bluuebunny/crossref_metadata_2025 huggingface dataset:
A Second Outer-Core Region in
Klebsiella pneumoniae
Lipopolysaccharide
Authors: Regué Miguel , Izquierdo Luis , Fresno Sandra , Piqué Núria , Corsaro Maria Michela , Naldi Teresa , De Castro Cristina , Waidelich Dietmar , Merino Susana , Tomás Juan M.
Published: June 2005

Up to now only one major type of core oligosaccharide has been found in the lipopolysaccharide of all
Klebsiella pneumoniae
strains analyzed. Applying a different screening approach, we identified a novel
Klebsiella pneumoniae
core (type 2). Both
Klebsiella
core types share the same inner core and the outer-core-proximal disaccharide, GlcN-(1,4)-GalA, but they differ in the GlcN substituents. In core type 2, the Glc
p
N residue is substituted at the O-4 position by the disaccharide β-Glc
p
(1-6)-α-Glcp(1, while in core type 1 the Glc
p
N residue is substituted at the O-6 position by either the disaccharide α-He
p
(1-4)-α-Kdo(2 or a Kdo residue (Kdo is 3-deoxy-
d
-manno-octulosonic acid). This difference correlates with the presence of a three-gene region in the corresponding core biosynthetic clusters. Engineering of both core types by interchanging this specific region allowed studying the effect on virulence. The replacement of
Klebsiella
core type 1 in a highly type 2 virulent strain (52145) induces lower virulence than core type 2 in a murine infection model.
Defense against Protein Carbonylation by DnaK/DnaJ and Proteases of the Heat Shock Regulon
Authors: Fredriksson Åsa , Ballesteros Manuel , Dukan Sam , Nyström Thomas
Published: June 2005

Protein carbonylation is an irreversible oxidative modification that increases during organism aging and bacterial growth arrest. We analyzed whether the heat shock regulon has a role in defending
Escherichia coli
cells against this deleterious modification upon entry into stationary phase. Providing the cell with ectopically elevated levels of the heat shock transcription factor, σ
32
, effectively reduced stasis-induced carbonylation. Separate overproduction of the major chaperone systems, DnaK/DnaJ and GroEL/GroES, established that the former of these is more important in counteracting protein carbonylation. Deletion of the heat shock proteases Lon and HslVU enhanced carbonylation whereas a
clpP
deletion alone had no effect. However, ClpP appears to have a role in reducing protein carbonyls in cells lacking Lon and HslVU. Proteomic immunodetection of carbonylated proteins in the wild-type,
lon
, and
hslVU
strains demonstrated that the same spectrum of proteins displayed a higher load of carbonyl groups in the
lon
and
hslVU
mutants. These proteins included the β-subunit of RNA polymerase, elongation factors Tu and G, the E1 subunit of the pyruvate dehydrogenase complex, isocitrate dehydrogenase, 6-phosphogluconate dehydrogenase, and serine hydroxymethyltranferase.
Crystal Structure of the
Staphylococcus aureus
pI258 CadC Cd(II)/Pb(II)/Zn(II)-Responsive Repressor
Authors: Ye Jun , Kandegedara Ashoka , Martin Philip , Rosen Barry P.
Published: June 2005

The
Staphylococcus aureus
plasmid pI258
cadCA
operon encodes a P-type ATPase, CadA, that confers resistance to the heavy metals Cd(II), Zn(II), and Pb(II). Expression of this heavy-metal efflux pump is regulated by CadC, a homodimeric repressor that dissociates from the
cad
operator/promoter upon binding of Cd(II), Pb(II), or Zn(II). CadC is a member of the ArsR/SmtB family of metalloregulatory proteins. Here we report the X-ray crystal structure of CadC at 1.9 Å resolution. The dimensions of the protein dimer are approximately 30 Å by 40 Å by 70 Å. Each monomer contains six α-helices and a three-stranded β-sheet. Helices 4 and 5 form a classic helix-turn-helix motif that is the putative DNA binding region. The α1 helix of one monomer crosses the dimer to approach the α4 helix of the other monomer, consistent with the previous proposal that these two regulatory metal binding sites for the inducer cadmium or lead are each formed by Cys-7 and Cys-11 from the N terminus of one monomer and Cys-58 and Cys-60 of the other monomer. Two nonregulatory metal binding sites containing zinc are formed between the two antiparallel α6 helices at the dimerization interface. This is the first reported three-dimensional structure of a member of the ArsR/SmtB family with regulatory metal binding sites at the DNA binding domain and the first structure of a transcription repressor that responds to the heavy metals Cd(II) and Pb(II).
Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate SymbiontBuchnera aphidicola
Authors: Moran Nancy A. , Dunbar Helen E. , Wilcox Jennifer L.
Published: June 2005

