bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of the cysteine residues in Arabidopsis thaliana cyclophilin CYP20-3 in peptidyl-prolyl cis–trans isomerase and redox-related functions
Authors: Laxa Miriam , König Janine , Dietz Karl-Josef , Kandlbinder Andrea 
Published: December 2006

Cyps (cyclophilins) are ubiquitous proteins of the immunophilin superfamily with proposed functions in protein folding, protein degradation, stress response and signal transduction. Conserved cysteine residues further suggest a role in redox regulation. In order to get insight into the conformational change mechanism and functional properties of the chloroplast-located CYP20-3, site-directed mutagenized cysteine→serine variants were generated and analysed for enzymatic and conformational properties under reducing and oxidizing conditions. Compared with the wild-type form, elimination of three out of the four cysteine residues decreased the catalytic efficiency of PPI (peptidyl-prolyl cis–trans isomerase) activity of the reduced CYP20-3, indicating a regulatory role of dithiol–disulfide transitions in protein function. Oxidation was accompanied by conformational changes with a predominant role in the structural rearrangement of the disulfide bridge formed between Cys54 and Cys171. The rather negative Em (midpoint redox potential) of −319 mV places CYP20-3 into the redox hierarchy of the chloroplast, suggesting the activation of CYP20-3 in the light under conditions of limited acceptor availability for photosynthesis as realized under environmental stress. Chloroplast Prx (peroxiredoxins) were identified as interacting partners of CYP20-3 in a DNA-protection assay. A catalytic role in the reduction of 2-Cys PrxA and 2-Cys PrxB was assigned to Cys129 and Cys171. In addition, it was shown that the isomerization and disulfide-reduction activities are two independent functions of CYP20-3 that both are regulated by the redox state of its active centre.
Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data
Authors: Lerman Gilad , McQuown Joseph , Blais Alexandre , Dynlacht Brian D. , Chen Guangliang , Mishra Bud 
Published: December 2006

AbstractWe present a fast, versatile and adaptive-multiscale algorithm for analyzing a wide-variety of DNA microarray data. Its primary application is in normalization of array data as well as subsequent identification of ‘enriched targets’, e.g. differentially expressed genes in expression profiling arrays and enriched sites in ChIP-on-chip experimental data.We show how to accommodate the unique characteristics of ChIP-on-chip data, where the set of ‘enriched targets’ is large, asymmetric and whose proportion to the whole data varies locally.Contact: lerman@umn.eduSupplementary information: Supplementary figures, related preprint, free software as well as our raw DNA microarray data with PCR validations are available at as well as Bioinformatics online.
Is correction for protein concentration appropriate for protein adduct dosimetry? Hypothesis and clues from an aflatoxin B1‐exposed population
Authors: Peng Tao , Li Le‐Qun , Peng Min‐Hao , Liu Zhi‐Ming , Liu Tang‐Wei , Yan Lu‐Nan , Shen Han‐Ming , Wang LianWen , Wang Qiao , Wang Kai‐bo , Liang Ren‐xiang , Wei Zong‐liang , Ong Choon Nam , Santella Regina M. 
Published: December 2006

Protein adducts are useful biomarkers for assessing exposure, metabolism and risk of carcinogens. Aflatoxin B1–albumin adducts (AAA) and protein carbonyl content (PCC) have long been used for assessing aflatoxin exposure and oxidative stress to proteins, and the quantitative data are almost exclusively expressed per mg protein. Given the large variation in protein concentrations in plasma among populations, this may not be the most appropriate method. The objective was to test the hypothesis that AAA and PCC should be expressed per mL plasma in population studies. AAA and PCC were analyzed among 402 subjects from three regions of China with a gradient in hepatocellular carcinoma (HCC) mortality ranging from 21 to 97 per 100 000. When biomarker values were expressed per mL plasma, the AAA level was significantly associated with plasma PCC (r = 0.262, P < 0.001), and adjusted levels of AAA and PCC paralleled HCC mortalities in the three regions, suggesting a role for aflatoxin‐related oxidative stress in hepatocarcinogenesis in this population. In addition, there were statistically significant associations between both protein biomarkers, expressed per mL plasma, and the levels of alanine aminotransferase and aspartate aminotransferase in hepatitis B virus‐infected subjects, suggesting roles for aflatoxin exposure, oxidative stress and hepatitis B virus infection in the development of HCC. The present data suggest that interindividual variation in plasma protein concentration may influence the dosimetry and relevant interpretation of protein biomarkers. (Cancer Sci 2007; 98: 140–146)
Role of habitat in determining macroinvertebrate production in an intermittent‐stream system
Authors: CHADWICK MICHAEL A. , HURYN ALEXANDER D. 
Published: December 2006

