bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of diet in renal disease and Cockcroft–Gault formulas do not predict mortality (ZODIAC‐6)
Authors: Bilo H. J. G. , Logtenberg S. J. J. , Joosten H. , Groenier K. H. , Ubink‐Veltmaat L. J. , Kleefstra N. 
Published: March 2009

AbstractAims  An inverse relationship between estimates of renal function, with formulas such as the Modification of diet in renal disease (MDRD) study equation or the Cockcroft–Gault formula, and mortality has been suggested. These formulas both contain the variables sex, serum creatinine and age and the latter also contains body weight. We investigated whether these formulas predict mortality better than the variables they contain together in patients with Type 2 diabetes.Methods  In 1998, 1143 primary care patients with Type 2 diabetes participated in the Zwolle Outpatient Diabetes project Integrating Available Care (ZODIAC) Study, in the Netherlands. Clinical and laboratory data were collected at baseline. Life status was assessed after 6 years. We used Cox proportional hazard modelling to investigate the association between estimates of renal function (continuous data) and the variables they contain and mortality, adjusting for confounders. Both formulas were compared with models consisting of the variables present in the formulas. Predictability was assessed using Bayesian information criterion (BIC) and Harrell’s C statistics.Results  At follow‐up, 335 patients had died. All variables, except sex, influenced mortality. Predictive capability, indicated by lower BIC values and higher Harrell’s C values, was up to 10% better for models containing the separate variables as compared with Cockcroft–Gault or MDRD.Conclusions  Using estimates of renal function to assess mortality risk decreases predictability as compared with the combination of the risk factors they contain. These formulas, therefore, could be used to estimate renal function; however, they should not be used as a tool to predict mortality risk.
Relationship of Type 2 diabetes to the prevalence, incidence and progression of age‐related hearing loss
Authors: Mitchell P. , Gopinath B. , McMahon C. M. , Rochtchina E. , Wang J. J. , Boyages S. C , Leeder S. R 
Published: March 2009

AbstractAims  Type 2 diabetes and associated microvascular abnormalities are postulated to affect hearing. Our study reports on the relationship between Type 2 diabetes and the prevalence, 5‐year incidence and progression of hearing impairment in a representative, older, Australian population.Methods  The Blue Mountains Hearing Study is a population‐based survey of age‐related hearing loss conducted in a defined suburban area, west of Sydney. Hearing loss was defined as the pure‐tone average of frequencies 0.5, 1.0, 2.0 and 4.0 kHz > 25 decibels hearing level (dB HL) in the better ear (bilateral hearing loss). Type 2 diabetes was defined from reported physician‐diagnosed diabetes or fasting blood glucose ≥ 7.0 mmol/l.Results  Age‐related hearing loss was present in 50.0% of diabetic participants (n = 210) compared with 38.2% of non‐diabetic participants (n = 1648), odds ratio (OR) 1.55 [95% confidence interval (CI) 1.11–2.17], after adjusting for multiple risk factors. A relationship of diabetes duration with hearing loss was also demonstrated. After 5 years, incident hearing loss occurred in 18.7% of participants with, and 18.0% of those without diabetes, adjusted OR 1.01 (CI 0.54–1.91). Progression of existing hearing loss (> 5 dB HL), however, was significantly greater in participants with newly diagnosed diabetes (69.6%) than in those without diabetes (47.8%) over this period, adjusted OR 2.71 (CI 1.07–6.86).Conclusions  Type 2 diabetes was associated with prevalent, but not incident hearing loss in this older population. Accelerated hearing loss progression over 5 years was more than doubled in persons newly diagnosed with diabetes. These data explore further reported links between Type 2 diabetes and age‐related hearing loss.
Emissions Trading, Wealth Transfers and the Wounded Bull Scenario in Power Generation
Authors: Simshauser Paul , Doan Thao 
Published: March 2009

Abstract Electricity generators accept that emissions trading is fundamental to meeting CO2 reduction targets. But unless a percentage of permits are allocated, existing generators will face non‐trivial wealth transfers. Seldom contemplated in academic works are the adverse economic consequences of an all‐auction approach to emissions trading. Using Victoria to illustrate, we find that once CO2 prices exceed $17.50/t, the marginal coal generator facing large wealth transfers will withhold generating capacity to raise prices and recoup stranded investments, thus becoming a ‘wounded bull’ in the market place. This has material welfare implications with modelling results indicate an intermediate‐run 300 per cent increase in wholesale power prices.
Cellular calcium deficiency plays a role in neuronal death caused by proteasome inhibitors
Authors: Wu Shengzhou , Hyrc Krzysztof L. , Moulder Krista L. , Lin Ying , Warmke Timothy , Snider B. Joy 
Published: March 2009