Buchnera aphidicola, the obligate symbiont of aphids, has an extremely reduced genome, of which about 10% is devoted to the biosynthesis of essential amino acids needed by its hosts. Most regulatory genes for these pathways are absent, raising the question of whether and how transcription of these genes responds to the major shifts in dietary amino acid content encountered by aphids. Using full-genome microarrays forB. aphidicolaof the hostSchizaphis graminum, we examined transcriptome responses to changes in dietary amino acid content and then verified behavior of individual transcripts using quantitative reverse transcriptase PCR. The only gene showing a consistent and substantial (>twofold) response wasmetE, which underlies methionine biosynthesis and which is the only amino acid biosynthetic gene retaining its ancestral regulator (metR). In another aphid host,Acyrthosiphon pisum,B. aphidicolahas no functionalmetRand shows no response inmetEtranscript levels to changes in amino acid concentrations. Thus, the only substantial transcriptional response involves the one gene for which an ancestral regulator is retained. This result parallels that from a previous study on heat stress, in which only the few genes retaining the global heat shock promoter showed responses in transcript abundance. The irreversible losses of transcriptional regulators constrain ability to alter gene expression in the context of environmental fluctuations affecting the symbiotic partners.
Overproduction of CcmG and CcmFH
Rc
Fully Suppresses the
c
-Type Cytochrome Biogenesis Defect of
Rhodobacter capsulatus
CcmI-Null Mutants
Authors: Sanders Carsten , Deshmukh Meenal , Astor Doniel , Kranz Robert G. , Daldal Fevzi
Published: June 2005

Gram-negative bacteria like
Rhodobacter capsulatus
use intertwined pathways to carry out the posttranslational maturation of
c
-type cytochromes (Cyts). This periplasmic process requires at least 10 essential components for apo-Cyt
c
chaperoning, thio-oxidoreduction, and the delivery of heme and its covalent ligation. One of these components, CcmI (also called CycH), is thought to act as an apo-Cyt
c
chaperone. In
R. capsulatus
, CcmI-null mutants are unable to produce
c
-type Cyts and thus sustain photosynthetic (Ps) growth. Previously, we have shown that overproduction of the putative heme ligation components CcmF and CcmH
Rc
(also called Ccl1 and Ccl2) can partially bypass the function of CcmI on minimal, but not on enriched, media. Here, we demonstrate that either additional overproduction of CcmG (also called HelX) or hyperproduction of CcmF-CcmH
Rc
is needed to completely overcome the role of CcmI during the biogenesis of
c
-type Cyts on both minimal and enriched media. These findings indicate that, in the absence of CcmI, interactions between the heme ligation and thioreduction pathways become restricted for sufficient Cyt
c
production. We therefore suggest that CcmI, along with its apo-Cyt chaperoning function, is also critical for the efficacy of holo-Cyt
c
formation, possibly via its close interactions with other components performing the final heme ligation steps during Cyt
c
biogenesis.
A Phosphohexomutase from the Archaeon
Sulfolobus solfataricus
Is Covalently Modified by Phosphorylation on Serine
Authors: Ray W. Keith , Keith Sabrina M. , DeSantis Andrea M. , Hunt Jeremy P. , Larson Timothy J. , Helm Richard F. , Kennelly Peter J.
Published: June 2005

A phosphoserine-containing peptide was identified from tryptic digests from
Sulfolobus solfataricus
P1 by liquid chromatography-tandem mass spectrometry. Its amino acid sequence closely matched that bracketing Ser-309 in the predicted protein product of open reading frame sso0207, a putative phosphohexomutase, in the genome of
S. solfataricus
P2. Open reading frame sso0207 was cloned, and its protein product expressed in
Escherichia coli
. The recombinant protein proved capable of interconverting mannose 1-phosphate and mannose 6-phosphate, as well as glucose 1-phosphate and glucose 6-phosphate, in vitro. It displayed no catalytic activity toward glucosamine 6-phosphate or
N
-acetylglucosamine 6-phosphate. Models constructed using the X-ray crystal structure of a homologous phosphohexomutase from
Pseudomonas aeruginosa
predicted that Ser-309 of the archaeal protein lies within the substrate binding site. The presence of a phosphoryl group at this location would be expected to electrostatically interfere with the binding of negatively charged phosphohexose substrates, thus attenuating the catalytic efficiency of the enzyme. Using site-directed mutagenesis, Ser-309 was substituted by aspartic acid to mimic the presence of a phosphoryl group. The
V
max
of the mutationally altered protein was only 4% that of the unmodified form. Substitution of Ser-309 with larger, but uncharged, amino acids, including threonine, also decreased catalytic efficiency, but to a lesser extent—three- to fivefold. We therefore predict that phosphorylation of the enzyme in vivo serves to regulate its catalytic activity.
Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human PathogenBurkholderia pseudomallei
Authors: Ou Keli , Ong Catherine , Koh Shze Yung , Rodrigues Fiona , Sim Siew Hoon , Wong Daniel , Ooi Chia Huey , Ng Kim Chong , Jikuya Hiroyuki , Yau Chin Chin , Soon Sou Yen , Kesuma Djohan , Lee May Ann , Tan Patrick
Published: June 2005

