dihexylfluorene (CFC), and 2,7-bis(N-octylcarbazol-2-yl)-N-octylcarbazole (CCC) are reported. From ZINDO/S calculations performed on the optimized ground state geometries (HF/6-31G*), the S1← S0and S2← S0electronic transitions of CPC, CFC, and CCC are weakly allowed, whereas the S3← S0electronic transition is dipole-allowed (x axis) and possesses a high value of the oscillator strength. On the other hand, for CTC, the dipole-allowed electronic transition is S1← S0. For the four derivatives, the dipole-allowed transition corresponds mainly to the promotion of an electron from the HOMO to the LUMO. The first absorption band of each derivative can be assigned to the dipole-allowed transition. The geometry optimization of the excited states has been done with RCIS/6-31G* ab initio calculations. For CPC, CFC, and CCC, S3is much more stabilized than S1and S2, causing a crossing of the singlet excited states (S3becomes lower in energy than S1and S2). Emission energies from the first relaxed excited states (S1→ S0) have been obtained from ZINDO/S calculations performed on the optimized S1geometries (RCIS/6-31G*). It is found that these energies are in very good agreement with those determined from the fluorescence spectra. Going from CPC to CTC, the replacement of a phenylene ring by a thiophene unit induces a red shift in the absorption and fluorescence spectra. This behavior is interpreted in terms of the electron donor properties of the thiophene ring. The increase of the oligomer chain (CFC and CCC compared to CPC) also induces bathochromic shifts in the spectra because of a longer electronic delocalization along the molecular frame. From fluorescence data, it is observed that a more planar conformation is favored in the relaxed excited states. RCIS/6-31G* ab initio calculations performed on the S1relaxed excited states confirm this statement. Finally, the photophysical properties of CTC are mainly governed by nonradiative processes (knr), whereas the variation in the photophysics of CPC, CFC, and CCC mainly involves radiative processes (kF).Key words: electronic spectroscopy, fluorescence, photophysics, ab initio calculations, excited states.
A facile synthesis of 3,4-dialkyl-3,4-dihydro-2H-1,3-benzoxazin-2-ones and naphthoxazin-2-ones and their reactions with organolithium and Grignard reagents  Preparation of N-[1-(2′-hydroxyphenyl)alkyl]amides
Authors: Cimarelli Cristina , Palmieri Gianni , Volpini Emanuela
Published: November 2004

A facile and simple method for the preparation of 3,4-dialkyl-3,4-dihydro-2H-1,3-benzoxazin-2-ones or naphthoxazin-2-ones in high yields from aminoalkylphenols and aminoalkylnaphthols is described. The reactions of the products obtained with organolithium and Grignard reagents were studied, and a method for the preparation of N-[1-(2-hydroxyphenyl)alkyl]-N-alkylamides, which are of pharmaceutical interest, from benzoxazinones was developed. A possible reaction mechanism is also proposed. The relative configuration of chiral products was determined from conformational analysis of 1H NMR spectra.Key words: benzoxazinones, naphthoxazinones, organometallic reagents, amide preparation, aminoalkylphenols.
BOSE-EINSTEIN CONDENSATION OF ATOMS WITH ATTRACTIVE INTERACTION
Authors: AKHMEDIEV N. , DAS M. P. , VAGOV A. V.
Published: November 2004

We suggest that crucial effect on Bose-Einstein condensation in systems with attractive potential is three-body interaction. We investigate stationary solutions of the Gross-Pitaevskii equation with negative scattering length and a higher-order stabilising term in presence of an external parabolic potential. Stability properties of the condensate are similar to those for thermodynamic systems in statistical physics which have first order phase transitions. We have shown that there are three possible type of stationary solutions corresponding to stable, metastable and unstable phases. Results are discussed in relation to recently observed 7 Li condensate.
A THEORETICAL REVISIT ON 2-NORBORNYL CATION
Authors: ZUO TIANMING , HUANG THOMAS
Published: November 2004

The 2-norbornyl cation is an old topic in physical-organic chemistry. Whether in classical or non-classical form (partial bridged form) it has been one of the focus of discussion. Currently the experimental data and theoretical calculations favorably support the idea that 2-norbornyl cation is not in the classical form in the stable-ion condition. In this paper, first, we will show that a 3-center-2-electron π-complex is formed by the collapse of 2-norbornyl cation. Further, using different theoretical methods (B3LYP, MP2) with different basis sets (6-31+ G , 6-31 G (d,p), 6-311 G (d,p), 6-311 G (2d,p)), we find that there is a trend for the 3-center-2-electron π-complex to approach the Cs symmetry, and this π-complex oscillates within the numerical limits of the perfect Cs symmetrical configuration. The stabilization energies of the π-complex are 13.87 Kcal/mol and 19.47 Kcal/mol by B3LYP/6-31+G and MP2/6-31+G, respectively. Second, our calculations also show that the transition state between 2-norbornyl cation and 3-norbornyl cation is formed by a 3, 2-proton shift, not the generally accepted 3, 2-hydride shift. The activation energy of this 3, 2-proton shift is 10.9 Kcal/mol. Detailed structural changes in the optimization process and the formation of transition state (also a 3-center-2-electron π-complex) between 2-norbornyl cation and 3-norbornyl cation will also be included.
MFCC-DOWNHILL SIMPLEX METHOD FOR MOLECULAR STRUCTURE OPTIMIZATION
Authors: CHEN X. H. , ZHANG J. Z. H.
Published: November 2004