AbstractCytosolic Ca2+concentration ([Ca2+]i) is reduced in cultured neurons undergoing neuronal death caused by inhibitors of the ubiquitin proteasome system. Activation of calcium entry via voltage‐gated Ca2+channels restores cytosolic Ca2+levels and reduces this neuronal death (Snideret al.2002). We now show that this reduction in [Ca2+]iis transient and occurs early in the cell death process, before activation of caspase 3. Agents that increase Ca2+influx such as activation of voltage‐gated Ca2+channels or stimulation of Ca2+entry via the plasma membrane Na–Ca exchanger attenuate neuronal death only if applied early in the cell death process. Cultures treated with proteasome inhibitors had reduced current density for voltage‐gated Ca2+channels and a less robust increase in [Ca2+]iafter depolarization. Levels of endoplasmic reticulum Ca2+were reduced and capacitative Ca2+entry was impaired early in the cell death process. Mitochondrial Ca2+was slightly increased. Preventing the transfer of Ca2+from mitochondria to cytosol increased neuronal vulnerability to this death while blockade of mitochondrial Ca2+uptake via the uniporter had no effect. Programmed cell death induced by proteasome inhibition may be caused in part by an early reduction in cytosolic and endoplasmic reticulum Ca2+,possibly mediated by dysfunction of voltage‐gated Ca2+channels. These findings may have implications for the treatment of disorders associated with protein misfolding in which proteasome impairment and programmed cell death may occur.
Tumor necrosis factor‐α‐induced neutral sphingomyelinase‐2 modulates synaptic plasticity by controlling the membrane insertion of NMDA receptors
Authors: Wheeler David , Knapp Edward , Bandaru Veera V. R. , Wang Yue , Knorr David , Poirier Christophe , Mattson Mark P. , Geiger Jonathan D. , Haughey Norman J. 
Published: March 2009

AbstractThe insertion and removal of NMDA receptors from the synapse are critical events that modulate synaptic plasticity. While a great deal of progress has been made on understanding the mechanisms that modulate trafficking of NMDA receptors, we do not currently understand the molecular events required for the fusion of receptor containing vesicles with the plasma membrane. Here, we show that sphingomyelin phosphodiesterase 3 (also known as neutral sphingomyelinase‐2) is critical for tumor necrosis factor (TNF) α‐induced trafficking of NMDA receptors and synaptic plasticity. TNFα initiated a rapid increase in ceramide that was associated with increased surface localization of NMDA receptor NR1 subunits and a specific clustering of NR1 phosphorylated on serines 896 and 897 into lipid rafts. Brief applications of TNFα increased the rate and amplitude of NMDA‐evoked calcium bursts and enhanced excitatory post‐synaptic currents. Pharmacological inhibition or genetic mutation of neutral sphingomyelinase‐2 prevented TNFα‐induced generation of ceramide, phosphorylation of NR1 subunits, clustering of NR1, enhancement of NMDA‐evoked calcium flux and excitatory post‐synaptic currents.
Towards sustainable Text Concept Mapping
Authors: Conlon Tom 
Published: March 2009

AbstractPrevious experimental studies have indicated that young people's text comprehension and summarisation skills can be improved by techniques based on text concept mapping (TCM). However, these studies have done little to elucidate a practical pedagogy that can make the techniques adoptable within the context of typical secondary school classrooms. This paper explains how a collaborative research approach has developed a new pedagogy, named TCM/4, for TCM, along with new technology that supports this pedagogy in effective ways. Case studies of the strategy indicate that pupils enjoyed their lessons and shared their teachers' views that it was helpful in comprehending texts.
New generation sequencers as a tool for genotyping of highly polymorphic multilocus MHC system
Authors: BABIK WIESŁAW , TABERLET PIERRE , EJSMOND MACIEJ JAN , RADWAN JACEK 
Published: March 2009