Natural isolates of pathogenic bacteria can exhibit a broad range of phenotypic traits. To investigate the molecular mechanisms contributing to such phenotypic variability, we compared the genomes, transcriptomes, and proteomes of two natural isolates of the gram-negative bacteriumBurkholderia pseudomallei, the causative agent of the human disease melioidosis. Significant intrinsic genomic, transcriptional, and proteomic variations were observed between the two strains involving genes of diverse functions. We identified 16 strain-specific regions in theB. pseudomalleiK96243 reference genome, and for eight regions their differential presence could be ascribed to either DNA acquisition or loss. A remarkable 43% of the transcriptional differences between the strains could be attributed to genes that were differentially present between K96243 and Bp15682, demonstrating the importance of lateral gene transfer or gene loss events in contributing to pathogen diversity at the gene expression level. Proteins expressed in a strain-specific manner were similarly correlated at the gene expression level, but up to 38% of the global proteomic variation between strains comprised proteins expressed in both strains but associated with strain-specific protein isoforms. Collectively, >65 hypothetical genes were transcriptionally or proteomically expressed, supporting their bona fide biological presence. Our results provide, for the first time, an integrated framework for classifying the repertoire of natural variations existing at distinct molecular levels for an important human pathogen.
Biochemical Characterization of a Prokaryotic Phenylalanine Ammonia Lyase
Authors: Xiang Longkuan , Moore Bradley S.
Published: June 2005

The committed biosynthetic reaction to benzoyl-coenzyme A in the marine bacterium “
Streptomyces maritimus
” is carried out by the novel prokaryotic phenylalanine ammonia lyase (PAL) EncP, which converts the primary amino acid
l
-phenylalanine to
trans
-cinnamic acid. Recombinant EncP is specific for
l
-phenylalanine and shares many biochemical features with eukaryotic PALs, which are substantially larger proteins by ∼200 amino acid residues.
Evolutionary Changes of the
flhDC
Flagellar Master Operon in
Shigella
Strains
Authors: Tominaga Akira , Lan Ruiting , Reeves Peter R.
Published: June 2005

Shigella
strains are nonmotile. The master operon of flagellar synthesis,
flhDC
, was analyzed for genetic damage in 46
Shigella
strains representing all known serotypes. In 11 strains (B1, B3, B6, B8, B10, B18, D5, F1B, D10, F3A, and F3C) the
flhDC
operon was completely deleted. PCR and sequence analysis of the
flhDC
region of the remaining 35 strains revealed many insertions or deletions associated with insertion sequences, and the majority of the strains were found to be defective in their
flhDC
genes. As these genes also play a role in regulation of nonflagellar genes, the loss may have other consequences or be driven by selection pressures other than those against flagellar motility. It has been suggested that
Shigella
strains fall mostly into three clusters within
Escherichia coli
, with five outlier strains, four of which are also within
E. coli
(G. M. Pupo, R. Lan, and P. R. Reeves, Proc. Natl. Acad. Sci. USA 97:10567-10572, 2000). The distribution of genetic changes in the
flhDC
region correlated very well with the three clusters and outlier strains found using housekeeping gene DNA sequences, enabling us to follow the sequence of mutational change in the
flhDC
locus. Two cluster 2 strains were found to have unique
flhDC
sequences, which are most probably due to recombination during the exchange of the adjacent O-antigen gene clusters.
A population based study of reporting patterns and characteristics of men who abuse their female partners
Authors: Peek-Asa C , Zwerling C , Young T , Stromquist A M , Burmeister L F , Merchant J A
Published: June 2005

Objective:This study estimates the prevalence of male abusive behavior reported by men and their female partners and identifies characteristics of abusive men.

Design:Baseline survey from a population based cohort study of general health.

Setting:A rural county in Iowa, USA.

Subjects:572 men and their cohabitating female partners.

Main outcome measures:Male-to-female physical, emotional, and sexual abuse reported by either partner.

Results:In this cohort, 13.6% of men had performed at least one act of physical abuse and 34.9% emotional abuse. More than 45% of abusive men reported their own behaviors. Alcohol problems, antisocial personality characteristics, depressive symptoms, and financial stress were all positively associated with both physical and emotional abuse, but suicidal thoughts were less likely among abusers.

Conclusion:Identification of common characteristics of abusive men may predict proclivity towards partner violence and barriers to behavior modification.
Traffic calming policy can reduce inequalities in child pedestrian injuries: database study
Authors: Jones S J , Lyons R A , John A , Palmer S R
Published: June 2005

Objectives:To determine whether area wide traffic calming distribution reflects known inequalities in child pedestrian injury rates. To determine whether traffic calming is associated with changes in childhood pedestrian injury rates.

Design:Small area ecological study, longitudinal analysis of injury rates with cross sectional analysis of traffic calming and method of travel to school.

Settings:Two cities in the United Kingdom.

Participants:4–16 year old children between 1992 and 2000.

Main outcome measures:Area wide traffic calming distribution by area deprivation status and changes in injury rate/1000.

Results:The most deprived fourth of city A had 4.8 times (95% CI 3.71 to 6.22) the number of traffic calming features per 1000 population compared with the most affluent fourth. Injury rates among the most deprived dropped from 9.42 to 5.07 from 1992–94 to 1998–2000 (95% CI for change 2.82 to 5.91). In city B, the traffic calming ratio of the most to least deprived fourth was 1.88 (95% CI 1.46 to 2.42); injury rates in the deprived areas dropped from 8.92 to 7.46 (95% CI for change −0.84 to 3.77). Similar proportions of 9–12 year olds walked to school in both cities.

Conclusions:Area wide traffic calming is associated with absolute reductions in child pedestrian injury rates and reductions in relative inequalities in child pedestrian injury rates.
Group interventions for the prevention of injuries in young children: a systematic review
Authors: Bruce B , McGrath P
Published: June 2005

Objective:This systematic review examined group based injury prevention interventions that targeted young children to determine the effectiveness of such strategies in enhancing children’s safety behaviors.

