bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal arteritis in Hong Kong
Authors: TAM Stanley , WONG T. C.
Published: July 2008

Objective:  To evaluate Chinese patients with biopsy‐proven temporal arteritis in Hong Kong, focusing on clinical presentation, frequency of occurrence, treatment regimen and complications, management and outcome of these patients.

Design:  A retrospective study.

Method:  A retrospective study was undertaken in which patients with biopsy‐proven temporal arteritis were identified from: (i) Statistical records of Hospital Authority (1996–1999); (ii) pathology records of regional hospitals in Hong Kong (1996–2000); and (iii) case records from rheumatologists in two university hospitals. Indexed hospital and out‐patient records were reviewed and analysed.

Results:  Nineteen patients with biopsy‐proven temporal arteritis were identified from 1996 to 2000 and the calculated annual incidence was 0.34 patients in 100,000 people aged 50 and above per year. There were six male and 13 female patients (male : female ratio 1:2.2). Sixteen (84%) patients were older than 70 years. The common presentations were similar to overseas studies and included headache (79%), muscular symptoms (42%), constitutional symptoms (37%), scalp tenderness (37%), visual loss (32%), jaw claudication (32%), abnormal temporal artery (32%), and fever (26%). The mean erythrocyte sedimentation rate before treatment was 104 mm/h (SD = 30 mm/h). Anemia (Hb < 12 g/dL) was present in 79% of patients. The mean duration of symptoms before diagnosis was 8.4 weeks. Seventeen (89%) patients received high‐dose steroid therapy but none received steroid‐sparing agents. Only 33% of patients reached a physiological dose of steroid (prednisolone 5 mg/day) after 1 year.

Conclusion:  Temporal arteritis is rare among Hong Kong Chinese. A rough estimate of annual incidence yielded less than one per 100,000 people aged ≥ 50. Overall clinical presentation was similar to overseas studies but there were: (i) longer duration of steroid therapy given; and (ii) more complications from steroid use. Steroid‐sparing agents should be considered early in difficult‐to‐control cases.
Wegener's granulomatosis and acute upper limb digital ischemia
Authors: KEJRIWAL Ritwik , LIM Tien Ming , KUMAR Sunil
Published: July 2008

Wegener's granulomatosis is a rare disease which occasionally causes digital gangrene. We describe a patient who developed gangrene in an upper limb despite being on adequate treatment with intravenous cyclophosphamide and corticosteroids. Further management included administration of prostacyclin analogue (Iloprost) resulting in stabilization of disease.
Churg–Strauss syndrome with peripheral gangrene and severe renal failure
Authors: BOOPATHY K. Seerala , RAJENDRAN C. Panchapakesa , RUKMANGATHARAJAN S. , RAJESWARI S. , RAVICHANDRAN R. , VASANTHY N.
Published: July 2008

A 32‐year‐old man, known asthmatic since childhood, presented with multiple ulcers over lower legs, burning sensation over fingers and blackish discoloration of left little finger. On examination, he had systemic hypertension, tenderness over maxillary sinuses, left‐sided foot drop and gangrene of left little finger. The investigations showed anemia, eosinophilia, elevated serum immunoglobulin E level, elevated myeloperoxidase level, proteinuria and raised creatinine. A diagnosis of Churg‐Strauss syndrome with rare manifestations of gangrene and severe renal failure was made with the above features.
Psoriatic arthritis with ANCA‐positive vasculitis: a rare association
Authors: CHEWOOLKAR Vaibhav , BICHILE Lata S. , JAIN Neeraj , RAJ Pranesh
Published: July 2008

Psoriatic arthritis is an inflammatory arthropathy in patients with psoriasis. Although 8% of patients affected with psoriasis without vasculitic manifestations are positive for perinuclear antineutrophilic cytoplasmic antibody (P‐ANCA), cutaneous vasculitis in psoriatic arthritis with a positive P‐ANCA is rare. We report a case of a 46‐year‐old‐man with a 25‐year history of plaque psoriasis admitted with joint pain and rash. He was subsequently diagnosed as having psoriatic arthritis and leucocytoclastic vasculitis with positive ANCA and was treated with methotrexate and corticosteroids. We hereby highlight the association of vasculitis with positive ANCA in a patient with psoriatic arthritis.
THE INTRINSIC QUALITATIVE PROPERTIES OF THE CLASSICAL OPTIMAL STOPPING PROBLEM ARE INVARIANT TO THE FUNCTIONAL FORM OF THE DISCOUNT FUNCTION
Authors: CAPUTO MICHAEL R.
Published: July 2008

Abstract The intrinsic qualitative properties of a generic optimal stopping model are shown to be invariant to the functional form of the discount function. If the discount function is assumed to be a member of particular infinite parametric family—a family that includes the exponential and classical hyperbolic discount functions as special cases—an additional refutable comparative statics result is produced that holds for the entire family. Consequently, if one limits econometric tests of the model to its qualitative properties, one cannot determine the form of the discount function used by the decision maker. It is also shown that the only discount function that yields a time‐consistent stopping rule is the exponential function with a constant rate of discount.
ON THE ECONOMICS OF BIOLOGICAL INVASION: AN APPLICATION TO RECREATIONAL FISHING
Authors: OLAUSSEN JON OLAF , SKONHOFT ANDERS
Published: July 2008

