bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional response to nitrosative stress in Saccharomyces cerevisiae
Authors: Horan Susannah , Bourges Ingrid , Meunier Brigitte 
Published: May 2006

AbstractNitric oxide and NO‐derived species (RNS) are defence molecules with broad antimicrobial activity. Microorganisms have developed strategies to sense RNS and counteract their damaging effects. We used Saccharomyces cerevisiae, harbouring a deletion of YHB1 that encodes the main NO scavenger enzyme, to study consequences of RNS exposure on whole‐genome transcriptional response. The expression of > 700 genes was altered on RNS treatment. No major role for ROS‐scavenging enzymes was found, and the respiratory chain, the main site of ROS production, had only minor involvement in the RNS‐induced stress. The changes were generally transient and also found after treatment with the respiratory inhibitor myxothiazol. However, 117 genes showed a persistent response that was not observed after myxothiazol treatment. Of these, genes of the glutathione and DNA repair systems, iron homeostasis and transport were found to be upregulated. Severe repression of genes of respiratory chain enzymes was observed. Many of these genes are known to be regulated by the transcription factor Hap1p, suggesting that RNS might interfere with Hap1p activity. We showed also that Msn2/4p and Yap1p, key regulators of the response to general stress and oxidative stress, respectively, played a role in mediating the RNS‐induced response. Copyright © 2006 John Wiley & Sons, Ltd.
The effect of hunger level on predation dynamics in the spiderNesticodes rufipes: a functional response study
Authors: Rossi Marcelo N. , Reigada Carolina , Godoy Wesley A.C. 
Published: May 2006

AbstractIt is well known that a predator has the potential to regulate a prey population only if the predator responds to increases in prey density and inflicts greater mortality rates. Predators may cause such density‐dependent mortality depending on the nature of the functional and numerical responses. As spiders are usually faced with a shortage of prey, the killing behavior of the spiderNesticodes rufipesat varying densities ofMusca domesticawas examined here through laboratory functional response experiments where spiders were deprived of food for 5 (well‐fed) or 20 days (hungry). An additional laboratory experiment was also carried out to assess handling time of spiders. The number of prey killed by spiders over 24‐ and 168‐h periods of predator–prey interaction was recorded. Logistic regression analyses revealed the type II functional response for both well‐fed and hungry spiders. We found that the lower predation of hungry spiders during the first hours of experimentation was offset later by an increase in predation (explained by estimated handling times), resulting in similarity of functional response curves for well‐fed and hungry spiders. It was also observed that the higher number of prey killed by well‐fed spiders over a 24‐h period of spider–prey interaction probably occurred due to their greater weights than hungry spiders. We concluded that hungry spiders may be more voracious than well‐fed spiders only over longer time periods, since hungry spiders may spend more time handling their first prey items than well‐fed spiders.
Soil composition affects the nesting behavior of blue‐tailed bee‐eaters (Merops philippinus) on Kinmen Island
Authors: Yuan Hsiao‐Wei , Wang Ming‐Kuang , Chang Wen‐Lian , Wang Lee‐Ping , Chen Yue‐Min , Chiou Chyi‐Rong 
Published: May 2006

AbstractThe blue‐tailed bee‐eater (Merops philippinus) is a summer migrant that breeds on Kinmen Island, located off the west coast of Taiwan, about 5 km from the southern coast of mainland China. The aim of this study was to investigate why blue‐tailed bee‐eaters build their nests in sandy loam and sandy clay loam, but not in clay loam. Soil chemical and physical properties, and mineralogical composition were measured for the different soil types. Clay loam had a significantly lower pH, Na, and base saturation than did sandy loam or sandy clay loam. Clay loam had a significantly higher N, cation‐exchange capacity (CEC), K, and free iron (Fed) and aluminum oxide (Ald) contents than the other soil types. Clay loam had significantly lower sand and higher clay content, and higher bulk density and penetration resistance than the other soil types. The correlation coefficients (r 2) between penetration resistance and Fed, Ald, and clay contents were 0.997, 0.848, and 0.779, respectively. Soil strength and compaction are important criteria for bee‐eaters’ nesting‐site selection. The lower pH of clay loam would enhance the exchangeable Al and acidity, further increasing the soil aggregation. Thus, it might prevent the bee‐eaters from excavating nesting burrows.
Algal toxin yessotoxin signalling pathways involve immunocyte mussel calcium channels
Authors: Malagoli Davide , Casarini Livio , Ottaviani Enzo 
Published: May 2006