Methods:A comprehensive (manual and electronic) search of the literature was performed using the following study selection criteria: (1) intervention engaged children under the age of 6 years; (2) included a control group; (3) used a group intervention approach; (4) study written in English language; (5) addressed unintentional injuries; and (6) outcomes included injuries, knowledge, or safety behaviors. Data abstraction was performed independently by two researchers using a standardized approach.

Results:Nine studies met the criteria that included safety interventions of road crossing (4), car restraint (2), spinal cord safety (1), poison safety (1), and 911/stranger danger/street crossing (1). The types of interventions included videos, interactive activities, cartoons, stories, puppets, singing, coloring, games, simulation games, demonstrations, modeling/role playing, and rehearsal practice using seat belts, models, and real street crossing. The intensity and duration of interventions varied substantially and only two studies randomly assigned participants. The review revealed a positive effect (knowledge, behaviour, and/or attitude) for five of the studies, three had mixed effect, and one reported no effect.

Conclusions:Although no clear conclusions can be drawn from the limited number of studies of diverse design and rigor, researchers should attempt to minimize shortcomings occurring in community based research. Engaging community partners including teachers and parents who influence relationships and outcomes could provide opportunity for more rigorous, comprehensive, and integrated approach to longitudinal research that could identify key factors of successful strategies.
Carotid and vertebral artery dissection syndromes
Authors: Thanvi B , Munshi S K , Dawson S L , Robinson T G
Published: June 2005

Cervicocerebral arterial dissections (CAD) are an important cause of strokes in younger patients accounting for nearly 20% of strokes in patients under the age of 45 years. Extracranial internal carotid artery dissections comprise 70%–80% and extracranial vertebral dissections account for about 15% of all CAD. Aetiopathogenesis of CAD is incompletely understood, though trauma, respiratory infections, and underlying arteriopathy are considered important. A typical picture of local pain, headache, and ipsilateral Horner’s syndrome followed after several hours by cerebral or retinal ischaemia is rare. Doppler ultrasound, MRI/MRA, and CT angiography are useful non-invasive diagnostic tests. The treatment of extracranial CAD is mainly medical using anticoagulants or antiplatelet agents although controlled studies to show their effectiveness are lacking. The prognosis of extracranial CAD is generally much better than that of the intracranial CAD. Recurrences are rare in CAD.
Practical experience and confidence in managing emergencies among preregistration house officers
Authors: Clayton R A E , Henderson J , McCracken S E , Wigmore S J , Paterson-Brown S
Published: June 2005

Objectives

To assess the experience gained by pre-registration house officers (PRHOs) at the end of their first post. To assess confidence in managing common emergencies and experience gained in practical procedures. To compare traditional six month posts with four month posts and to compare the experiences of PRHOs posted in teaching hospitals (THs) with those based in district general hospitals (DGHs).

Design

Interview questionnaire.

Participants

152 graduates from Edinburgh University Medical School in 2000 who had completed their first PRHO post by February 2001.

Results

There were few significant differences in confidence in managing emergencies and in numbers of practical procedures attempted between respondents from four and six month posts or between those holding TH and DGH posts. PRHOs had gained little experience in practical procedures: fewer than 15% had performed five or more of a number of procedures including lumbar puncture, pleural aspiration, chest drainage, and insertion of nasogastric tube. A high proportion of PRHOs indicated that they felt confident initiating management of conditions in specialties of which they had little or no experience.

Conclusions

Rotations of three four month posts do not seem to reduce overall experience in the PRHO year. There is little difference in experience gained between TH and DGH posts. PRHOs perform few practical procedures and some may be overconfident in their own abilities.
Cost of ambulatory care of diabetes mellitus: a study from north India
Authors: Grover S , Avasthi A , Bhansali A , Chakrabarti S , Kulhara P
Published: June 2005

Background

Diabetes mellitus is a chronic and potentially disabling disease that represents an important public health and clinical concern because of the economic burden it imposes on the person, family, and society. Despite this, data regarding cost of care of diabetes mellitus from developing countries are scarce. This study aimed to assess the cost of care of Indian patients with diabetes mellitus.

Methods

Cost of illness in 50 outpatients with diabetes mellitus (diagnosed according to WHO criteria, Expert Committee, 1997) was assessed over a six month period using a specially designed questionnaire, together with structured assessments of disability.

Results

Total annual cost of care was 14 508 rupees (263.78 euros). The largest proportion of the total cost was made up of direct costs (68%), followed by indirect costs (28.76%) and provider’s costs (2.8%). Drug costs were high. Total treatment cost was significantly higher in those who were more educated, those who visited the hospital more often, and those receiving a greater number of drugs.