In this paper, a MFCC-downhill simplex method is proposed to study binding structures of small molecules or ions in large molecular complex systems. This method employs the Molecular Fractionation with Conjugated Caps (MFCC) approach in computing inter-molecular energy and implements the downhill simplex algorithm for structural optimization. The method is numerically tested on a system of [KCp(18-crown-6)] to optimize the position of the potassium cation in a fixed coordination sphere. The result of MFCC-downhill simplex optimization method shows good agreement with both the crystal structure and with the full-system downhill simplex optimized structure. The effect of the initial structure of the simplex and the method/basis-set levels of the quantum chemical calculation on the MFCC-downhill simplex optimization are also discussed. This method should be applicable to structure optimization of large complex molecular systems such as proteins or other biopolymers.
ON DIRECTLY SOLVING RADIAL SCHRÖDINGER EQUATION FOR THE GROUND STATES OF TWO ELECTRON ATOMS OR IONS BY GENETIC ALGORITHM
Authors: SAHA RAJENDRA , BHATTACHARYYA S. P.
Published: November 2004

A recipe is proposed for solving the radial Schrödinger equation (SE) for two electron atoms and ions in their ground states by genetic algorithm (GA). The recipe is tested for the isoelectronic series of H -, He , Li +, Be 2+ atoms and ions. The strong and weak features of the method are analyzed, and possible directions of improvement suggested.
PROTEIN FORCE-FIELD PARAMETERS OPTIMIZED WITH THE PROTEIN DATA BANK I: FORCE-FIELD OPTIMIZATIONS
Authors: SAKAE YOSHITAKE , OKAMOTO YUKO
Published: November 2004

We optimized five existing sets of force-field parameters for protein systems by our recently proposed method. The five force fields are AMBER parm94, AMBER parm96, AMBER parm99, CHARMM version 22, and OPLS-AA. The method consists of minimizing the sum of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank (PDB). We selected the partial-charge and backbone torsion-energy parameters for this optimization, and 100 molecules from the PDB were used. We gave detailed comparisons of the optimized force fields and found that there is a tendency of convergence towards the same function for the torsion-energy term.
LINEAR SCALING FOR DENSITY FUNCTIONAL CALCULATIONS ON LARGE MOLECULES WITH THE DEFT SOFTWARE PACKAGE
Authors: SHAW DAWN M. , ST-AMANT ALAIN
Published: November 2004

The new methods implemented within the DeFT density functional software package are outlined. Where appropriate, they are benchmarked against the conventional methods, which are prohibitively expensive for large systems due to their poor scaling with system size. Benchmark calculations on extended glycine polypeptides clearly demonstrate that linear scaling has been achieved for these first principles electronic structure calculations. Within the DeFT software package, a divide-and-conquer approach is instrumental in attaining this goal. The errors introduced by our divide-and-conquer approach are quantified and shown to be insignificant when compared to the inherent error in even the most accurate density functionals presently available. Calculations on molecules within the G2 dataset highlight the overall accuracy of the exchange-correlation functionals, orbital basis sets, auxiliary density fitting basis sets, and grids used within DeFT.
Neuromedin B and its receptor are mitogens in both normal and malignant epithelial cells lining the colon
Authors: Matusiak Damien , Glover Sarah , Nathaniel Rajkumar , Matkowskyj Kristina , Yang Jianxin , Benya Richard V.
Published: November 2004

Bombesin-like peptides are uniformly thought to act as mitogens in cancer. Yet by studying human tissues, we have recently shown that bombesin and its mammalian homologue gastrin-releasing peptide act as morphogens, promoting tumor differentiation when aberrantly upregulated in colon cancer. In contrast, little is known about the bombesin-like peptide neuromedin B (NMB) and its receptor (NMB-R) in the human gastrointestinal tract. We therefore studied their presence and function in normal and malignant human colonic epithelia. Anti-NMB monoclonal antibodies were made against keyhole limpet hemocyanin (KLH)-conjugated human NMB, whereas anti-NMB-R antibodies were raised in rabbits against KLH-conjugated peptides corresponding to the third intracellular loop and COOH-terminal tail of the receptor protein. NMB antibody recognized two bands at ∼1.2 kDa and ∼1.5 kDa. NMB-R antibodies recognized a band at 80 kDa (predicted 43 kDa); whereas treatment with the deglycosylating agent peptide- N-glycosidase generated bands at 65, 47, and 43 kDa. By immunohistochemistry, both NMB and NMB-R were expressed in normal and cancerous colonic epithelial tissues. In cancer, the amount of NMB was similar to that expressed by proliferating epithelial cells located within the crypt. In contrast, NMB-R expression was increased in cancer, with higher levels detected in better differentiated tumor cells. To assess NMB function, proliferation was determined in the nonmalignant human colonic epithelial cell line NCM-460 and in the colon cancer cell lines Caco-2 and HT-29. Exogenously added NMB was 50–100% more efficacious than gastrin-releasing peptide in causing tumor cell proliferation, whereas only NMB increased NCM-460 cell proliferation. These findings indicate that NMB and its receptor are coexpressed by proliferating cells in which they act in an autocrine fashion with similar and modest potency in both normal and malignant colonic epithelial cells.