Abstract The paper demonstrates four general mechanisms that may affect economically valuable species when exposed to biological invasion. We distinguish between an ecological level effect and an ecological growth effect. In addition, we present an economic quantity effect working through demand. Finally, we suggest that there is an economic quality effect that reflects the possibility that invasions affect the harvesting agents directly through demand‐side forces. For example, this may occur because the state of the original species or the ecosystem is altered. We depart from the existing literature by revealing ecological and economic forces that explain why different agents may lack incentives to control invasions. The theoretical model is illustrated by the case where escaped farmed salmon (EFS) influence wild Atlantic salmon fisheries.
REBUILDING THE EASTERN BALTIC COD STOCK UNDER ENVIRONMENTAL CHANGE (PART II): TAKING INTO ACCOUNT THE COSTS OF A MARINE PROTECTED AREA
Authors: RÖCKMANN CHRISTINE , TOL RICHARD S. J. , SCHNEIDER UWE A. , JOHN MICHAEL A. ST.
Published: July 2008

Abstract This study adds a cost analysis of the Eastern Baltic cod fishery to the existing model presented in Röckmann et al. [2007a]. As cost data on this international fishery do not exist, data from Denmark are extrapolated to the whole international fishery. Additionally, unit and total variable costs are simulated, and the sensitivity to a set of different cost–stock and cost–output elasticities is tested. The study supports preliminary conclusions that a temporary marine reserve policy, which focuses on protecting the Eastern Baltic cod spawning stock in the International Council for the Exploration of the Sea (ICES) subdivision 25, is a valuable fisheries management tool to (i) rebuild the overexploited Eastern Baltic cod stock and (ii) increase operating profits. The negative effects of climate change can be postponed for at least 20 years—depending on the assumed rate of future climate change. Including costs in the economic analysis does not change the ranking of management policies as proposed in the previous study where costs were neglected.
Emergence and Acquisition of Fluoroquinolone-Resistant Gram-Negative Bacilli in the Intestinal Tracts of Mice Treated with Fluoroquinolone Antimicrobial Agents
Authors: Pultz Michael J. , Nerandzic Michelle M. , Stiefel Usha , Donskey Curtis J.
Published: July 2008

After mice received orogastric administration of a fluoroquinolone-resistant
Klebsiella pneumoniae
strain, subcutaneous treatment with ciprofloxacin, levofloxacin, and moxifloxacin promoted persistent low-density colonization in 10% to 40% of the mice, whereas treatment with clindamycin consistently promoted high-density colonization. No emergence of fluoroquinolone-resistant gram-negative bacilli was detected in the mice during or after treatment with the fluoroquinolone antimicrobial agents.
Microbiological and Genotypic Analysis of Methicillin-Resistant
Staphylococcus aureus
Bacteremia
Authors: McCalla Carlo , Smyth Davida S. , Robinson D. Ashley , Steenbergen Judith , Luperchio Steven A. , Moise Pamela A. , Fowler Vance G. , Sakoulas George
Published: July 2008

In a recent landmark trial of bacteremia caused by methicillin-resistant
Staphylococcus aureus
(MRSA) isolates, vancomycin MICs were ≥1 μg/ml for only 16% of the isolates, and accessory gene regulator (
agr
) function as measured by delta-hemolysin activity was absent or reduced in only 28.1% of the isolates. This clinical study did not capture a population of MRSA isolates predictive of vancomycin treatment failure.
Effect of Flagellar Mutations on
Yersinia enterocolitica
Biofilm Formation
Authors: Kim Tae-Jong , Young Briana M. , Young Glenn M.
Published: July 2008

Yersinia enterocolitica
biovar 1B is one of a number of strains pathogenic to humans in the genus
Yersinia
. It has three different type III secretion systems, Ysc, Ysa, and the flagella. In this study, the effect of flagella on biofilm formation was evaluated. In a panel of 31 mutant
Y. enterocolitica
strains, we observed that mutations that abolish the structure or rotation of the flagella greatly reduce biofilm formation when the bacteria are grown under static conditions. These results were further evaluated by assessing biofilm formation under continuous culture using a flow cell chamber. The results confirmed the important contribution of flagella to the initiation of biofilm production but indicated that there are differences in the progression of biofilm development between static growth and flow conditions. Our results suggest that flagella play a critical role in biofilm formation in
Y. enterocolitica
.
A RecombinantSaccharomyces cerevisiaeStrain Overproducing Mannoproteins Stabilizes Wine against Protein Haze
Authors: Gonzalez-Ramos Daniel , Cebollero Eduardo , Gonzalez Ramon
Published: July 2008

Stabilization against protein haze was one of the first positive properties attributed to yeast mannoproteins in winemaking. In previous work we demonstrated that deletion ofKNR4leads to increased mannoprotein release in laboratorySaccharomyces cerevisiaestrains. We have now constructed strains withKNR4deleted in two different industrial wine yeast backgrounds. This required replacement of two and three alleles ofKNR4for the EC1118 and T73-4 backgrounds, respectively, and the use of three different selection markers for yeast genetic transformation. The actual effect of the genetic modification was dependent on both the genetic background and the culture conditions. The fermentation performance of T73-4 derivatives was clearly impaired, and these derivatives did not contribute to the protein stability of the wine, even though they showed increased mannoprotein release in vitro. In contrast, the EC1118 derivative with both alleles ofKNR4deleted released increased amounts of mannoproteins both in vitro and during wine fermentation assays, and the resulting wines were consistently less susceptible to protein haze. The fermentation performance of this strain was slightly impaired, but only with must with a very high sugar content. These results pave the way for the development of new commercial strains with the potential to improve several mannoprotein-related quality and technological parameters of wine.
Candidate Stress Genes ofNitrosomonas europaeafor Monitoring Inhibition of Nitrification by Heavy Metals
Authors: Park Sunhwa , Ely Roger L.
Published: July 2008

Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury onNitrosomonas europaeawere studied in quasi-steady-state batch reactors. When cells were exposed to 1 μM CdCl2, 6 μM HgCl2, or 8 μM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses ofN. europaeato cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 μM CdCl2for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 μM CdCl2, withmerA(mercuric reductase) showing 297-fold upregulation. InN. europaeacells exposed to 6 μM HgCl2or to 8 μM CuCl2,merAshowed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes andamoA, but no such recovery was evident in Cd2+-exposed cells even thoughmerTPCADEwere highly upregulated. We suggest that the upregulation ofmerAin response to CdCl2and HgCl2exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.
Prevalence and Characterization of Enterotoxin Gene-CarryingClostridium perfringensIsolates from Retail Meat Products in Japan
Authors: Miki Yasuhiro , Miyamoto Kazuaki , Kaneko-Hirano Ikuko , Fujiuchi Kanako , Akimoto Shigeru
Published: July 2008

Clostridium perfringensis an important anaerobic pathogen causing food-borne gastrointestinal (GI) diseases in humans and animals. It is thought thatC. perfringensfood poisoning isolates typically carry the enterotoxin gene (cpe) on their chromosome, while isolates from other GI diseases, such as antibiotic-associated diarrhea, carrycpeon a transferable plasmid. However, food-borne GI disease outbreaks associated withC. perfringensisolates carrying plasmid-bornecpe(plasmidcpeisolates) were recently reported in Japan and Europe. To investigate whether retail food can be a reservoir for food poisoning generally, we evaluated Japanese retail meat products for the presence of two genotypes of enterotoxigenicC. perfringens. Our results demonstrated that approximately 70% of the Japanese retail raw meat samples tested were contaminated with low numbers ofC. perfringensbacteria and 4% were contaminated withcpe-positiveC. perfringens. Most of thecpe-positiveC. perfringensisolates obtained from Japanese retail meat carriedcpeon a plasmid. The plasmidcpeisolates exhibited lower spore heat resistance than did chromosomalcpeisolates. Collectively, these plasmidcpeisolates might be causative agents of food poisoning when foods are contaminated with these isolates from equipment and/or the environment after cooking, or they may survive in food that has not been cooked at a high enough temperature.
Development of a Novel Biofilm Continuous Culture Method for Simultaneous Assessment of Architecture and Gaseous Metabolite Production
Authors: Yawata Yutaka , Nomura Nobuhiko , Uchiyama Hiroo
Published: July 2008

The way that gaseous metabolite production changes along with biofilm architecture development is poorly understood. To address this question, we developed a novel flow reactor biofilm culture method that allows for simultaneous assessment of gaseous metabolite production and architecture visualization. In this report, we establish the utility of this method using denitrification by
Pseudomonas aeruginosa
biofilms as a model system. Using this method, we were able to collect and analyze gaseous metabolites produced by denitrification and also visualize biofilm architecture in a nondestructive manner. Thus, we propose that this novel method is a powerful tool to investigate potential relationships between biofilm architecture and the gas-producing metabolic activity of biofilms, providing new insights into biofilm ecology.
Global Transcriptional Response of the Alkali-Tolerant CyanobacteriumSynechocystissp. Strain PCC 6803 to a pH 10 Environment
Authors: Summerfield Tina C. , Sherman Louis A.
Published: July 2008

Many cyanobacterial strains are able to grow at a pH range from neutral to pH 10 or 11. Such alkaline conditions favor cyanobacterial growth (e.g., bloom formation), and cyanobacteria must have developed strategies to adjust to changes in CO2concentration and ion availability.Synechocystissp. strain PCC 6803 exhibits similar photoautotrophic growth characteristics at pH 10 and pH 7.5, and we examined global gene expression following transfer from pH 7.5 to pH 10 to determine cellular adaptations at an elevated pH. The strategies used to develop homeostasis at alkaline pH had elements similar to those of many bacteria, as well as components unique to phototrophic microbes. Some of the response mechanisms previously identified in other bacteria included upregulation of Na+/H+antiporters, deaminases, and ATP synthase. In addition, upregulated genes encoded transporters with the potential to contribute to osmotic, pH, and ion homeostasis (e.g., a water channel protein, a large-conductance mechanosensitive channel, a putative anion efflux transporter, a hexose/proton symporter, and ABC transporters of unidentified substrates). Transcriptional changes specific to photosynthetic microbes involved NADH dehydrogenases and CO2fixation. The pH transition altered the CO2/HCO3−ratio within the cell, and the upregulation of three inducible bicarbonate transporters (BCT1, SbtA, and NDH-1S) likely reflected a response to this perturbed ratio. Consistent with this was increased transcript abundance of genes encoding carboxysome structural proteins and carbonic anhydrase. Interestingly, the transition to pH 10 resulted in increased abundance of transcripts of photosystem II genes encoding extrinsic and low-molecular-weight polypeptides, although there was little change in photosystem I gene transcripts.
Rapid Identification and Typing of
Listeria
Species by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Barbuddhe Sukhadeo B. , Maier Thomas , Schwarz Gerold , Kostrzewa Markus , Hof Herbert , Domann Eugen , Chakraborty Trinad , Hain Torsten
Published: July 2008