Conclusion

From this study it can be concluded that diabetes mellitus is an expensive illness to treat even in developing countries. The main brunt of financial burden is borne by the family. Any efforts at cost reduction should, therefore, have the family as its focus, and relieving the family of this financial burden needs to be prioritised.
Direct thrombin inhibitors: novel antithrombotics on the horizon in the thromboprophylactic management of atrial fibrillation
Authors: Katira R , Chauhan A , More R S
Published: June 2005

Antithrombotic agents have verified efficacy in reducing the thromboembolic risk associated with atrial fibrillation. This article focuses on the emergence of a new oral direct thrombin inhibitor, ximelagatran, into the arena of atrial fibrillation thromboprophylaxis. This review does not cover atrial fibrillation in the context of valvular heart disease. The efficacy of aspirin and warfarin will be discussed briefly.
Management of chronic hepatitis C
Authors: Lo Re V , Kostman J R
Published: June 2005

Hepatitis C virus (HCV) infection is transmitted primarily through percutaneous exposure to blood, and most infections are associated with injection drug use. Progression to chronic HCV occurs in 55% to 86% of infected people, and persistent infection is a major cause of cirrhosis, end stage liver disease, and hepatocellular carcinoma. The detection of HCV antibodies should be performed initially to screen at risk populations. In those who are seropositive, HCV viraemia should be assessed to determine if chronic HCV is present. The HCV genotype should also be determined, as this is the strongest predictor of response to available treatment. A liver biopsy is very often helpful because it can estimate degree of hepatic fibrosis, identify concurrent diseases that might contribute to hepatic injury, and aid in selection of patients for treatment. The decision to start antiviral therapy should take into account potential contraindications to therapy, patient motivation, severity of disease, age, and HCV genotype. Combination therapy with weekly subcutaneous pegylated interferon and daily oral ribavirin is the standard of care for treating patients with chronic HCV.
Evaluation of the status of tuberculosis as part of the clinical case definition of AIDS in India
Authors: Attili V S S , Singh V P , Rai M , Varma D V , Sundar S
Published: June 2005

Aim

To assess HIV associated tuberculosis in a high tuberculosis prevalence setting and its status in the clinical case definition of AIDS.

Methods

All HIV patients attending the infectious disease clinic, Varanasi, India between January 2001 and December 2003 were included in the study. They were stratified into three distinct immunological categories depending on their CD4 levels in accordance to Centers for Disease Control (CDC) classification. Tuberculosis of different organs was defined as detailed below.

Results

Tuberculosis was the commonest opportunistic disease, seen in 163 patients. Of these, 68 had exclusively pulmonary tuberculosis, 55 extrapulmonary disease, and 40 the disseminated form. Pulmonary and extrapulmonary tuberculosis had low positive predictive value (PPV) (51% and 42%) for CD4 levels of <200 when compared with the disseminated form (specificity 87% and PPV 75%). Among 86 patients with radiological evidence of tuberculosis, typical radiological features of post-primary tuberculosis were present in 60 cases (70%). Other features such as effusion (14 patients, 16%) and miliary shadows (12 patients, 14%) were comparatively rare.

Conclusion

Keeping pulmonary and extrapulmonary forms of tuberculosis in AIDS defining illness should be reconsidered. In a similar way tuberculosis in HIV patients from areas endemic with tuberculosis occurs in patients with a wide range of immune status and has a better prognosis than other AIDS defining illnesses. Therefore the inclusion of tuberculosis in clinical case definition of AIDS is not justified.
Advances in wound healing: topical negative pressure therapy
Authors: Jones S M , Banwell P E , Shakespeare P G
Published: June 2005

In clinical practice many wounds are slow to heal and difficult to manage. The recently introduced technique of topical negative pressure therapy (TNP) has been developed to try to overcome some of these difficulties. TNP applies a controlled negative pressure to the surface of a wound that has potential advantages for wound treatment and management. Although the concept itself, of using suction in wound management is not new, the technique of applying a negative pressure at the surface of the wound is. This paper explores the origins and proposed mechanisms of action of TNP therapy and discusses the types of wounds that are thought to benefit most from use of this system.
Cognitive aging and Alzheimer’s disease
Authors: Vandenberghe R , Tournoy J
Published: June 2005

Cognitive aging and clinically probable Alzheimer’s disease can be discriminated by means of clinical and neuropsychological testing, and structural and functional imaging techniques. Research at the level of cognitive brain systems and at the molecular level provides exciting new insights into the relation between aging and neurodegeneration. The advances at the clinical and at the basic research levels are necessary if we wish to meet the formidable challenge that the increasing prevalence of Alzheimer’s disease poses to the medical community.
Pathogenesis and treatment of Clostridium difficile infection
Authors: Tonna I , Welsby P D
Published: June 2005

This paper reviews the pathogenesis and management of Clostridium difficile diarrhoea, in particular the management of recurrent episodes.
Divergent impacts of experimental lake-level drawdown on planktonic and benthic plant communities in a boreal forest lake
Authors: Turner Michael A , Huebert David B , Findlay David L , Hendzel Leonard L , Jansen Wolfgang A , Bodaly RA (Drew) , Armstrong Llwellyn M , Kasian Susan EM
Published: June 2005

Water-surface elevation in lake 226 (L226) of the Experimental Lakes Area in northwestern Ontario, Canada, was lowered experimentally by 23 m during each of three successive winters, and increased naturally but incompletely during the ensuing summers. Our objective was to compare the responses of the littoral and pelagic plant communities to this physical disturbance. Water-chemistry changes were muted, and neither nitrogen nor phosphorus concentration changed. Phytoplankton biomass, species assemblages, productivity, and nutrient status were largely unaffected except for small changes in species diversity and relative abundance of cyanobacteria and cryptophytes. Despite possible transient changes in functional and structural properties, the principal disruption for benthic algae was loss of colonizable surfaces. Floating-leaved and submersed macrophytes (hydrophytes) responded initially with large decreases in biomass and cover. The subsequent response of hydrophytes to drawdown varied: relative frequency of isoetids such as Eriocaulon septangulare decreased, while that of pondweeds such as Potamogeton spirillus increased. The trophic impacts of declining lake levels, whether due to hydroelectric reservoir manipulations or climate change, are likely to be much greater in the littoral zone than in the pelagic zone if major nutrients are unaltered.
Comparison of size-at-age of larval Atlantic cod (Gadus morhua) from different populations based on size- and temperature-dependent growth models
Authors: Folkvord A
Published: June 2005