Summary1. The effect of channel drying on macroinvertebrate production was studied at the habitat and reach scale in a catchment drained by intermittent streams in Maine, U.S.A. The catchment includes two first‐order streams and their second‐order confluence. Six reaches were selected for study based on differences in channel slope and habitat cover (bedrock, riffle/run, debris dam and pool). Stream water in each reach was acidic and oligotrophic.2. The study reaches had different degrees of channel drying. In the first‐order reaches, surface flow ceased earlier in the season and for longer periods than second‐order reaches. Regardless of reach, pool and debris dam habitats retained water longer than riffle/runs and bedrock. Unlike other habitats, debris dams retained moisture for relatively long periods following cessation of surface flow.3. Reach‐specific macroinvertebrate production ranged from approximately 1.7 to 2.9 g AFDM m−2 year−1 which are among the lowest values ever reported. Habitat‐specific production ranged from approximately 0.5 to 5.0 g AFDM m−2 year−1 (bedrock and debris dams, respectively).4. At the reach scale, quantities of stored benthic organic matter (range approximately 200–600 g AFDM−2) decreased in a downstream direction.5. A combination of differences in the timing and duration of channel drying, habitat structure and detritus standing stocks appeared to influence levels of invertebrate production among the study reaches.6. Our interpretation of a canonical correspondence analysis indicates that drying is more important than habitat in affecting macroinvertebrate production in this intermittent stream system.
Should research ethics triumph over clinical ethics?
Authors: Kottow Michael H. 
Published: December 2006

AbstractEvidence‐based medicine (EBM) and its main strategy, randomized clinical trials, have had less impact on medical practice than might be expected. Of the various reasons that make practitioners wary of applying research results, this paper explores some consequences of scientists’ and research sponsors’ adamant insistence that reliable science can only be achieved if protocols adhere exclusively to the ethics of investigation basically reduced to obtaining informed consent and avoiding risks as far as possible. This means, and has been explicitly contended, that neither patients nor doctors should fall prey to the therapeutic fallacy which leads them to expect that research will also take care of patient‐subjects’ medical welfare. Doctors would betray their profession if they allowed clinical research to disregard their therapeutic obligations in favour of strict scientific methodology, as is bound to happen when using placebos in spite of existing therapy, disregarding equipoise, disallowing benefit claims, emphasizing the distinction between research ethics and clinical ethics but denying any difference between therapeutic and non‐therapeutic trials. That scientists and practitioners should not agree on needs and priorities in the medical context, constitutes an additional factor in the less than optimal reception of EBM by the health care professions.
Pressure ulcer prevalence in Europe: a pilot study
Authors: Vanderwee Katrien , Clark Michael , Dealey Carol , Gunningberg Lena , Defloor Tom 
Published: December 2006

AbstractRationale and aims  Numerous prevalence studies have been conducted. The problem with these studies is that prevalence proportions cannot be compared with each other, because of differences in performance of each survey. There is no agreed standardized method for determining prevalence proportions. This study aimed to develop and pilot a uniform data collection instrument and methodology to measure the pressure ulcer prevalence and to get some insight into pressure ulcer prevalence across different patient groups in Europe.Methods  Pressure ulcer experts from different European countries developed a data collection instrument, which included five categories of data: general data, patient data, risk assessment, skin observation and prevention. A convenience sample of university and general hospitals of Belgium, Italy, Portugal, UK and Sweden participated in the study. In each participating hospital, teams of two trained nurses who collected the data on the wards were established. All patients admitted before midnight on the day of the survey and older than 18 years were included.Results  The data collection instrument and study procedure of the survey were found to be effective by all participants. 5947 patients were surveyed in 25 hospitals in five European countries. The pressure ulcer prevalence (grade 1–4) was 18.1% and if grade 1 ulcers were excluded, it was 10.5%. The sacrum and heels were the most affected locations. Only 9.7% of the patients in need of prevention received fully adequate preventive care.Conclusion  The methodology is sufficiently robust to measure and compare pressure ulcer prevalence in different countries. The pressure ulcer prevalence was higher than expected and relatively few patients received adequate prevention. This indicates that more attention to prevention is needed in Europe.
Pre-main-sequence stars in the Lagoon Nebula (M8)
Authors: Arias J. I. , Barbá R. H. , Morrell N. I. 
Published: December 2006