AbstractA fragment of a putative L‐type Ca2+ channel has been identified by molecular biology experiments in immunocytes from the mussel Mytilus galloprovincialis. Using the cell permeable and Ca2+‐specific fluorochrome FURA 2‐AM, we have demonstrated that the algal toxin yessotoxin (YTX) is able to increase intracellular Ca2+ concentration in M. galloprovincialis immunocytes. The YTX effect on Ca2+ increase is inhibited by the L‐type Ca2+ channel inhibitor, verapamil, which is cAMP‐ and cGMP‐dependent, but PKA‐ and nitric oxide‐independent. On the basis of these observations, a possible role for YTX as a potential disturber of mussel immune efficiency is suggested.
CD38 expression enhances sensitivity of lymphoma T and B cell lines to biochemical and receptor‐mediated apoptosis
Authors: Gregorini Armando , Tomasetti Marco , Cinti Cristina , Colomba Daniela , Colomba Stella 
Published: May 2006

AbstractCD38 has been widely characterised both as an ectoenzyme and as a receptor. In the present paper, we investigated the role of CD38 as possible modulator of apoptosis. CD38‐positive (CD38+) and negative (CD38−) fractions, obtained by sorting CD38+ cells from lymphoma T (Jurkat) and lymphoma B (Raji) and by transfecting lymphoma LG14 and myeloid leukemia K562 cell lines, were used. Cellular subpopulations were exposed to different triggers (H2O2, UV‐B, α‐TOS and hrTRAIL) and the extent of apoptosis was determined by Annexin V‐FITC/PI assay. Our data showed that, in lymphoma cells, propensity to apoptosis was significantly linked to CD38 expression and that, remarkably, such response was independent of the nature of the trigger used. Inhibition of CD38 expression by antisense oligonucleotides treatment resulted in CD38‐silenced fractions which were as prone to apoptosis as CD38− ones. Notably, susceptibility of K562 to apoptosis‐inducing challenges was not affected by CD38 expression.
Can heterotopic gastric mucosa present as globus pharyngeus?
Authors: Lancaster J L , Gosh S , Sethi R , Tripathi S 
Published: May 2006

We present a series of four patients presenting with symptoms leading to a provisional diagnosis of globus pharyngeus. On further investigation, they were all found to have small areas of abnormal mucosa in either their hypopharynx or proximal oesophagus, which on biopsy were reported as containing gastric-type mucosa. Following anti-reflux treatment, all patients eventually reported a cessation of symptoms. All but one patient was followed up with repeat endoscopies. We highlight the fact that biopsies reporting gastric epithelium at this anatomical site are in keeping with the diagnosis of heterotopic gastric mucosa. We review the literature and report the high incidence and natural history of this condition.Heterotopic gastric mucosa can only be diagnosed on endoscopy and is easily missed, even during such an investigation. We raise the question of whether this condition may be one of a number of factors in the aetiology of globus pharyngeus.
Observational study of bone-anchored hearing aid infection rates using different post-operative dressings
Authors: Doshi J , Karagama Y , Buckley D , Johnson I 
Published: May 2006

Introduction: Avoidance of infection at the implant site is a crucial element to the success of bone-anchored hearing aid (BAHA) implantation. However, little evidence exists to suggest the best post-operative wound dressing to use.Material and methods: We report our experience with 160 consecutive BAHA patients, using four types of post-operative BAHA wound dressing (Tri-adcortyl®, Mepitel®, Allevyn®, and Acticoat 7® with Allevyn). Patients were reviewed at week one and week two post-operatively. Infection was defined as a positive wound swab culture or evidence of cellulitis at the BAHA site.Results: Post-operative BAHA infection rates were 16 per cent, 50 per cent, 10 per cent and 5 per cent, for each of the four dressings respectively, and the mean number of additional visits to wound care clinic were 1.5, 3.7, one and 0.4, respectively.Discussion: Acticoat 7 with Allevyn produced the lowest infection rate and thus became the dressing of choice for our BAHA programme.
Firth's early phonological views and prosodic analysis: a reply to Coleman (2004)
Authors: Battaner-Moro Elena 
Published: May 2006

