bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative measurement of specific biomarkers for protein oxidation, nitration and glycation in Arabidopsis leaves
Authors: Bechtold Ulrike , Rabbani Naila , Mullineaux Philip M. , Thornalley Paul J. 
Published: April 2009

SummaryHigher plants are continually exposed to reactive oxygen and nitrogen species during their lives. Together with glucose and reactive dicarbonyls, these can modify proteins spontaneously, leading to protein oxidation, nitration and glycation. These reactions have the potential to damage proteins and have an impact on physiological processes. The levels of protein oxidation, nitration and glycation adducts were assayed, using liquid chromatography coupled with tandem mass spectrometry, in total leaf extracts over a diurnal cycle and when exposed to conditions that promote oxidative stress. Changes in the levels of oxidation, glycation and nitration adducts were found between the light and dark phases under non‐stress conditions. A comparison between wild‐type plants and a mutant lacking peptide methionine sulfoxide reductase (pmsr2‐1) showed increased protein oxidation, nitration and glycation of specific amino acid residues during darkness in pmsr2‐1. Short‐term excess light exposure, which promoted oxidative stress, led to increased protein glycation, specifically by glyoxal. This suggested that any increased oxidative damage to proteins was within the repair capacity of the plant. The methods developed here provide the means to simultaneously detect a range of protein oxidation, nitration and glycation adducts within a single sample. Thus, these methods identify a range of biomarkers to monitor a number of distinct biochemical processes that have an impact on the proteome and therefore the physiological state of the plant.
The cell morphogenesis gene SPIRRIG in Arabidopsis encodes a WD/BEACH domain protein
Authors: Saedler Rainer , Jakoby Marc , Marin Birger , Galiana‐Jaime Elena , Hülskamp Martin 
Published: April 2009

SummaryWD40/BEACH domain proteins have been implicated in membrane trafficking and membrane composition events in Dictyostelium and Drosophila. In this paper, we show that the Arabidopsis SPIRRIG (SPI) gene encodes a WD40/BEACH domain protein. The cellular analysis revealed fragmented vacuoles in root hairs similar to those found in the corresponding Dictyostelium mutants, suggesting a related cellular function. The phenotypic analysis revealed that spi mutants share all phenotypic aspects of mutants in the actin polymerization‐regulating ARP2/3 pathway, including distorted trichomes, less lobing of epidermal pavement cells, disconnected epidermal cells on various organs, and shorter root hairs. This complete phenotypic overlap suggests that this WD40/BEACH domain protein and the actin‐regulating ARP2/3 pathway are involved in similar growth processes.
THE HERMENEUTICS OF INTER‐FAITH RELATIONS: RETRIEVING MODERATION AND PLURALISM AS UNIVERSAL PRINCIPLES IN QUR'ANIC EXEGESES
Authors: Afsaruddin Asma 
Published: May 2009

ABSTRACTThis article discusses the exegeses of two Qur'anic verses: Qur'an 2:143, which describes righteous Muslims as constituting a “middle/moderate community” (umma wasat) and Qur'an 5:66, which similarly describes righteous Jews and Christians as constituting a “balanced/moderate community” (umma muqtasida). Taken together, these verses clearly suggest that it is subscription to some common standard of righteousness and ethical conduct that determines the salvific nature of a religious community and not the denominational label it chooses to wear. Such a perspective offers the possibility of formulating universal principles of ethical and moral conduct, which may contribute to the formation of a genuinely pluralist global society today. Through a close study of Qur'anic exegeses of these verses from the late first/seventh century to modern times, I retrieve some of the most prevalent Muslim understandings of “moderation” through time and dwell on their contemporary implications.
Neurophysiological investigations of hepatic encephalopathy: ISHEN practice guidelines
Authors: Guerit Jean‐Michel , Amantini Aldo , Fischer Catherine , Kaplan Peter W. , Mecarelli Oriano , Schnitzler Alfons , Ubiali Emilio , Amodio Piero ,   the members of the ISHEN commission on Neurophysiological Investigations
Published: May 2009