Abstract
We report the discovery of new pre-main-sequence (PMS) stars in the Lagoon Nebula (M8) at a distance of 1.25 kpc, based on intermediate-resolution spectra obtained with the Boller & Chivens spectrograph at the 6.5-m Magellan I Telescope (Las Campanas Observatory, Chile). According to the spectral types, the presence of emission lines and the lithium λ 6708 absorption line, we are able to identify 27 classical T Tauri stars, seven weak-lined T Tauri stars and three PMS emission objects with spectral type G, which we include in a separate stellar class denominated ‘PMS Fe/Ge class’. Using near-infrared photometry either from the Two-Micron All-Sky Survey or from our own previous work, we derive effective temperatures and luminosities for these stars and locate them in the Hertzsprung–Russell diagram, in order to estimate their masses and ages. We find that almost all of our sample stars are younger than 3 × 106 yr and span over a range of masses between 0.8 and 2.5 M⊙. A cross-correlation between our spectroscopic data and the X-ray sources detected with the Chandra ACIS instrument is also presented.
A SNARE‐protein has opposing functions in penetration resistance and defence signalling pathways
Authors: Zhang Ziguo , Feechan Angela , Pedersen Carsten , Newman Mari‐Anne , Qiu Jin‐long , Olesen Karen L. , Thordal‐Christensen Hans 
Published: December 2006

SummaryPenetration resistance is often the first line of defence against fungal pathogens. Subsequently induced defences are mediated by the programmed cell death (PCD) reaction pathway and the salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) signalling pathways. We previously demonstrated that full penetration resistance in Arabidopsis against the non‐host barley powdery mildew fungus (Blumeria graminis f.sp. hordei) requires the syntaxin SYP121 (PEN1). Here we report that SYP121, together with SYP122, functions as a negative regulator of subsequently induced defence pathways. The SA level in the syntaxin double mutant syp121–1 syp122–1 is dramatically elevated, resulting in necrosis and dwarfism. This phenotype is partially rescued by introducing the SA‐signalling mutations eds1–2, eds5–3, sid2–1 and npr1–1 as well as the NahG transgene. These partially rescued triple mutants have an unknown defence to Pseudomonas syringae pv. tomato, and have increased HR‐like responses to non‐host and host powdery mildew fungi. The HR‐like responses cause efficient resistance to the latter. These defence pathways are SA‐independent. Furthermore, the JA/ET signalling marker, PDF1.2, is highly upregulated in the triple mutants. Thus SYP121 and SYP122 are negative regulators of PCD, SA, JA and ET pathways through a molecular function distinct from that of SYP121 in penetration resistance. Our data suggest that individual cells preferentially express either penetration resistance or the subsequently induced defences.
Rapid differentiation of Candida albicans from non‐albicans species by germ tube test directly from BacTAlert blood culture bottles
Authors: Terlecka Jolanta A. , Du Cros Philipp A. , Orla Morrissey C. , Spelman Denis 
Published: December 2006

SummaryBloodstream infections (BSIs) caused by Candida species are increasing in incidence, and are associated with high mortality rates, which are due in part to a delay in the administration of appropriate antifungal therapy. Earlier identification of yeast isolates from blood cultures may improve clinical outcomes. Identification of a Candida as albicans or non‐albicans species depends on the presence or absence of germ tubes. Conventionally, germ tube test (GTT) is performed on colonies grown on agar plate after 24–48 h of incubation. In the present study, the GTT was performed earlier on an aliquot taken from blood culture bottle, after yeast cells were seen in Gram stain and the results were compared with the GTT using the conventional method. Thirty‐one consecutive bloodstream isolates of yeast were included in this prospective study over 10 months. There was 100% concordance between the two GTT methods. Final identification was confirmed by standard laboratory procedures. The performance of GTT directly from blood culture bottles has important implications for early, appropriate therapy in patients with candidaemia.
High‐risk febrile neutropenia in Auckland 2003–2004: the influence of the microbiology laboratory on patient treatment and the use of pathogen‐specific therapy
Authors: Ritchie S. , Palmer S. , Ellis‐Pegler R. 
Published: December 2006