In a previous issue of this journal, John Coleman (2004) reviewed the written-up version of a poster I presented at the 15th International Congress of Phonetic Sciences, Barcelona (Battaner-Moro 2003, henceforth BM). The aim of the poster was to discuss the evolution of Firthian prosodic analysis. In his review, Coleman derives from it ‘an ignorance or a neglect of Firth's publications prior to 1948' on my part (p. 211). He focusses his criticisms on the following three statements:
‘Firth never did prosodic analysis.’‘There is a complete absence of programmatic work in Firth's works.’‘Prosodic analysis was developed by the members of the London School and not at all by John Firth.’
Towards an integrated model of expertise in medical imaging – Part II Three dimensions of expert practice
Authors: Yielder Jill 
Published: May 2006

The nature of professional expertise has been widely debated in the literature. However it has been examined primarily from a dichotomy of perspectives – either from an experiential or a cognitive focus, without the attempt to integrate these, and other aspects of expertise into an integrated and coherent model. This article series explicates the nature of professional expertise specifically in the field of medical imaging. It represents a section of the outcomes of a larger study which formulated and illustrated an integrated model of professional expertise also applicable to other professions. It has been written in two parts, Part I of which overviews the study and presents two of the five aspects of expertise identified. Part II presents the other three aspects.The study used data gathered from interviews and critical incident recording from expert medical imaging practitioners in Auckland, New Zealand, over an extended time frame.Findings showed that while expertise is situated in the context of practice, it incorporates several dimensions working together in an integrated, seamless fashion through the medium of the individual practitioner. The participants identified and illustrated that expertise in medical imaging is a synthesis of a particular knowledge base, the cognitive processes, personality and internal processes of the practitioner. It manifests through, and builds on, interpersonal relationships with patients and other professionals, and is expressed through the actual doing of professional practice. It is through the reflexive examination of practice and management of change that professionals may transform these integrated aspects into the qualitative state of expertise.
The career of radiography: information on the web
Authors: Glennie E. , Kirby A. 
Published: May 2006

Purpose: To establish whether or not the quantity and quality of information available on the internet about the career of diagnostic radiography is of a good or satisfactory standard.Methods: Four search engines with four different search terms were used and the top twenty hits for each group were read. The applicable sites were scored to determine the quality of each site.Results: Only 12% (37) of the 320 sites read were applicable. Out of the 37 there were 4 sites that gained a good score from the scoring sheet and therefore were classed as high quality, but 21 out of 37 sites did gain half marks or over.Conclusions: In conclusion, the quantity and quality of sites about the career of radiography was not of a satisfactory standard and more attention from both the government and professional bodies is needed if the profession is to gain attention and the staff shortage problem is to be solved.
Progress in Neurotherapeutics and Neuropsychopharmacology 2007
Authors: Cummings Jeffrey L. 
Published: May 2006

ABSTRACTThere continues to be progress in neurotherapeutics and neuropsychopharmacology with each advancing year. Production of new molecular entities (NME's) remains small, but advances are being made in repurposing agents and extending their indications, obtaining more safety and tolerability data in long term and extension studies, introducing novel trial methodologies that provide insight into how to best to conduct trials and how best to treat diseases, and developing new formulations that improve adherence and decrease the barriers to patient compliance. Advances in how to test potential disease-modifying agents in patients with progressive neurological illnesses is advancing. Promising biomarkers have been identified in some neurological diseases.
Identification of norharman as the cytotoxic compound produced by the sponge (Hymeniacidon perleve)‐associated marine bacterium Pseudoalteromonas piscicida and its apoptotic effect on cancer cells
Authors: Zheng Li , Yan Xiaojun , Han Xiaotian , Chen Haimin , Lin Wei , Lee Frank S. C. , Wang Xiaoru 
Published: May 2006