AbstractBy studying neuronal activity through neuronal electrogenesis, neurophysiological investigations provide a functional assessment of the nervous system and, therefore, has been used for quantitative assessment and follow‐up of hepatic encephalopathy (HE). The different clinical neurophysiological approaches can be classified depending on the function to explore and their sensitivity to HE. The reliable techniques are those that reflect cortical function, i.e., cognitive‐evoked potentials (EPs) (P300 paradigm), electroencephalogram (EEG), visual EPs (latency>100 ms) and somatosensory EPs (SEPs) (latency between 25 and 100 ms). Short‐latency EPs (brainstem acoustic EPs, SEPs of a latency<25 ms) are in principle insensitive to HE, but can disclose brainstem conduction deficits due to oedema. SEPs and motor EPs can disclose myelopathies. Because of its parallelism to the clinical examination, clinical neurophysiology can complement the neurological examination: (i) to provide evidence of HE in patients who have normal consciousness; (ii) to rule out, at least under some conditions, disturbances of consciousness due to other causes (e.g. drug‐induced disturbances, non‐convulsive status epilepticus) with the reservation that the mildest degrees of encephalopathy might be associated with an EEG pattern similar to that induced by drugs; and (iii) to demonstrate the worsening or, conversely improvement, of HE in the follow‐up period.
High kallikrein‐related peptidase 6 in non‐small cell lung cancer cells: an indicator of tumour proliferation and poor prognosis
Authors: Nathalie Heuzé‐Vourc’h , Chris Planque , Serge Guyetant , Catherine Coco , Benjamin Brillet , Claire Blechet , Christelle Parent , Briollais Laurent , Pascale Reverdiau , Marie‐Lise Jourdan , Yves Courty 
Published: May 2009

AbstractThe human kallikrein‐related peptidases (KLK) are serine proteases whose concentrations are often abnormal in common human malignancies and contribute to neoplastic progression through multifaceted roles. However, little attention has been paid to their synthesis and involvement in the development and dissemination of lung cancer, the leading cause of cancer mortality worldwide. We have analysed the production of KLK6 in normal lung and tumour tissues from patients with non‐small cell lung cancer (NSCLC). KLK6 immunoreactivity was restricted to epithelial cells of the normal bronchi, but most of the cancer samples were moderately or highly immunoreactive, regardless of the histological subtype. In contrast, little or no KLK6 was detected in NSCLC cells. We have developed NSCLC lines expressing wild‐type KLK6 in order to investigate the role of KLK6 in lung cancer biology, and analysed its impact on proliferation. Ectopic KLK6 dramatically enhanced NSCLC cell growth and KLK6‐producing NSCLC cells had accelerated cell cycles, between the G1 and S phases. This was accompanied by a marked increase in cyclin E and decrease in p21. KLK6 production was also associated with enhanced synthesis of c‐Myc, which is known to promote cell‐cycle progression. Finally, examination of specimens from patients with NSCLC revealed that KLK6 mRNA is overexpressed in tumour tissue, and high KLK6 concentrations were associated with lower survival rates. We conclude that a high concentration of KLK6 is an indicator of tumour proliferation and an independent predictive factor in NSCLC.
A systematic review of the 5‐year survival and complication rates of implant‐supported single crowns
Authors: Jung Ronald E. , Pjetursson Bjarni E. , Glauser Roland , Zembic Anja , Zwahlen Marcel , Lang Niklaus P. 
Published: May 2009