This study presents the first intraspecific evaluation of larval growth performance across several different experimental scales, environments, and regions of a marine fish species. Size- and temperature-dependent growth models for larval and early juvenile Atlantic cod (Gadus morhua) are developed based on selected laboratory experiments with cod fed in excess. Observed sizes-at-age of cod from several experiments and stocks are compared with predictions from the models using initial size and ambient temperature history as inputs. Comparisons with results from other laboratory experiments reveal that the model predictions represent relatively high growth rates. Results from enclosure experiments under controlled seminatural conditions generally provide growth rates similar to those predicted from the models. The models therefore produce suitable reference growth predictions against which field-based growth estimates can be compared. These comparisons suggest that surviving cod larvae in the sea typically grow at rates close to their size- and temperature-dependent capacity. This suggests that climatic influences will strongly affect the year-to-year variations in growth of cod during their early life history owing to their markedly temperature-dependent growth potential.
Disruption of the hypothalamo-pituitary-interrenal axis in 1+ yellow perch (Perca flavescens) chronically exposed to metals in the environment
Authors: Gravel A , Campbell P GC , Hontela A
Published: June 2005

Although it has been reported that adult yellow perch (Perca flavescens) chronically exposed to metals in the environment exhibit endocrine impairment characterized by blunted cortisol secretion, little is known about the vulnerability of early life stages. Young-of-the-year (YOY) and 1+ yellow perch were captured, subjected to a standardized stress test or adrenocorticotropic-hormone stimulation in lakes situated along a contamination gradient of Cd, Cu, and Zn in the mining region of Abitibi, Quebec. For the first time, whole-body cortisol concentrations were measured. The 1+ fish with elevated whole-body Cd, Cu, and Zn concentrations had an impaired capacity to respond to an acute stress challenge. Although YOY perch had similar whole-body Cd concentrations to 1+ perch, no effects on physiological status were detected in relation to body burdens of metals. Metal contamination did not affect whole-body thyroid-hormone concentrations, condition factor, or hepatosomatic index in 1+ or YOY perch. These results indicate that effects of Cd, Cu, and Zn on the functional integrity of the hypothalamo-pituitary-interrenal axis in yellow perch are detectable after only 1 year of environmental exposure.
The use of moored inverted echo sounders for monitoring meso-zooplankton and fish near the ocean surface
Authors: Trevorrow Mark V
Published: June 2005

This study evaluates the effectiveness of a 200-kHz inverted echo sounder for monitoring the abundance and behavior of near-surface zooplankton and fish. Data from both oceanic and littoral environments are examined: first from an 81-day deployment at Ocean Station Papa (OSP) in the northeast Pacific Ocean during the spring of 1996, and second from an 8-day deployment in the southern Strait of Georgia in September 1998. The analysis combines calibrated backscatter intensity, echo-amplitude statistics, and acoustic-scattering models to produce estimates of mean scatterer size and abundance. The identity of the various scatterer classes is deduced from local net trawls and reference to previous studies. At the OSP site the dominant scatterers were found to be euphausiids, pteropods, and myctophid fishes, with mean lengths of 15, 1.5, and 28 mm, respectively. At the Strait of Georgia site three fish size classes were identified: juvenile herring with mean length near 10 cm, juvenile salmon with mean length of 20 cm, and there was weak evidence for an adult salmon class. Overall, the acoustically derived abundance estimates were in reasonable agreement with the local net trawls and results from previous studies. The usefulness of sustained monitoring over diurnal and seasonal time scales is demonstrated with the OSP zooplankton data.
Relating plaice (Pleuronectes platessa) recruitment to deteriorating habitat quality: effects of macroalgal blooms in coastal nursery grounds
Authors: Pihl Leif , Modin Johan , Wennhage Håkan
Published: June 2005

Concentration of juveniles of marine fishes in nurseries may act as a bottleneck during the life cycle, where quantity and quality of nurseries determine population size. Macroalgal blooms have become a common phenomenon in eutrophic shallow waters worldwide, and matforming algae may now cover many essential nursery habitats. In this investigation, the aim was to assess the quantitative effect of algal mats on the recruitment of plaice (Pleuronectes platessa) from nurseries in the Swedish Skagerrak archipelago. A model was constructed using data on nursery size, settling density, and mortality of plaice combined with data on algal distribution. Recruitment of 0-group plaice from nurseries could be reduced by 30%40% due to algae. The largest negative effect occurred during high settlement, reducing the important influence of strong year classes on stock size. The model predicted a reduction of juveniles due to algae of 4546 × 106 individuals at high settlement. This amounts to 68% of the output at medium settlement and equals the amount of plaice produced during 5 years of low settlement. Up to 75% of the total reduction could occur in one quarter of the study area. With limiting resources, management actions should not be generally applied but rather be concentrated to optimize the cost-benefit of measures taken.
Spawning behaviour and success of mature male Atlantic salmon (Salmo salar) parr of farmed and wild origin
Authors: Weir Laura K , Hutchings Jeffrey A , Fleming Ian A , Einum Sigurd
Published: June 2005

