bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quality of life after surgery for benign disease of the parotid gland
Authors: Erkan A N , Yavuz H , Ozer C , Ozer F , Ozluoglu L 
Published: May 2007

AbstractObjective:To evaluate quality of life after surgery for benign neoplastic disease of the parotid gland.Patients and methods:A quality of life questionnaire, which was created from the Hebrew version of the University of Washington Quality of Life prototype, was applied to 55 patients who underwent surgery for benign neoplastic parotid disease. All patients were examined in Baskent University Adana Teaching and Medical Research Center, where all except 10 subjects (who responded by phone) completed the quality of life questionnaire.Results:The highest overall score was 96.3 indicating no salivary fistula. Only one patient complained of salivary secretion through the wound scar. The lowest overall score was 59.5 indicating loss of sensation. Although no post-surgical pain was reported by 32 (58 per cent) patients, 16 (29 per cent) patients reported a post-surgical change in their appearance. Scarring and surgical site depression were reported by 26 (47 per cent) and 17 patients (30 per cent), respectively. Facial nerve impairment was reported by seven patients (13 per cent) during the early post-operative period; these patients recovered from that impairment. The only significant statistical correlations were noted between general health and gender, and between post-surgical pain and gender. There was not any statistical correlation between all data and age, tumour type and education level.Conclusion:The general status of patients who have undergone surgery for a benign parotid neoplasm can be assessed with a quality of life questionnaire. Patients' post-surgical quality of life can be improved by the correct choice of surgical approach and reconstructive method.
Is there an association between blood group O and epistaxis?
Authors: Reddy V M , Daniel M , Bright E , Broad S R , Moir A A 
Published: May 2007

AbstractIntroduction:Blood group O is associated with lower expression of von Willebrand factor suggesting a relative bleeding tendency. A lower admission rate for epistaxis among Asians compared with Caucasians has also been noted, with one explanation being higher prevalence of blood group O among Caucasians. This study investigates whether blood group O is over-represented in patients admitted with epistaxis.Methods:A retrospective study was conducted, using computerised hospital in-patient and blood bank databases to identify Caucasians admitted with epistaxis between January 2000 and December 2005 inclusive. The control group consisted of 500 consecutive patients who had a primary total hip arthroplasty and 500 consecutive patients who gave birth within the delivery suite.Results:1261 Caucasians admitted with epistaxis were identified. Among epistaxis patients, 50.44 per cent were blood group O but among the control group this was 45.10 per cent (chi-square testp = 0.008).Conclusion:Blood group O appears over-represented in Caucasian patients admitted with epistaxis, compared with the control population, raising the possibility that blood group O is a risk factor for epistaxis.
Genomic plasticity in prokaryotes: the case of the square haloarchaeon
Authors: Cuadros-Orellana Sara , Martin-Cuadrado Ana-Belen , Legault Boris , D'Auria Giuseppe , Zhaxybayeva Olga , Papke R Thane , Rodriguez-Valera Francisco 
Published: May 2007

Abstract
The variability in genome content among closely related strains of prokaryotes has been one of the most remarkable discoveries of genomics. One way to approach the description of this so-called pan-genome is to compare one reference strain genome with metagenomic sequences from the environment. We have applied this approach to one extreme aquatic habitat, saturated brines in a solar saltern. The genome of Haloquadratum walsbyi strain DSM 16790 was compared to an environmental metagenome obtained from the exact site of its isolation. This approach revealed that some regions of the strain genome were scarcely represented in the metagenome. Here we have analyzed these genomic islands (GI) in the genome of DSM 16790 and compared them with the complete sequence of some fosmids from the environmental library. Two of the islands, GI 2 and GI 4, overlapped with two large guanine and cytosine (GC)-rich regions that showed evidence of high variability through mobile elements. GI 3 seemed to be a phage or phage-remnant acquired by the reference genome, but not present in most environmental lineages. Most differential gene content was related to small molecule transport and detection, probably reflecting adaptation to different pools of organic nutrients. GI 1 did not possess traces of mobile elements and had normal GC content. This island contained the main cluster of cell envelope glycoproteins and the variability found was different from the other GIs. Rather than containing different genes it consisted of homologs with low similarity. This variation might reflect a phage evasion strategy.
Public computer surfaces are reservoirs for methicillin-resistant staphylococci
Authors: Kassem Issmat I , Sigler Von , Esseili Malak A 
Published: May 2007