AbstractAccurate genotyping of complex systems, such as the major histocompatibility complex (MHC) often requires simultaneous analysis of multiple co‐amplifying loci. Here we explore the utility of the massively parallel 454 sequencing method as a universal tool for genotyping complex MHC systems in nonmodel vertebrates. The power of this approach stems from the use of tagged polymerase chain reaction (PCR) primers to identify individual amplicons which can be simultaneously sequenced to the arbitrarily chosen coverage. However, the error‐prone sequencing technology poses considerable challenges as it may be difficult to discriminate between sequencing errors and true rare alleles; due to complex nature of artefacts and errors, efficient quality control is required. Nevertheless, our study demonstrates the parallel 454 sequencing can be an efficient genotyping platform for MHC and provides an alternative to classical genotyping methods. We introduced procedures to identify the threshold that can be used to reduce number of genotyping errors by eliminating most of artefactual alleles (AA) representing PCR or sequencing errors. Our procedures are based on two expectations: first, that AA should be relatively rare, both overall and on per‐individual basis, and second, that most AA result from errors introduced to sequences of true alleles. In our data set, alleles with an average per‐individual frequency below 3% most likely represented artefacts. This threshold will vary in other applications according to the complexity of the genotyped system. We strongly suggest direct assessment of genotyping error in every experiment by running a fraction of duplicates: individuals amplified in independent PCRs.
Proliferation of Antibiotic-Producing Bacteria and Concomitant Antibiotic Production as the Basis for the Antibiotic Activity of Jordan's Red Soils
Authors: Falkinham Joseph O. , Wall Thomas E. , Tanner Justin R. , Tawaha Khaled , Alali Feras Q. , Li Chen , Oberlies Nicholas H. 
Published: March 2009

ABSTRACTAnecdotes, both historical and recent, recount the curing of skin infections, including diaper rash, by using red soils from the Hashemite Kingdom of Jordan. Following inoculation of red soils isolated from geographically separate areas of Jordan,Micrococcus luteusandStaphylococcus aureuswere rapidly killed. Over the 3-week incubation period, the number of specific types of antibiotic-producing bacteria increased, and high antimicrobial activity (MIC, ∼10 μg/ml) was observed in methanol extracts of the inoculated red soils. Antibiotic-producing microorganisms whose numbers increased during incubation included actinomycetes,Lysobacterspp., andBacillusspp. The actinomycetes produced actinomycin C2and actinomycin C3. No myxobacteria or lytic bacteriophages with activity against eitherM. luteusorS. aureuswere detected in either soil before or after inoculation and incubation. Although protozoa and amoebae were detected in the soils, the numbers were low and did not increase over the incubation period. These results suggest that the antibiotic activity of Jordan's red soils is due to the proliferation of antibiotic-producing bacteria.
Glycerol Utilization Gene Cluster in
Streptomyces clavuligerus
Authors: Baños Sonia , Pérez-Redondo Rosario , Koekman Bert , Liras Paloma 
Published: March 2009

ABSTRACT

The
Streptomyces clavuligerus
ATCC 27064 glycerol cluster
gylR-glpF1K1D1
is induced by glycerol but is not affected by glucose.
S. clavuligerus
growth and clavulanic acid production are stimulated by glycerol, but this does not occur in a
glpK1
-deleted mutant. Amplification of
glpK1D1
results in transformants yielding larger amounts of clavulanic acid in the wild-type strain and in overproducer
S. clavuligerus
Gap15-7-30 or
S. clavuligerus
Δ
relA
strains.
Negative Fitness Consequences and Transmission Dynamics of a Heritable Fungal Symbiont of a Parasitic Wasp
Authors: Gibson Cara M. , Hunter Martha S. 
Published: March 2009