Listeria monocytogenes
is a food-borne pathogen that is the causative agent of human listeriosis, an opportunistic infection that primarily infects pregnant women and immunologically compromised individuals. Rapid, accurate discrimination between
Listeria
strains is essential for appropriate therapeutic management and timely intervention for infection control. A rapid method involving matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) that shows promise for identification of
Listeria
species and typing and even allows for differentiation at the level of clonal lineages among pathogenic strains of
L. monocytogenes
is presented. A total of 146 strains of different
Listeria
species and serotypes as well as clinical isolates were analyzed. The method was compared with the pulsed-field gel electrophoresis analysis of 48
Listeria
strains comprising
L. monocytogenes
strains isolated from food-borne epidemics and sporadic cases, isolates representing different serotypes, and a number of
Listeria
strains whose genomes have been completely sequenced. Following a short inactivation/extraction procedure, cell material from a bacterial colony was deposited on a sample target, dried, overlaid with a matrix necessary for the MALDI process, and analyzed by MALDI-TOF MS. This technique examines the chemistry of major proteins, yielding profile spectra consisting of a series of peaks, a characteristic “fingerprint” mainly derived from ribosomal proteins. Specimens can be prepared in a few minutes from plate or liquid cultures, and a spectrum can be obtained within 1 minute. Mass spectra derived from
Listeria
isolates showed characteristic peaks, conserved at both the species and lineage levels. MALDI-TOF MS fingerprinting may have potential for
Listeria
identification and subtyping and may improve infection control measures.
Aspergillus fumigatusRasA Regulates Asexual Development and Cell Wall Integrity
Authors: Fortwendel Jarrod R. , Fuller Kevin K. , Stephens Timothy J. , Bacon W. Clark , Askew David S. , Rhodes Judith C.
Published: July 2008

The Ras family of proteins is a large group of monomeric GTPases. Members of the fungal Ras family act as molecular switches that transduce signals from the outside of the cell to signaling cascades inside the cell.A. fumigatusRasA is 94% identical to the essential RasA gene ofAspergillus nidulansand is the Ras family member sharing the highest identity to Ras homologs studied in many other fungi. In this study, we report thatrasAis not essential inA. fumigatus, but its absence is associated with slowed germination and a severe defect in radial growth. The ΔrasAhyphae were more than two times the diameter of wild-type hyphae, and they displayed repeated changes in the axis of polarity during hyphal growth. The deformed hyphae accumulated numerous nuclei within each hyphal compartment. The ΔrasAmutant conidiated poorly, but this phenotype could be ameliorated by growth on osmotically stabilized media. The ΔrasAmutant also showed increased susceptibility to cell wall stressors, stained more intensely with calcofluor white, and was refractory to lysing enzymes used to make protoplasts, suggesting an alteration of the cell wall. All phenotypes associated with deletion ofrasAcould be corrected by reinsertion of the wild-type gene. These data demonstrate a crucial role for RasA in both hyphal growth and asexual development inA. fumigatusand provide evidence that RasA function is linked to cell wall integrity.
Genetic Analysis of Trimethylamine
N
-Oxide Reductases in the Light Organ Symbiont
Vibrio fischeri
ES114
Authors: Dunn Anne K. , Stabb Eric V.
Published: July 2008

Trimethylamine
N
-oxide (TMAO) reductases are widespread in bacteria and often function in anaerobic respiration. The regulation and expression of TMAO reductase operons have been well studied in model genera such as
Escherichia
,
Shewanella
, and
Rhodobacter
, although TMAO reductases are present in many other bacteria, including the marine
Vibrio
species. The genome sequence of
Vibrio fischeri
revealed three putative TMAO reductase operons, and a previous report identified TMAO reductase activity in symbiotic
V. fischeri
isolates associated with the light organs of adult Hawaiian bobtail squid,
Euprymna scolopes
. We examined the roles and regulation of these three operons using mutational analyses and promoter-reporter fusions. We found that the
torECA
promoter, and to a lesser extent the
torYZ
and
dmsABC
promoters, were active during symbiotic colonization of juvenile
E. scolopes
; however, a
V. fischeri
strain lacking TMAO reductase activity displays no discernible colonization defect over the first 48 h. Our studies also revealed that
torECA
has the most active promoter of the putative TMAO reductase operons, and TorECA is the major contributor to TMAO-dependent growth in
V. fischeri
under the conditions tested. Interestingly, the transcriptional regulation of TMAO reductase operons in
V. fischeri
appears to differ from that in previously studied organisms, such as
Escherichia coli
, which may reflect differences in gene arrangement and bacterial habitat. This study lays the foundation for using
V. fischeri
as a model system for studying TMAO reductases in the
Vibrionaceae
.
Lawsonia intracellularisContains a Gene Encoding a Functional Rickettsia-Like ATP/ADP Translocase for Host Exploitation
Authors: Schmitz-Esser Stephan , Haferkamp Ilka , Knab Silvia , Penz Thomas , Ast Michelle , Kohl Christian , Wagner Michael , Horn Matthias
Published: July 2008