AbstractObjectives: The objective of this systematic review was to assess the 5‐year survival of implant‐supported single crowns (SCs) and to describe the incidence of biological and technical complications.Methods: An electronic MEDLINE search complemented by manual searching was conducted to identify prospective and retrospective cohort studies on SCs with a mean follow‐up time of at least 5 years. Failure and complication rates were analyzed using random‐effects Poisson's regression models to obtain summary estimates of 5‐year proportions.Results: Twenty‐six studies from an initial yield of 3601 titles were finally selected and data were extracted. In a meta‐analysis of these studies, survival of implants supporting SCs was 96.8% [95% confidence interval (CI): 95.9–97.6%] after 5 years. The survival rate of SCs supported by implants was 94.5% (95% CI: 92.5–95.9%) after 5 years of function. The survival rate of metal–ceramic crowns, 95.4% (95% CI: 93.6–96.7%), was significantly (P=0.005) higher than the survival rate, 91.2% (95% CI: 86.8–94.2%), of all‐ceramic crowns.Peri‐implantitis and soft tissue complications occurred adjacent to 9.7% of the SCs and 6.3% of the implants had bone loss exceeding 2 mm over the 5‐year observation period. The cumulative incidence of implant fractures after 5 years was 0.14%. After 5 years, the cumulative incidence of screw or abutment loosening was 12.7% and 0.35% for screw or abutment fracture. For supra‐structure‐related complications, the cumulative incidence of ceramic or veneer fractures was 4.5%.Conclusion: It can be concluded that after an observation period of 5 years, high survival rates for implants and implant‐supported SCs can be expected. However, biological and particularly technical complications are frequent.
Cerebral MRI findings in a cohort of ex‐preterm and control adolescents
Authors: Nagy Zoltan , Jónsson Baldvin 
Published: May 2009

AbstractAim: Newborn infants were entered between 1988 and 1993 into a prospective, long‐term, follow‐up study. We aimed to investigate how the outcome of preterm‐born individuals on cerebral magnetic resonance imaging (MRI) compared to that reported on similar cohorts internationally.Methods: The 74 ex‐preterm (12.38–17.7 years, 51% girls) and 69 control participants (12.18–16.47 years, 53% girls) underwent a MRI examination on a 1.5T scanner. Two experienced neuroradiologists examined the T1‐ and T2‐weigthed images first independently and then in consensus without knowledge of group adherence.Results: Only 21 (4 controls) of the 143 sets of scans showed any abnormalities. All but one of these were of mild extent. Among the ex‐preterm adolescents two showed only incidental findings while the other 15 had either gliosis or white matter loss. Eleven subjects had white matter loss, seven of which had no other abnormalities. Four subjects had gliosis, three of which had no other abnormalities. The extent, severity or frequency of injury was not related to being born small for gestational age.Conclusion: Although the rate of structural abnormalities was higher in the group of adolescents born preterm, this rate was well below that reported from other centres around the world. We attribute this to the minimally invasive neonatal care and to different social structures in Sweden compared to that of other reports on similar cohorts.
A primary care provider’s guide to preventive and acute care management of adults and children with sickle cell disease
Authors: Pack‐Mabien Ardie , Haynes Johnson 
Published: May 2009

AbstractPurpose: To familiarize primary care providers (PCPs) with the pathophysiological processes, diagnostic evaluation, and medical management of sickle hemoglobinopathies and their complications. Current standards of care, clinical research advances, and new treatment options will also be addressed to assist PCPs in the management of sickle cell disease (SCD).Data sources: A selective search and review of the current literature on SCD and the authors’ experience.Conclusions: Management of individuals with SCD is very complex, requiring a multidisciplinary approach that includes the patient or parent, PCP, specialist, nurse, and social worker. More patients living with SCD are relying on PCPs in nonspecialty practices for comprehensive disease management.Implications for practice: Newborn screening detects new cases of SCD annually. The median life expectancy has more than doubled for individuals with sickle cell anemia. Healthcare providers are now in an era of increased routine screening, assessment, and management of chronic complications from this illness not previously seen in the care of adults with SCD.
Current understanding and management of dilated cardiomyopathy in Duchenne and Becker muscular dystrophy
Authors: Kaspar Rita Wen , Allen Hugh D. , Montanaro Federica 
Published: May 2009