ABSTRACT

Heritable bacterial symbionts are widespread in insects and can have many important effects on host ecology and fitness. Fungal symbionts are also important in shaping their hosts' behavior, interactions, and evolution, but they have been largely overlooked. Experimental tests to determine the relevance of fungal symbionts to their insect hosts are currently extremely rare, and to our knowledge, there have been no such tests for strictly predacious insects. We investigated the fitness consequences for a parasitic wasp (
Comperia merceti
) of an inherited fungal symbiont in the Saccharomycotina (Ascomycota) that was long presumed to be a mutualist. In comparisons of wasp lines with and without this symbiont, we found no evidence of mutualism. Instead, there were significant fitness costs to the wasps in the presence of the yeast; infected wasps attacked fewer hosts and had longer development times. We also examined the relative competitive abilities of the larval progeny of infected and uninfected mothers, as well as horizontal transmission of the fungal symbiont among larval wasps that shared a single host cockroach egg case. We found no difference in larval competitive ability when larvae whose infection status differed shared a single host. We did find high rates of horizontal transmission of the fungus, and we suggest that this transmission is likely responsible for the maintenance of this infection in wasp populations.
Migratory Response of Soil Bacteria to
Lyophyllum
sp. Strain Karsten in Soil Microcosms
Authors: Warmink J. A. , van Elsas J. D. 
Published: March 2009

ABSTRACT

In this study, the selection of bacteria on the basis of their migration via fungal hyphae in soil was investigated in microcosm experiments containing
Lyophyllum
sp. strain Karsten (DSM2979). One week following inoculation with a bacterial community obtained from soil, selection of a few specific bacterial types was noticed at 30 mm in the growth direction of
Lyophyllum
sp. strain Karsten in sterile soil. Cultivation-based analyses showed that the migration-proficient types encompassed 10 bacterial groups, as evidenced by (GTG)
5
genomic fingerprinting as well as 16S rRNA gene sequencing. These were (>97% similarity)
Burkholderia terrae
BS001,
Burkholderia sordidicola
BS026,
Burkholderia sediminicola
BS010, and
Burkholderia phenazinium
BS028;
Dyella japonica
BS013, BS018, and BS021; “
Sphingoterrabacterium pocheensis
” BS024;
Sphingobacterium daejeonense
BS025; and
Ralstonia basilensis
BS017. Migration as single species was subsequently found for
B. terrae
BS001,
D. japonica
BS018 and BS021, and
R. basilensis
BS017. Typically, migration occurred only when these organisms were introduced at the fungal growth front and only in the direction of hyphal growth. Migration proficiency showed a one-sided correlation with the presence of the
hrcR
gene, used as a marker for the type III secretion system (TTSS), as all single-strain migrators were equipped with this system and most non-single-strain migrators were not. The presence of the TTSS stood in contrast to the low prevalence of TTSSs within the bacterial community used as an inoculum (<3%). Microscopic examination of
B. terrae
BS001 in contact with
Lyophyllum
sp. strain Karsten hyphae revealed the development of a biofilm surrounding the hyphae. Migration-proficient bacteria interacting with
Lyophyllum
sp. strain Karsten may show complex behavior (biofilm formation) at the fungal tip, leading to their translocation and growth in novel microhabitats in soil.
prtH2
, Not
prtH
, Is the Ubiquitous Cell Wall Proteinase Gene in
Lactobacillus
helveticus
Authors: Genay M. , Sadat L. , Gagnaire V. , Lortal S. 
Published: March 2009

ABSTRACT

Lactobacillus
helveticus
strains possess an efficient proteolytic system that releases peptides which are essential for lactobacillus growth in various fermented dairy products and also affect textural properties or biological activities. Cell envelope proteinases (CEPs) are bacterial enzymes that hydrolyze milk proteins. In the case of
L
.
helveticus
, two CEPs with low percentages of amino acid identity have been described, i.e., PrtH and PrtH2. However, the distribution of the genes that encode CEPs still remains unclear, rendering it difficult to further control the formation of particular peptides. This study evaluated the diversity of genes that encode CEPs in a collection of strains of
L
.
helveticus
isolated from various biotopes, both in terms of the presence or absence of these genes and in terms of nucleotide sequence, and studied their transcription in dairy matrices. After defining three sets of primers for both the
prtH
and
prtH2
genes, we studied the distribution of the genes by using PCR and Southern blotting experiments. The
prtH2
gene was ubiquitous in the 29 strains of
L
.
helveticus
studied, whereas only 18 of them also exhibited the
prtH
gene. Sequencing of a 350-bp internal fragment of these genes revealed the existence of intraspecific diversity. Finally, expression of these two CEP-encoding genes was followed during the growth in dairy matrices of two strains, ITG LH77 and CNRZ32, which possess one and two CEP-encoding genes, respectively. Both genes were shown to be expressed by
L
.
helveticus
at each stage of growth in milk and at different stages of mini-Swiss-type cheese making and ripening.
Suppression of the Bacterial Spot PathogenXanthomonas euvesicatoriaon Tomato Leaves by an Attenuated Mutant ofXanthomonas perforans
Authors: Hert A. P. , Marutani M. , Momol M. T. , Roberts P. D. , Olson S. M. , Jones J. B. 
Published: March 2009