Marine invertebrates harbour a wealth of micro‐organisms in their bodies. Most of these micro‐organisms can catabolize antibiotic compounds as chemical‐defence compounds. These compounds not only play an important protective role for their producer and for their hosts, but also have high potential in medicinal applications. In order to discover natural anticancer products, 29 marine bacterial strains have been isolated from the sponge Hymeniacidon perleve, samples of which were collected from the intertidal zone during low tide off Nanji island in Eastern China. By means of a cytotoxicity bioassay, one strain, NJ6‐3‐1, with significant cytotoxic activity, was selected for culture in a 30‐litre fermentation tank. The major cytotoxic compound in the metabolites of NJ6‐3‐1, separated by means of a bioassay‐guided fractionation process, has been identified as norharman (a β‐carboline alkaloid) by electron‐impact MS and NMR analyses. Norharman showed cytotoxicity towards both the HeLa cervical‐cancer cell line and the BGC‐823 stomach‐cancer cell line, with an IC50 of 5 μg/ml. Several methods were used to study the mechanism by which norharman is cytotoxic to HeLa cells. By means of an Acridine Orange/ethidium bromide dual‐staining assay, condensation of chromatin was observed. A TUNEL (terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labelling) assay showed degradation of DNA. Flow‐cytometric analysis indicated that norharman could arrest cells at the G2/M phase of the cell cycle. These results demonstrate the cytotoxic mechanism of norharman involves the induction of apoptosis in HeLa cells.
Rho/ROCK‐dependent pseudopodial protrusion and cellular blebbing are regulated by p38 MAPK in tumour cells exhibiting autocrine c‐Met activation
Authors: Jia Zongjian , Vadnais Julie , Lu Michael L. , Noël Josette , Nabi Ivan R. 
Published: May 2006

Background information. The c‐Met‐dependent, β‐actin‐rich, blebbed pseudopodia of MSV‐MDCK‐INV (invasive Moloney‐sarcoma‐virus‐transformed Madin—Darby canine kidney) cells are induced by Rho/ROCK (Rho kinase) activation, and are morphologically distinct from flat extended lamellipodia.Results. Microtubules were shown to extend to these actin‐rich pseudopodial domains, and microtubule depolymerization by nocodazole treatment resulted in progressive cellular blebbing, initiating in the pseudopodial domains and resulting in transient cellular rounding and blebbing after 30 min. The blebbing response was dependent on autocrine HGF (hepatocyte growth factor) activation of c‐Met and prevented by inhibition of RhoA, ROCK and p38 MAPK (p38 mitogen‐activated protein kinase), but not ERK (extracellular‐signal‐regulated kinase) or PI3K (phosphoinositide 3‐kinase). Phospho‐p38 MAPK was present in pseudopodia, localizing activation of this signalling pathway to this protrusive membrane structure. In serum‐starved cells, LPA (lysophosphatidic acid) activation of RhoA induced p38 MAPK‐dependent pseudopodial protrusions, and inhibition of p38 MAPK prevented pseudopodial protrusion and displacement of MSV‐MDCK‐INV cells. MSV‐MDCK‐INV cells exhibited intermittent blebbing and rounding, which may represent an integral part of their motile behaviour.Conclusions. The localized activation of an autocrine HGF/c‐Met loop regulates Rho/ROCK activation of p38 MAPK signalling to stimulate both membrane blebbing and pseudopod formation.
Subcellular translocation signals regulate Geminin activity during embryonic development
Authors: Boos Aline , Lee Amy , Thompson Dominic M. , Kroll Kristen L. 
Published: May 2006