AbstractBackground: International guidelines recommend routine microbiological assessment of patients with febrile neutropenia, but do not recommend a change from broad‐spectrum antibiotic therapy to pathogen‐specific therapy when a clinically relevant organism has been isolated. The aim of the study was to determine the aetiology of febrile neutropenia in adult haematology patients at Auckland City Hospital, to document the changes in treatment made following isolation of a clinically relevant organism and to assess adverse outcomes in any patient who received pathogen‐specific therapy after a positive culture result.Methods: The results of all microbiological tests together with antibiotic therapy were recorded from consecutive patients with fever and a neutrophil count <0.5 × 109/L over 1 year beginning in May 2003.Results: One thousand one hundred and ninety‐six specimens were collected from 81 patients during 116 episodes of febrile neutropenia. A pathogen was isolated from blood cultures in 40 episodes: Gram‐positive cocci accounted for 46% of isolates and Gram‐negative bacilli for 35%. Isolation of a pathogen from blood cultures resulted in a change of treatment in 25 of 40 (62.5%, 95%CI 46–77%) episodes. In 12 of these episodes, antibiotic therapy was optimized to a single pathogen‐specific agent. No adverse events or subsequent changes in antibiotic therapy occurred in any of these 12 patients. Isolation of a pathogen from specimens other than blood seldom led to a change in therapy.Conclusion: Isolation of a pathogen from blood cultures often allows antibiotic therapy to be simplified to a pathogen‐specific regimen. Further study of this approach is warranted.
Selective 5‐HT1B receptor inhibition of glutamatergic and GABAergic synaptic activity in the rat dorsal and median raphe
Authors: Lemos Julia C. , Pan Yu‐Zhen , Ma Xiaohong , Lamy Christophe , Akanwa Adaure C. , Beck Sheryl G. 
Published: December 2006

AbstractThe dorsal (DR) and median (MR) raphe nuclei contain 5‐hydroxytryptamine (5‐HT) cell bodies that give rise to the majority of the ascending 5‐HT projections to the forebrain. The DR and MR have differential roles in mediating stress, anxiety and depression. Glutamate and GABA activity sculpt putative 5‐HT neuronal firing and 5‐HT release in a seemingly differential manner in the MR and DR, yet isolated glutamate and GABA activity within the DR and MR has not been systematically characterized. Visualized whole‐cell voltage‐clamp techniques were used to record excitatory and inhibitory postsynaptic currents (EPSC and IPSC) in 5‐HT‐containing neurons. There was a regional variation in action potential‐dependent (spontaneous) and basal [miniature (m)] glutamate and GABAergic activity. mEPSC activity was greater than mIPSC activity in the DR, whereas in the MR the mIPSC activity was greater. These differences in EPSC and IPSC frequency indicate that glutamatergic and GABAergic input have distinct cytoarchitectures in the DR and MR. 5‐HT1B receptor activation decreased mEPSC frequency in the DR and the MR, but selectively inhibited mIPSC activity only in the MR. This finding, in concert with its previously described function as an autoreceptor, suggests that 5‐HT1B receptors influence the ascending 5‐HT system through multiple mechanisms. The disparity in organization and integration of glutamatergic and GABAergic input to DR and MR neurons and their regulation by 5‐HT1B receptors may contribute to the distinction in MR and DR regulation of forebrain regions and their differential function in the aetiology and pharmacological treatment of psychiatric disease states.
Brain activity associated with fear renewal
Authors: Bruchey A. K. , Gonzalez‐Lima F. 
Published: December 2006