ABSTRACTA bacteriocin-producing strain of the bacterial spot of tomato plant pathogen,Xanthomonas perforans, with attenuated pathogenicity was deployed for biocontrol of a bacteriocin-sensitive strain of the genetically closely related bacterial spot of tomato plant pathogen,X.euvesicatoria. The attenuated mutant (91-118ΔopgHΔbcnB) ofX.perforanswas tested in leaf tissue and shown to significantly inhibit internal populations of the wild-typeX.euvesicatoriastrain although significantly less than the wild-type 91-118 strain, whereas in a phyllosphere inhibition assay, the mutant strain reduced epiphytic populations comparably to 91-118. Thus, the attenuated mutant limited the sensitive bacterium more efficiently on the leaf surface than inside the leaf. In field experiments, weekly application of 91-118ΔopgHΔbcnBsignificantly reducedX.euvesicatoriapopulations compared to the growers’ standard control (copper hydroxide and mancozeb applied weekly and acibenzolar-S-methyl applied every 2 weeks). The biological control agent, 91-118ΔopgHΔbcnB, applied every 2 weeks also significantly reducedX.euvesicatoriapopulations in one season but was not significantly different from the growers’ standard control. Potentially, attenuated pathogenic strains could be deployed as biological control agents in order to improve disease control of foliar plant pathogens.
Characterization of a New Plasmid-Like Prophage in a Pandemic
Vibrio parahaemolyticus
O3:K6 Strain
Authors: Lan Shih-Feng , Huang Chung-Ho , Chang Chuan-Hsiung , Liao Wei-Chao , Lin I-Hsuan , Jian Wan-Neng , Wu Yueh-Gin , Chen Shau-Yan , Wong Hin-chung 
Published: March 2009

ABSTRACT

Vibrio parahaemolyticus
is a common food-borne pathogen that is normally associated with seafood. In 1996, a pandemic O3:K6 strain abruptly appeared and caused the first pandemic of this pathogen to spread throughout many Asian countries, America, Europe, and Africa. The role of temperate bacteriophages in the evolution of this pathogen is of great interest. In this work, a new temperate phage, VP882, from a pandemic O3:K6 strain of
V
.
parahaemolyticu
s was purified and characterized after mitomycin C induction. VP882 was a
Myoviridae
bacteriophage with a polyhedral head and a long rigid tail with a sheath-like structure. It infected and lysed high proportions of
V
.
parahaemolyticus
,
Vibrio vulnificus
, and
Vibrio cholerae
strains. The genome of phage VP882 was sequenced and was 38,197 bp long, and 71 putative open reading frames were identified, of which 27 were putative functional phage or bacterial genes. VP882 had a linear plasmid-like genome with a putative protelomerase gene and cohesive ends. The genome does not integrate into the host chromosome but was maintained as a plasmid in the lysogen. Analysis of the reaction sites of the protelomerases in different plasmid-like phages revealed that VP882 and ΦHAP-1 were highly similar, while N15, ΦKO2, and PY54 made up another closely related group. The presence of DNA adenine methylase and quorum-sensing transcriptional regulators in VP882 may play a specific role in this phage or regulate physiological or virulence-associated traits of the hosts. These genes may also be remnants from the bacterial chromosome following transduction.
Activation and Transfer of the Chromosomal Phage Resistance Mechanism AbiV in
Lactococcus lactis
Authors: Haaber Jakob , Moineau Sylvain , Hammer Karin 
Published: March 2009

ABSTRACT

AbiV is a chromosomally encoded phage resistance mechanism that is silent in the wild-type phage-sensitive strain
Lactococcus lactis
subsp.
cremoris
MG1363. Spontaneous phage-resistant mutants of
L. lactis
MG1363 were analyzed by reverse transcriptase PCR and shown to express AbiV. This expression was related to a reorganization in the upstream region of
abiV
. Transfer of
abiV
between two lactococcal strains, most likely by conjugation, was also demonstrated. To our knowledge, this is the first report of natural transfer of a chromosomally encoded phage resistance mechanism.