ATP/ADP translocases are a hallmark of obligate intracellular pathogens related to chlamydiae and rickettsiae. These proteins catalyze the highly specific exchange of bacterial ADP against host ATP and thus allow bacteria to exploit their hosts' energy pool, a process also referred to as energy parasitism. The genome sequence of the obligate intracellular pathogenLawsonia intracellularis(Deltaproteobacteria), responsible for one of the most economically important diseases in the swine industry worldwide, revealed the presence of a putative ATP/ADP translocase most similar to known ATP/ADP translocases of chlamydiae and rickettsiae (around 47% amino acid sequence identity). The gene coding for the putative ATP/ADP translocase ofL. intracellularis(L. intracellularisnucleotide transporter 1 [NTT1Li]) was cloned and expressed in the heterologous hostEscherichia coli. The transport properties of NTT1Liwere determined by measuring the uptake of radioactively labeled substrates byE. coli. NTT1Litransported ATP in a counterexchange mode with ADP in a highly specific manner; the substrate affinities determined were 236.3 (± 36.5) μM for ATP and 275.2 (± 28.1) μM for ADP, identifying this protein as a functional ATP/ADP translocase. NTT1Liis the first ATP/ADP translocase from a bacterium not related toChlamydiaeorRickettsiales, showing that energy parasitism by ATP/ADP translocases is more widespread than previously recognized. The occurrence of an ATP/ADP translocase inL. intracellularisis explained by a relatively recent horizontal gene transfer event with rickettsiae as donors.
RNase Activity of Polynucleotide Phosphorylase Is Critical at Low Temperature inEscherichia coliand Is Complemented by RNase II
Authors: Awano Naoki , Inouye Masayori , Phadtare Sangita
Published: July 2008

InEscherichia coli, the cold shock response is exerted upon a temperature change from 37°C to 15°C and is characterized by induction of several cold shock proteins, including polynucleotide phosphorylase (PNPase), during acclimation phase. InE. coli, PNPase is essential for growth at low temperatures; however, its exact role in this essential function has not been fully elucidated. PNPase is a 3′-to-5′ exoribonuclease and promotes the processive degradation of RNA. Our screening of anE. coligenomic library for an in vivo counterpart of PNPase that can compensate for its absence at low temperature revealed only one protein, another 3′-to-5′ exonuclease, RNase II. Here we show that the RNase PH domains 1 and 2 of PNPase are important for its cold shock function, suggesting that the RNase activity of PNPase is critical for its essential function at low temperature. We also show that its polymerization activity is dispensable in its cold shock function. Interestingly, the third 3′-to-5′ processing exoribonuclease, RNase R ofE. coli, which is cold inducible, cannot complement the cold shock function of PNPase. We further show that this difference is due to the different targets of these enzymes and stabilization of some of the PNPase-sensitive mRNAs, likefis, in the Δpnpcells has consequences, such as accumulation of ribosomal subunits in the Δpnpcells, which may play a role in the cold sensitivity of this strain.
Toxic Introns and Parasitic Intein in
Coxiella burnetii
: Legacies of a Promiscuous Past
Authors: Raghavan Rahul , Hicks Linda D. , Minnick Michael F.
Published: July 2008

The genome of the obligate intracellular pathogen
Coxiella burnetii
contains a large number of selfish genetic elements, including two group I introns (Cbu.L1917 and Cbu.L1951) and an intervening sequence that interrupts the 23S rRNA gene, an intein (Cbu.DnaB) within
dnaB
and 29 insertion sequences. Here, we describe the ability of the intron-encoded RNAs (ribozymes) to retard bacterial growth rate (toxicity) and examine the functionality and phylogenetic history of Cbu.DnaB. When expressed in
Escherichia coli
, both introns repressed growth, with Cbu.L1917 being more inhibitory. Both ribozymes were found to associate with ribosomes of
Coxiella
and
E. coli
. In addition, ribozymes significantly reduced in vitro luciferase translation, again with Cbu.L1917 being more inhibitory. We analyzed the relative quantities of ribozymes and genomes throughout a 14-day growth cycle of
C. burnetii
and found that they were inversely correlated, suggesting that the ribozymes have a negative effect on
Coxiella
's growth. We determined possible sites for ribozyme associations with 23S rRNA that could explain the observed toxicities. Further research is needed to determine whether the introns are being positively selected because they promote bacterial persistence or whether they were fixed in the population due to genetic drift. The intein, Cbu.DnaB, is able to self-splice, leaving the host protein intact and presumably functional. Similar inteins have been found in two extremophilic bacteria (
Alkalilimnicola ehrlichei
and
Halorhodospira halophila
) that are distantly related to
Coxiella
, making it difficult to determine whether the intein was acquired by horizontal gene transfer or was vertically inherited from a common ancestor.
ON HAAG DUALITY FOR PURE STATES OF QUANTUM SPIN CHAINS
Authors: KEYL M. , MATSUI TAKU , SCHLINGEMANN D. , WERNER R. F.
Published: July 2008

In this note, we consider quantum spin chains and their translationally invariant pure states. We prove Haag duality for quasilocal observables localized in semi-infinite intervals (-∞ , 0] and [1, ∞) when the von Neumann algebra generated by observables localized in [0, ∞) is non-type I.
ON APPROXIMATE SOLUTIONS OF SEMILINEAR EVOLUTION EQUATIONS II: GENERALIZATIONS, AND APPLICATIONS TO NAVIER–STOKES EQUATIONS
Authors: MOROSI CARLO , PIZZOCCHERO LIVIO
Published: July 2008