AbstractThis is the first mapping study of the brain activity associated with the renewal of an extinguished conditioned response. Rats were given radiolabeled fluorodeoxyglucose, a glucose analog, to map brain effects of an extinguished tone during context‐dependent renewal of conditioned fear. A tone conditioned stimulus was paired with a footshock unconditioned stimulus in a first context, followed by conditioned response extinction in a second context and conditioned response renewal in a third context. Control rats were treated identically, except that tone and shock were presented pseudorandomly. Compared with control subjects, rats with conditioned response renewal had increased tone‐evoked fluorodeoxyglucose uptake in the auditory system (auditory cortex, medial geniculate, inferior colliculus and lateral lemniscal nuclei), as well as somatic and visceral sensory nuclei (external cuneate, spinal trigeminal, solitary tract and vestibular nuclei). In addition, perirhinal cortex, anterior lateral hypothalamus and ventrolateral periaqueductal gray showed conditioned response renewal effects. Brain–behavior correlations indicated that the activity of the external cuneate nucleus strongly predicted the conditioned response in the renewal group. It is suggested that context‐dependent fear renewal is associated with (1) tone‐evoked activation of the excitatory conditioned stimulus representation in the auditory system, (2) associative activation of the unconditioned stimulus representation in somatic and visceral sensory nuclei in the absence of the unconditioned stimulus, and (3) neural activation of the perirhinal cortex, hypothalamus and periaqueductal gray. These findings support Pavlov's stimulus‐substitution theory as a neural mechanism contributing to the renewal effect.
Periodicity and frequency coding in human auditory cortex
Authors: Hall Deborah A. , Edmondson‐Jones A. Mark , Fridriksson Julius 
Published: December 2006

AbstractUnderstanding the neural coding of pitch and frequency is fundamental to the understanding of speech comprehension, music perception and the segregation of concurrent sound sources. Neuroimaging has made important contributions to defining the pattern of frequency sensitivity in humans. However, the precise way in which pitch sensitivity relates to these frequency‐dependent regions remains unclear. Single‐frequency tones also cannot be used to test this hypothesis as their pitch always equals their frequency. Here, temporal pitch (periodicity) and frequency coding were dissociated using stimuli that were bandpassed in different frequency spectra (centre frequencies 800 and 4500 Hz), yet were matched in their pitch characteristics. Cortical responses to both pitch‐evoking stimuli typically occurred within a region that was also responsive to low frequencies. Its location extended across both primary and nonprimary auditory cortex. An additional control experiment demonstrated that this pitch‐related effect was not simply caused by the generation of combination tones. Our findings support recent neurophysiological evidence for a cortical representation of pitch at the lateral border of the primary auditory cortex, while revealing new evidence that additional auditory fields are also likely to play a role in pitch coding.
Reduced presynaptic efficiency of excitatory synaptic transmission impairs LTP in the visual cortex of BDNF‐heterozygous mice
Authors: Abidin Ismail , Köhler Torben , Weiler Elke , Zoidl Georg , Eysel Ulf T. , Lessmann Volkmar , Mittmann Thomas 
Published: December 2006

AbstractThe neurotrophin brain‐derived neurotrophic factor (BDNF) plays an important role in neuronal survival, axonal and dendritic growth and synapse formation. BDNF has also been reported to mediate visual cortex plasticity. Here we studied the cellular mechanisms of BDNF‐mediated changes in synaptic plasticity, excitatory synaptic transmission and long‐term potentiation (LTP) in the visual cortex of heterozygous BDNF‐knockout mice (BDNF+/–). Patch‐clamp recordings in slices showed an ∼ 50% reduction in the frequency of miniature excitatory postsynaptic currents (mEPSCs) compared to wild‐type animals, in the absence of changes in mEPSC amplitudes. A presynaptic impairment of excitatory synapses from BDNF+/– mice was further indicated by decreased paired‐pulse ratio and faster synaptic fatigue upon prolonged repetitive stimulation at 40 Hz. In accordance, presynaptic theta‐burst stimulation (TBS) failed to induce LTP at layer IV to layers II‐III synapses during extracellular field‐potential recordings in BDNF+/– animals. Changes in postsynaptic function could not be detected, as no changes were observed in either the amplitudes of evoked EPSCs, the ratios of AMPA : NMDA currents or the kinetics of evoked AMPA and NMDA EPSCs. In line with this observation, an LTP pairing paradigm that relies on direct postsynaptic depolarization under patch‐clamp conditions could be induced successfully in BDNF+/– animals. These data suggest that a chronic reduction in the expression of BDNF to nearly 50% attenuates the efficiency of presynaptic glutamate release in response to repetitive stimulation, thereby impairing presynaptically evoked LTP in the visual cortex.