We examined genetic differences in the reproduction of an alternative maturation phenotype in Atlantic salmon (Salmo salar) by comparing the spawning behaviour and success among farmed, first-generation hybrid, and wild mature male parr raised in similar environments. Parr competed for spawning opportunities in the presence of either wild or farmed large males. There were no consistent differences among groups in aggression; however, there were differences in spawning participation with respect to large male origin and among parr types. There was a strong negative temporal effect on mature male parr spawning participation that differed by parr type; wild and farmed parr were most likely to participate in early spawnings, with hybrids being the most likely to participate in late spawnings. Overall, parr were also less likely to participate in spawnings involving large farmed males. Variance in reproductive success was higher among parr than among large males. Our results are consistent with the hypothesis that there are genetically based behavioural differences among mature male parr of farmed and wild origin that may potentially lead to differences in reproductive success.
Are marine protected areas a red herring or fisheries panacea?
Authors: Kaiser Michel J
Published: June 2005

Chronic failures in marine fisheries management have led some to suggest that marine protected areas (MPAs) are the solution to achieve sustainable fisheries. While such systems work for certain habitat-specific and nonmobile species, their utility for highly mobile stocks is questionable. Often the debate among proponents and critics of MPAs is confused by a lack of appreciation of the goals and objectives of such systems. The current consideration of MPAs as the basis of future fisheries management is a symptom of, and not the singular solution to, the problem of inappropriate implementation of fishing effort controls. The latter will provide greater overall conservation benefits if properly applied. Any future use of MPAs as an effective tool to achieve sustainable fisheries management in temperate systems should be treated as a large-scale, rigorously designed experiment to ensure that the outcome of using MPAs is interpreted correctly and not discredited for false reasons.
Age validation of canary rockfish (Sebastes pinniger) from off the Oregon coast (USA) using the bomb radiocarbon method
Authors: Piner Kevin R , Hamel Owen S , Menkel Jennifer L , Wallace John R , Hutchinson Charles E
Published: June 2005

The alternating translucent and opaque banding pattern in canary rockfish (Sebastes pinniger) otoliths, aged using a break-and-burn methodology, are annual markings. To validate age assignment, we compared measured radiocarbon levels in canary rockfish otolith cores with a reference chronology developed from known age Pacific halibut (Hippoglossus stenolepis). An average 2- to 3-year phase shift was detected between the canary rockfish and a Pacific halibut reference chronology that was likely the result of differences in the regional oceanography or underageing bias. The assumption of ageing bias consistency was tested with two sampling designs. The first design controled for age-related ageing error, and the second design related birth year to estimated age. No change in the magnitude of ageing bias as a function of age was detected.
Towards an absolute measurement of the 1S3S line in atomic hydrogen
Authors: Arnoult O , Nez F , Schwob C , Julien L , Biraben F
Published: June 2005

For very high-precision spectroscopy such as the two photon 1SnS transitions in hydrogen, the ability to measure precisely the absolute frequency of the excitation laser is required together with the best possible signal-to-noise ratio for the fluorescence signal. In the context of our experiment on the 1S3S transition, we present the specificities of our optical frequency comb apparatus, as well as a new detection scheme that makes use of the spatial information provided by a CCD camera detector.PACS No.: 39.30.+w
Proton Zemach radius and the hyperfine splitting of the ground state of muonic hydrogen
Authors: Bakalov D , Beswick A , Dupays A , Rizzo C
Published: June 2005

Recently, the Zemach radius of the proton has been calculated from experimental data using four different approaches, and the results do not agree with each other within the claimed accuracy. We assume that the puzzle might be solved by determining the Zemach radius from the hyperfine splitting of muonic hydrogen, and overview the present status of the theory of the hyperfine structure of muonic hydrogen as well as the possibilities to measure it with a satisfactory accuracy. PACS Nos.: 36.10.k, 32.10.Fn, 21.10.Ky, 13.40.Gp
PATH PROPERTIES OF THE LINEAR MULTIFRACTIONAL STABLE MOTION
Authors: STOEV STILIAN , TAQQU MURAD S.
Published: June 2005

The linear multifractional stable motion (LMSM) processes Y = {Y(t)}t∈ℝis an α-stable (0 < α < 2) stochastic process, which exhibits local self-similarity, has heavy tails and can have skewed distributions. The process Y is obtained from the well-known class of linear fractional stable motion (LFSM) processes by replacing their self-similarity parameter H by a function of time H(t).

We show that the paths of Y(t) are bounded on bounded intervals only if 1/α ≤ H(t) < 1, t ∈ ℝ. In particular, if 0 < α ≤ 1, then Y has everywhere discontinuous paths, with probability one. On the other hand, Y has a version with continuous paths if H(t) is sufficiently regular and 1/α < H(t), t ∈ ℝ. We study the Hölder regularity of the sample paths when these are continuous and establish almost sure bounds on the pointwise and uniform pointwise Hölder exponents of the (random) function Y(t,ω), t ∈ ℝ, in terms of the function H(t) and its corresponding Hölder exponents.