In our previous paper [12], a general framework was outlined to treat the approximate solutions of semilinear evolution equations; more precisely, a scheme was presented to infer from an approximate solution the existence (local or global in time) of an exact solution, and to estimate their distance. In the first half of the present work, the abstract framework of [12] is extended, so as to be applicable to evolutionary PDEs whose nonlinearities contain derivatives in the space variables. In the second half of the paper, this extended framework is applied to the incompressible Navier–Stokes equations, on a torus Tdof any dimension. In this way, a number of results are obtained in the setting of the Sobolev spaces ℍn(Td), choosing the approximate solutions in a number of different ways. With the simplest choices we recover local existence of the exact solution for arbitrary data and external forces, as well as global existence for small data and forces. With the supplementary assumption of exponential decay in time for the forces, the same decay law is derived for the exact solution with small (zero mean) data and forces. The interval of existence for arbitrary data, the upper bounds on data and forces for global existence, and all estimates on the exponential decay of the exact solution are derived in a fully quantitative way (i.e. giving the values of all the necessary constants; this makes a difference with most of the previous literature). Next, the Galerkin approximate solutions are considered and precise, still quantitative estimates are derived for their ℍndistance from the exact solution; these are global in time for small data and forces (with exponential time decay of the above distance, if the forces decay similarly).
CO-OCCURRENCE NETWORK OF REUTERS NEWS
Authors: ÖZGÜR ARZUCAN , CETIN BURAK , BINGOL HALUK
Published: July 2008

Networks describe various complex natural systems including social systems. We investigate the social network of co-occurrence in Reuters-21578 corpus, which consists of news articles that appeared in the Reuters newswire in 1987. People are represented as vertices and two persons are connected if they co-occur in the same article. The network has small-world features with power-law degree distribution. The network is disconnected and the component size distribution has power-law characteristics. Community detection on a degree-reduced network provides meaningful communities. An edge-reduced network, which contains only the strong ties has a star topology. "Importance" of persons are investigated. The network is the situation in 1987. After 20 years, a better judgment on the importance of the people can be done. A number of ranking algorithms, including Citation count and PageRank, are used to assign ranks to vertices. The ranks given by the algorithms are compared against how well a person is represented in Wikipedia. We find up to medium level Spearman's rank correlations. A noteworthy finding is that PageRank consistently performed worse than the other algorithms. We analyze this further and find reasons.
DISCRIMINATING 16 MUTUALLY ORTHOGONAL 4-ATOM CLUSTER STATES VIA CAVITY QED IN TELEPORTING ARBITRARY UNKNOWN TWO-ATOM STATE WITH A 4-ATOM CLUSTER STATE AS QUANTUM CHANNEL
Authors: ZHANG WEN , LIU YI-MIN , WANG ZHANG-YIN , ZHANG ZHAN-JUN
Published: July 2008

We propose a scheme for discriminating 16 mutually orthogonal 4-atom cluster entangled states (CES) via cavity QED in teleporting an arbitrary unknown two-atom state with a 4-atom CES as quantum channel. Utilizing the interaction of atoms with cavity and classical field, the complicated 4-atom CESs are transformed into the simple 4-atom product states. Hence the difficulty of measurement during the teleportation process is degraded. In the present scheme, we allow for the case of a strong classical driving field and the detuning between the atoms and the cavity is assumed large enough. Thereby the photon-number-dependent parts in the effective Hamiltonian can be neglected, and the scheme is insensitive to both the cavity decay and the thermal field.
DESIGN OF CHAOTIC PSEUDO-RANDOM BIT GENERATOR AND ITS APPLICATIONS IN STREAM-CIPHER CRYPTOGRAPHY
Authors: WANG XING-YUAN , WANG XIAO-JUAN
Published: July 2008

Because of the sensitivity of chaotic systems on initial conditions/control parameters, when chaotic systems are realized in a discrete space with finite states, the dynamical properties will be far different from the ones described by the continuous chaos theory, and some degradation will arise. This problem will cause the chaotic trajectory eventually periodic. In order to solve the problem, a new binary stream-cipher algorithm based on one-dimensional piecewise linear chaotic map is proposed in this paper. In the process of encryption and decryption, we employ a secret variant to perturb the chaotic trajectory and the control parameter to lengthen the cycle-length of chaotic trajectory. In addition, we design a nonlinear principle to generate a pseudo-random chaotic bit sequence as key stream. Cryptanalysis shows that the cryptosystem is of high security.
CFD SIMULATION OF FLOW THROUGH AN OPEN CELL FOAM
Authors: TABOR G. , YEO O. , YOUNG P. , LAITY P.
Published: July 2008

A sample of an open-celled plastic foam has been examined using a combination of experimental, microscopic and computational methods. The aim was to use image-based meshing techniques to generate for the first time geometrically faithful models of the microstructure of the foam, and to use Computational Fluid Dynamics (CFD) to compute flow properties and pressure drops across the sample. The microstructure of the foam was also investigated experimentally and using SEM to provide further information for the computational analysis. A comparison was made with existing experimental data on flows through foams, and the unit pressure drop was found to correlate with the flow speed in the appropriate manner.
IN-DEPTH ANALYSIS OF THE NAMING GAME DYNAMICS: THE HOMOGENEOUS MIXING CASE
Authors: BARONCHELLI ANDREA , LORETO VITTORIO , STEELS LUC
Published: July 2008