AbstractPurpose: To review the current understanding of the pathophysiology of dilated cardiomyopathy (DCM) in patients with Duchenne and Becker muscular dystrophies, assessment of cardiac dysfunction for these patients, and the recommended pharmacological treatment options and ongoing research directions.Data sources: Reviews and original research articles from scholarly journals and books.Conclusions: Duchenne and Becker muscular dystrophies are debilitating neuromuscular disorders, both caused by mutations in the dystrophin gene. Most patients develop DCM as part of the disease course; in fact, DCM is the leading cause of death among these patients. Cardiac surveillance, including routine monitoring of electrocardiograms, echocardiograms, and appropriate blood biomarkers, may detect early DCM development. Although previous studies have shown that early administration of cardiac medications may delay the development of DCM, current standard of care does not emphasize cardiac surveillance and timely treatment. This, in turn, limits clinicians, including advanced practice nurses, to be optimally engaged in providing the most aggressive and proactive patient care.Implications for practice: Implementing a routine cardiac assessment and timely pharmacological treatment in primary or specialty care settings is highlighted as an important step to optimize cardiac health among patients with Duchenne and Becker muscular dystrophies.
Carbon payments as a safeguard for threatened tropical mammals
Authors: Venter Oscar , Meijaard Erik , Possingham Hugh , Dennis Rona , Sheil Douglas , Wich Serge , Hovani Lex , Wilson Kerrie 
Published: May 2009

AbstractOne reason for the rapid loss of species‐rich tropical forests is the high opportunity costs of forest protection. In Kalimantan (Indonesian Borneo), the expansion of high‐revenue oil palm (Elaeis guineensis) plantations currently threatens 3.3 million ha of forest. We estimate that payments for Reduced Emissions from Deforestation and forest Degradation (REDD) could offset the costs of stopping this deforestation at carbon prices of US$10–33 per tonne of CO2, or $2–16 per tonne if forest conservation targets only cost‐efficient areas. Forty globally threatened mammals are found within these planned plantations, including the Bornean orangutan (Pongo pygmaeus) and Borneo pygmy elephant (Elephas maximus borneensis). Cost‐efficient areas for emissions reductions also contain higher‐than‐average numbers of threatened mammals, indicating that there may be synergies between mitigating climate change and conserving biodiversity. While many policy and implementation issues need clarification, our economic assessment suggests that REDD could offer a financially realistic lifeline for Kalimantan's threatened mammals if it is included in future climate agreements.
Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay
Authors: van Doorn R. , Sławiak M. , Szemes M. , Dullemans A. M. , Bonants P. , Kowalchuk G. A. , Schoen C. D. 
Published: April 2009

ABSTRACT

Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5′ and 3′ ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10
4
. A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.
Inactivation of Enteric Viruses in Minimally Processed Berries and Herbs
Authors: Butot S. , Putallaz T. , Amoroso R. , Sánchez G. 
Published: April 2009

ABSTRACT

Several hepatitis A virus (HAV) and human norovirus (HuNoV) outbreaks due to consumption of contaminated berries and vegetables have recently been reported. Model experiments were performed to determine the effectiveness of freeze-drying, freeze-drying combined with heating, and steam blanching for inactivation of enteric viruses that might be present on the surface of berries and herbs. Inactivation of HAV and inactivation of feline calicivirus, a surrogate for HuNoV, were assessed by viral culturing and quantitative reverse transcription PCR (RT-PCR), whereas HuNoV survival was determined only by quantitative RT-PCR. While freeze-drying barely reduced (<1.3 log
10
units) the amount of HAV RNA detected in frozen produce, a greater decline in HAV infectivity was observed. The resistance of HuNoV genogroup I (GI) to freeze-drying was significantly higher than that of HuNoV GII on berries. Addition of a terminal dry heat treatment at 120°C after freeze-drying enhanced virus inactivation by at least 2 log
10
units, except for HuNoV GII. The results suggest that steam blanching at 95°C for 2.5 min effectively inactivated infectious enteric viruses if they were present in herbs. Our results provide data for adjusting food processing technologies if viral contamination of raw materials is suspected.
Optimization of a Phage Amplification Assay To Permit Accurate Enumeration of Viable
Mycobacterium avium
subsp.
paratuberculosis
Cells
Authors: Foddai Antonio , Elliott Christopher T. , Grant Irene R. 
Published: April 2009