Background information. Geminin (Gem) is a protein with roles in regulating both the fidelity of DNA replication and cell fate during embryonic development. The distribution of Gem is predominantly nuclear in cells undergoing the cell cycle. Previous studies have demonstrated that Gem performs multiple activities in the nucleus and that regulation of Gem activation requires nuclear import in at least one context. In the present study, we defined structural and mechanistic features underlying subcellular localization of Gem and tested whether regulation of the subcellular localization of Gem has an impact on its activity in cell fate specification during embryonic development.Results. We determined that nuclear localization of Gem is dependent on a bipartite NLS (nuclear localization signal) in the N‐terminus of Xenopus Gem protein. This bipartite motif mapped to a Gem N‐terminal region previously shown to regulate neural cell fate acquisition. Microinjection into Xenopus embryos demonstrated that import‐deficient Gem was incapable of modulating ectodermal cell fate, but that this activity was rescued by fusion to a heterologous NLS. Cross‐species comparison of Gem protein sequences revealed that the Xenopus bipartite signal is conserved in many non‐mammalian vertebrates, but not in mammalian species assessed. Instead, we found that human Gem employs an alternative N‐terminal motif to regulate the protein's nuclear localization. Finally, we found that additional mechanisms contributed to regulating the subcellular localization of Gem. These included a link to Crm1‐dependent nuclear export and the observation that Cdt1, a protein in the pre‐replication complex, could also mediate nuclear import of Gem.Conclusions. We have defined new structural and regulatory features of Gem, and showed that the activity of Gem in regulating cell fate, in addition to its cell‐cycle‐regulatory activity, requires control of its subcellular localization. Our data suggest that rather than being constitutively nuclear, Gem may undergo nucleocytoplasmic shuttling through several mechanisms involving distinct protein motifs. The use of multiple mechanisms for modulating Gem subcellular localization is congruent with observations that Gem levels and activity must be stringently controlled during cell‐cycle progression and embryonic development.
Context-specific infinite mixtures for clustering gene expression profiles across diverse microarray dataset
Authors: Liu X. , Sivaganesan S. , Yeung K. Y. , Guo J. , Bumgarner R. E. , Medvedovic Mario 
Published: May 2006

AbstractMotivation: Identifying groups of co-regulated genes by monitoring their expression over various experimental conditions is complicated by the fact that such co-regulation is condition-specific. Ignoring the context-specific nature of co-regulation significantly reduces the ability of clustering procedures to detect co-expressed genes due to additional ‘noise’ introduced by non-informative measurements.Results: We have developed a novel Bayesian hierarchical model and corresponding computational algorithms for clustering gene expression profiles across diverse experimental conditions and studies that accounts for context-specificity of gene expression patterns. The model is based on the Bayesian infinite mixtures framework and does not require a priori specification of the number of clusters. We demonstrate that explicit modeling of context-specificity results in increased accuracy of the cluster analysis by examining the specificity and sensitivity of clusters in microarray data. We also demonstrate that probabilities of co-expression derived from the posterior distribution of clusterings are valid estimates of statistical significance of created clusters.Availability: The open-source package gimm is available atContact: Mario.Medvedovic@uc.eduSupplementary information:
Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
Authors: Huang De-Shuang , Zheng Chun-Hou 
Published: May 2006

Abstract
Motivation: Microarrays are capable of determining the expression levels of thousands of genes simultaneously. One important application of gene expression data is classification of samples into categories. In combination with classification methods, this technology can be useful to support clinical management decisions for individual patients, e.g. in oncology. Standard statistic methodologies in classification or prediction do not work well when the number of variables p (genes) far too exceeds the number of samples n. So, modification of existing statistical methodologies or development of new methodologies is needed for the analysis of microarray data.
Results: This paper proposes a new method for tumor classification using gene expression data. In this method, we first employ independent component analysis to model the gene expression data, then apply optimal scoring algorithm to classify them. Further speaking, this approach can first make full use of the high-order statistical information contained in the gene expression data. Second, this approach also employs regularized regression models to handle the situation of large numbers of correlated predictor variables. Finally, the predictive models are developed for classifying tumors based on the entire gene expression profile. To show the validity of the proposed method, we apply it to classify four DNA microarray datasets involving various human normal and tumor tissue samples. The experimental results show that the method is efficient and feasible.
Availability: Matlab scripts are available on request.
Contact: dshuang@iim.ac.cn