Language emergence and evolution have recently gained growing attention through multi-agent models and mathematical frameworks to study their behavior. Here we investigate further the Naming Game, a model able to account for the emergence of a shared vocabulary of form-meaning associations through social/cultural learning. Due to the simplicity of both the structure of the agents and their interaction rules, the dynamics of this model can be analyzed in great detail using numerical simulations and analytical arguments. This paper first reviews some existing results and then presents a new overall understanding.
APPLICATION OF CLENSHAW–CURTIS METHOD IN CONFINED TIME OF ARRIVAL OPERATOR EIGENVALUE PROBLEM
Authors: VITANCOL ROBERTO S. , GALAPON ERIC A.
Published: July 2008

The Clenshaw–Curtis method in discretizing a Fredholm integral operator is applied to solving the confined time of arrival operator eigenvalue problem. The accuracy of the method is measured against the known analytic solutions for the noninteracting case, and its performance compared against the well-known Nystrom method. It is found that Clenshaw–Curtis's is superior to Nystrom's. In particular, Nystrom method yields at most five correct decimal places for the eigenvalues and eigenfunctions, while Clenshaw–Curtis yields eigenvalues correct to 16 decimal places and eigenfunctions up to 15 decimal places for the same number of quadrature points. Moreover, Clenshaw–Curtis's accuracy in the eigenvalues is uniform over a determinable range of the computed eigenvalues for a given number of quadrature abscissas. Clenshaw–Curtis is then applied to the harmonic oscillator confined time of arrival operator eigenvalue problem.
The anatomy of prototypes
Authors: Lim Youn-Kyung , Stolterman Erik , Tenenberg Josh
Published: July 2008

The role of prototypes is well established in the field of HCI and Design. A lack of knowledge, however, about the fundamental nature of prototypes still exists. Researchers have attempted to identify different types of prototypes, such as low- vs. high-fidelity prototypes, but these attempts have centered on evaluation rather than support of design exploration. There have also been efforts to provide new ways of thinking about the activity of using prototypes, such as experience prototyping and paper prototyping, but these efforts do not provide a discourse for understanding fundamental characteristics of prototypes. In this article, we propose an anatomy of prototypes as a framework for prototype conceptualization. We view prototypes not only in their role in evaluation but also in their generative role in enabling designers to reflect on their design activities in exploring a design space. We base this framework on the findings of two case studies that reveal two key dimensions: prototypes as filters and prototypes as manifestations. We explain why these two dimensions are important and how this conceptual framework can benefit our field by establishing more solid and systematic knowledge about prototypes and prototyping.
Leveraging popular destinations to enhance Web search interaction
Authors: White Ryen W. , Bilenko Mikhail , Cucerzan Silviu
Published: July 2008

This article presents a novel Web search interaction feature that for a given query provides links to Web sites frequently visited by other users with similar information needs. These popular destinations complement traditional search results, allowing direct navigation to authoritative resources for the query topic. Destinations are identified using the history of the search and browsing behavior of many users over an extended time period, and their collective behavior provides a basis for computing source authority. They are drawn from the end of users' postquery browse trails where users may cease searching once they find relevant information. We describe a user study that compared the suggestion of destinations with the previously proposed suggestion of related queries as well as with traditional, unaided Web search. Results show that search enhanced by query suggestions outperforms other systems in terms of subject perceptions and search effectiveness for fact-finding search tasks. However, search enhanced by destination suggestions performs best for exploratory tasks with its best performance obtained from mining past user behavior at query-level granularity. We discuss the implications of these and other findings from our study for the design of search systems that utilize user behavior, in particular, user browse trails and popular destinations.
Models and framework for supporting runtime decisions in Web-based systems
Authors: Andreolini Mauro , Casolari Sara , Colajanni Michele
Published: July 2008

Efficient management of distributed Web-based systems requires several mechanisms that decide on request dispatching, load balance, admission control, request redirection. The algorithms behind these mechanisms typically make fast decisions on the basis of the load conditions of the system resources. The architecture complexity and workloads characterizing most Web-based services make it extremely difficult to deduce a representative view of a resource load from collected measures that show extreme variability even at different time scales. Hence, any decision based on instantaneous or average views of the system load may lead to useless or even wrong actions. As an alternative, we propose a two-phase strategy that first aims to obtain a representative view of the load trend from measured system values and then applies this representation to support runtime decision systems. We consider two classical problems behind decisions: how to detect significant and nontransient load changes of a system resource and how to predict its future load behavior. The two-phase strategy is based on stochastic functions that are characterized by a computational complexity that is compatible with runtime decisions. We describe, test, and tune the two-phase strategy by considering as a first example a multitier Web-based system that is subject to different classes of realistic and synthetic workloads. Also, we integrate the proposed strategy into a framework that we validate by applying it to support runtime decisions in a cluster Web system and in a locally distributed Network Intrusion Detection System.
Reusable software components
Authors: Levine Trudy
Published: July 2008

This column consists of our yearly listing of sources for reusable software components. As always, no recommendation or guarantee by this column is implied.
Gem # 3: Limited types in Ada 2005 --- constructor functions
Authors: Duff Bob
Published: July 2008

Ada Gem #3 --- Constructor functions may be used to create objects of limited types. The result of such function calls is built "in place" in the actual object being created.
Gem #6: The Ada95 multiple views idiom vs. Ada05 interfaces
Authors: Heaney Matthew
Published: July 2008