ABSTRACT

A commercially available phage amplification assay,
FASTPlaque
TB (Biotec Laboratories, Ipswich, United Kingdom), when used according to the manufacturer's instructions, does not permit accurate enumeration of
Mycobacterium avium
subsp.
paratuberculosis
. The aim of this study was to optimize the phage amplification assay conditions to permit accurate quantification of viable
M. avium
subsp.
paratuberculosis
cells. The burst time for
M. avium
subsp.
paratuberculosis
was initially determined to inform decisions about optimal incubation time before plating, and then other test parameters were altered to evaluate how the correlation between plaque and colony counts was affected. The D29 mycobacteriophage replicates more slowly in
M. avium
subsp.
paratuberculosis
than in
Mycobacterium smegmatis
(used to optimize the commercial test originally), and the mean burst time for four
M. avium
subsp.
paratuberulosis
strains was 210 ± 36.8 min at 37°C compared to 63 ± 17.5 min for
M. smegmatis
mc
2
155. To achieve 100% correlation between plaque and colony counts, the optimized phage assay includes the following: (i) resuspension of the samples to be tested in Middlebrook 7H9 broth containing 10% oleic acid-albumin-dextrose-catalase and 2 mM calcium chloride, followed by overnight incubation at 37°C before performance of the phage assay; (ii) a 2-h incubation of the sample with D29 mycobacteriophage before viricide treatment; and (iii) a further 90-min incubation after viricide treatment and neutralization up to the burst time (total incubation time, 210 min) before plating with
M. smegmatis
mc
2
155 in 7H9 agar. The optimized phage amplification assay was able to detect 1 to 10 CFU/ml of
M. avium
subsp.
paratuberculosis
in spiked milk or broth within 48 h, as demonstrated by the results of several blind trials.
Species-Specific Cell Wall Binding Affinity of the S-Layer Proteins of Mosquitocidal Bacterium
Bacillus sphaericus
C3-41
Authors: Li Jia , Hu Xiaomin , Yan Jianpin , Yuan Zhiming 
Published: April 2009

ABSTRACT

The binding affinities and specificities of six truncated S-layer homology domain (SLH) polypeptides of mosquitocidal
Bacillus sphaericus
strain C3-41 with the purified cell wall sacculi have been assayed. The results indicated that the SLH polypeptide comprised of amino acids 31 to 210 was responsible for anchoring the S-layer subunits to the rigid cell wall layer via a distinct type of secondary cell wall polymer and that a motif of the recombinant SLH polypeptide comprising amino acids 152 to 210 (rSLH
152-210
) was essential for the stable binding of the S-layer with the bacterial cell walls. The quantitative assays revealed that the

K
D

(equilibrium dissociation constant) values of rSLH
152-210
and rSLH
31-210
with purified cell wall sacculi were 1.11 × 10
−6
M and 1.40 × 10
−6
M, respectively. The qualitative assays demonstrated that the SLH domain of strain C3-41 could bind only to the cell walls or the cells treated with 5 M guanidinium hydrochloride of both toxic and nontoxic
B. sphaericus
strains but not to those from other bacteria, indicating the species-specific binding of the SLH polypeptide of
B. sphaericus
with bacterial cell walls.
Characterization of the Tn
916
Conjugative Transposon in a Food-Borne Strain of
Lactobacillus paracasei
Authors: Devirgiliis Chiara , Coppola Doriana , Barile Simona , Colonna Bianca , Perozzi Giuditta 
Published: April 2009

ABSTRACT

Food-borne antibiotic-resistant lactic acid bacteria have received growing attention in the past few years. We have recently identified tetracycline-resistant
Lactobacillus paracasei
in samples of milk and natural whey starter cultures employed in the manufacturing process of a typical Italian fermented dairy product, Mozzarella di Bufala Campana. In the present study, we have characterized at the molecular level the genetic context of tetracycline resistance determinants in these natural strains, which we have identified as
tet
(M). This gene was present in 21 independent isolates, whose fingerprinting profiles were distributed into eight different repetitive extragenic palindromic groups by cluster analysis. We provide evidence that the gene is associated with the broad-host, conjugative transposon Tn
916
, which had never before been described to occur in
L. paracasei
. PCR analysis of four independent isolates by use of specifically designed primer pairs detected the presence of a circular intermediate form of the transposon, carrying a coupling sequence (GGCAAA) located between the two termini of Tn
916
. This novel coupling sequence conferred low conjugation frequency in mating experiments with the recipient strain JH2-2 of
Enterococcus faecalis
.