The Gaussian multifractional Brownian motion (MBM) processes are LMSM processes when α = 2. We obtain some new results on the Hölder regularity of their paths.
QUADRATIC DYNAMICS IN MATRIX RINGS: TALES OF TERNARY NUMBER SYSTEMS
Authors: FISHBACK PAUL E. , HORTON MATTHEW D.
Published: June 2005

We describe the quadratic dynamics in certain three-component number systems, which like the complex numbers, can be expressed as rings of real matrices. This description is accomplished using the properties of the real quadratic family and its various first- and second-order phase and parameter derivatives. We demonstrate that the fundamental dichotomy of defining the Mandelbrot set either in terms of filled Julia sets or in terms of the orbit of the origin extends to these ternary number systems.
NONLINEAR FRACTAL INTERPOLATING FUNCTIONS OF ONE AND TWO VARIABLES
Authors: KOBES R. , PENNER A. J.
Published: June 2005

We consider nonlinear generalizations of fractal interpolating functions applied to functions of one and two variables. The use of such interpolating functions in representing images by an iterated function system is illustrated, particularly as applied to the problem of resizing images, or portions thereof.
EFFECT OF KEY PARAMETERS ON STRENGTH OF IN-FILLED STEEL-CONCRETE COMPOSITE COLUMNS
Authors: SHANMUGAM N. E. , LAKSHMI B.
Published: June 2005

This paper is concerned with the detailed study on the behavior of steel tubular columns in-filled with concrete. Moment–curvature–thrust relationships are generated for column cross-sections by an iterative process. Nonlinear equilibrium equations which include geometric and material nonlinearities are solved by an incremental-iterative numerical scheme based on generalized displacement control (GDC) method. The analytical model is used to investigate the effect of various parameters that could influence the behavior and ultimate load. Column end restraints are also considered as one of the parameters. The variables selected for the study cover a wide range of parameters arising from various loading conditions and column geometries.
DYNAMIC ANALYSIS OF ELASTOPLASTIC SHAKEDOWN OF STRUCTURES
Authors: CHALLAMEL NOËL
Published: June 2005

This paper deals with the dynamics of a single-degree-of-freedom elastoplastic oscillator. The model adopted herein is useful for understanding the dynamic behavior of civil engineering structures, such as steel structures, especially when plastic inelasticity is of concern. Using appropriate internal variables, the dynamic hysteretic system can be written as a singular autonomous system. The free vibration of such a nonlinear system reduces to periodic motion. The harmonic forced oscillator can exhibit periodic or quasi-periodic behaviors. A bifurcation diagram is numerically computed, which indicates that periodic elastoplastic limit cycles exist for some ranges of structural parameters. The bifurcation boundary separates the shakedown from other alternating plasticity phenomena.
The use of microgravity for cavity characterization in karstic terrains
Authors: Styles P. , McGrath R. , Thomas E. , Cassidy N.J.
Published: June 2005

Microgravity is the interpretation of changes in the subsurface density distribution from the measurement of minute variations in the gravitational attraction of the Earth. As a technique, it is particularly suited to the investigation of subsurface structures, mapping of geological boundaries and, most importantly in this case, the location and characterization of voids or cavities. Gravity variations due to the geological/petrophysical changes associated with fracturing and changes in pore composition are superimposed upon much larger variations due to elevation, latitude, topography, Earth tides and regional geological variations. However, these external changes can be modelled or monitored with sufficient accuracy to be removed from the data. With the recent development of high-resolution instruments, careful field acquisition techniques and sophisticated reduction, processing and analysis routines, anomalies as small as 10 microgal can be detected and interpreted effectively. This paper describes the ‘state-of-the-art’ application of the microgravity technique for the detection and characterization of karstic cavities in a variety of limestone terrains, including the Carboniferous Limestone of the United Kingdom and Eire and the coral limestones of the Bahamas. The case study examples show how the recorded gravity anomalies have revealed the location of density variations associated with underground cave systems and, ultimately, provided information on their depths, shapes and morphology from a combined analysis of their spectral content, characteristic gradient signatures and modelling responses. In addition, mass deficiencies have been estimated, directly from the anomaly map, by the use of Gauss's theorem without any prior knowledge of the exact location, or nature, of the causative bodies.
The engineering geology and characterization of Dublin Boulder Clay
Authors: Skipper J. , Follett B. , Menkiti C.O. , Long M. , Clark-Hughes J.
Published: June 2005

The ground investigation and construction for the North Cut and Cover Section of the Dublin Port Tunnel (north Dublin, Co. Dublin, Ireland) involved high resolution ground investigation and excavation logging. As a result, our interpretation of the glacially derived Quaternary geology encountered presents a more complex picture than previously described. A detailed description of the stratigraphy and lithology of the glacial deposits formerly known as the ‘Dublin Boulder Clay’ is presented, and palaeoenvironmental interpretations are suggested for the various units. The ‘Dublin Boulder Clay’ is reinterpreted to comprise four major units and associated subunits. Possible construction hazards, including discontinuities, lithological variability, glacio-tectonic rafting and the presence of large water-bearing units, are identified and linked with the stratigraphy. Preliminary data on the geotechnical and engineering behaviour of each unit are presented. The encountered lithologies generally demonstrated high
in-situ
strength and stiffness but low permeability and plasticity.