Ada Gem #6 --- The multiple views idiom is a technique that allows you to create the effect of deriving from multiple tagged types simultaneously. It is a powerful mechanism for composing abstractions that complements interface types.
Gem #9: Classwide operations, iterators, and generic algorithms
Authors: Heaney Matthew
Published: July 2008

Ada Gem #9 - A generic algorithm manipulates container elements in a way that is completely general, working with any container (including arrays) that provides a way to iterate over its elements. In this example we systematically alter an operation for copying containers within a common class, converting it to a generic algorithm that ultimately works for any kind of container.
Notes from the other side
Authors: Anonymous
Published: July 2008

Editor's note: I met Anonymous at a lunch---no cloak-and-dagger stuff here. He told me about his experiences as an online student and agreed to tell his story again in the article below. Because he is pursuing a position with the online faculty of the school at which he earned his master's degree, he asked to remain anonymous.
SIGACT news complexity theory column 59
Authors: Hemaspaandra Lane A.
Published: July 2008

I suspect that both those who have been lucky enough to hear Jin-Yi Cai speak about holographic algorithms and those who have not will find his article to be a great survey and a real treat. Warmest thanks to Jin-Yi, and more generally to all guest column writers, for their tremendous labors of love.
Probabilistic databases
Authors: Suciu Dan
Published: July 2008

Many applications today need to manage large data sets with uncertainties. In this paper we describe the foundations of managing data where the uncertainties are quantified as probabilities. We review the basic definitions of the probabilistic data model and present some fundamental theoretical results for query evaluation on probabilistic databases.
A novel combination: ranpirnase and rosiglitazone induce a synergistic apoptotic effect by down-regulating Fra-1 and Survivin in cancer cells
Authors: Ramos-Nino Maria E. , Littenberg Benjamin
Published: July 2008

Accumulating evidence supports the idea that two known phosphatidylinositol 3′-kinase (PI3K) downstream proteins, Fra-1 and Survivin, are potential targets for cancer therapy. Increased expression of Fra-1, a Fos family member of the transcription factor activator protein-1, has been implicated in both the maintenance and the progression of the transformed state of several cancer cells. In addition, high Survivin expression in tumors correlates with more aggressive behavior, lower response to chemotherapeutic drugs, and shortened survival time. Previously, we reported that, in malignant mesothelioma cells with increased PI3K activity, small-molecule inhibitors of the PI3K/AKT pathway acted cooperatively with the amphibian RNase chemotherapeutic drug ranpirnase to inhibit cell growth. Because the thiazolidinedione antidiabetic drug rosiglitazone targets the PI3K/AKT pathway, we investigated the effect of the combination of these two drugs in cell survival in several cancer cell lines. We show here that the combination of ranpirnase and rosiglitazone synergistically decreases cell viability and increases cell apoptosis in several cancer cell lines. Cell killing is associated with decreased Fra-1 and Survivin expression and knockdown of Fra-1 increases cell killing by ranpirnase in a dose-dependent manner but not by rosiglitazone. The drug combination does not have a synergistic effect on killing in Fra-1 knockdown cells, showing that Fra-1 modulation accounts in part for the synergism. The novel drug combination of ranpirnase and rosiglitazone is a promising combination to treat cancers with increased PI3K-dependent Fra-1 expression or Survivin. [Mol Cancer Ther 2008;7(7):1871–9]
Improved Survival After Out-of-Hospital Cardiac Arrest Is Associated With an Increase in Proportion of Emergency Crew–Witnessed Cases and Bystander Cardiopulmonary Resuscitation
Authors: Hollenberg Jacob , Herlitz Johan , Lindqvist Jonny , Riva Gabriel , Bohm Katarina , Rosenqvist Mårten , Svensson Leif
Published: July 2008

Background—

Out-of-hospital cardiac arrest (OHCA) is a major public health problem. We sought to describe changes in 1-month survival after OHCA in patients given cardiopulmonary resuscitation (CPR) during the last 14 years in Sweden.

Methods and Results—

All patients experiencing OHCA in whom CPR was attempted between 1992 and 2005 and who were reported to the Swedish Cardiac Arrest Register were included in the study. In all, 38 646 patients were included in this survey. The proportion of patients who were admitted alive to a hospital increased from 15.3% in 1992 to 21.7% in 2005 (
P
for trend <0.0001). The corresponding values for patients being alive after 1 month were 4.8% and 7.3%, respectively (
P
for trend <0.0001). The increase in 1-month survival was particularly evident among patients found with a shockable rhythm (increase from 12.7% in 1992 to 22.3% in 2005;
P
for trend <0.0001). The corresponding figures for patients found with a nonshockable rhythm were 1.2% in 1992 and 2.3% in 2005 (
P
for trend=0.044). Factors that potentially contributed to the improved survival rate were an increase in emergency medical crew–witnessed cases from 9% in 1992 to 15% in 2005 (
P
for trend <0.0001) and, to a lesser degree, an increase in bystander CPR from 31% in 1992 to 50% in 2005 (
P
for trend <0.0001). After adjustment for potential risk factors, the increase in survival remained significant.

Conclusions—

We found a significant increase in survival after OHCA in Sweden over the last 14 years. The increase was particularly marked among patients found with a shockable rhythm and was associated with an increase in the proportion of crew-witnessed cases and, to a lesser degree, an increase in the performance of bystander CPR.