Abstract
The role of computer keyboards used by students of a metropolitan university as reservoirs of antibiotic-resistant staphylococci was determined. Putative methicillin (oxacillin)-resistant staphylococci isolates were identified from keyboard swabs following a combination of biochemical and genetic analyses. Of 24 keyboards surveyed, 17 were contaminated with staphylococci that grew in the presence of oxacillin (2 mg l−1). Methicillin (oxacillin)-resistant Staphylococcus aureus (MRSA), -S. epidermidis (MRSE) and -S. hominis (MRSH) were present on two, five and two keyboards, respectively, while all three staphylococci co-contaminated one keyboard. Furthermore, these were found to be part of a greater community of oxacillin-resistant bacteria. Combined with the broad user base common to public computers, the presence of antibiotic-resistant staphylococci on keyboard surfaces might impact the transmission and prevalence of pathogens throughout the community.
Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays
Authors: Wu Chunlei , Zhao Haitao , Baggerly Keith , Carta Roberto , Zhang Li 
Published: May 2007

AbstractMotivation: In microarray experiments, probe design is critical to the specific and accurate measurement of target concentrations. Current designs select suitable probes through in silico scanning of transcriptome/genome based on first principles. However, due to lack of tools, the observed microarray data have not been used to assess the performance of individual probes to provide feedback to improve future designs.Result: In this study, we describe a probe performance assessment method based on the concordance of the observed signals from probes that share common targets. Using this method, we found that probes containing multiple guanines in a row (G-stacks) have abnormal binding behavior compared with other probes, both in gene expression assays and genotyping assays using Affymetrix microarrays. These probes are less likely to covary with other probes that interrogate the same genes. Moreover, we found that these probes are much more likely to produce outliers when fitting the observed signals according to the positional dependent nearest neighbor model, which gives reasonable estimates of binding affinity for most other probes. These results suggest that probes containing G-stacks tend to have increased cross hybridization signals and reduced target-specific hybridization signals, presumably due to multiplex binding forming G-quartet structures. Our findings are expected to be useful in microarray design and data analysis.Availability: URL: http://odin.mdacc.tmc.edu/~zhangli/PerfectMatch/contains the computer program for calculating correlations of neighboring probes.Contact: lzhangli@mdanderson.orgSupplementary information: Bioinformatics online or http://odin.mdacc.tmc.edu/~zhangli/G-stack
Mining co-regulated gene profiles for the detection of functional associations in gene expression data
Authors: Gyenesei Attila , Wagner Ulrich , Barkow-Oesterreicher Simon , Stolte Etzard , Schlapbach Ralph 
Published: May 2007

AbstractMotivation: Association pattern discovery (APD) methods have been successfully applied to gene expression data. They find groups of co-regulated genes in which the genes are either up- or down-regulated throughout the identified conditions. These methods, however, fail to identify similarly expressed genes whose expressions change between up- and down-regulation from one condition to another. In order to discover these hidden patterns, we propose the concept of mining co-regulated gene profiles. Co-regulated gene profiles contain two gene sets such that genes within the same set behave identically (up or down) while genes from different sets display contrary behavior. To reduce and group the large number of similar resulting patterns, we propose a new similarity measure that can be applied together with hierarchical clustering methods.Results: We tested our proposed method on two well-known yeast microarray data sets. Our implementation mined the data effectively and discovered patterns of co-regulated genes that are hidden to traditional APD methods. The high content of biologically relevant information in these patterns is demonstrated by the significant enrichment of co-regulated genes with similar functions. Our experimental results show that the Mining Attribute Profile (MAP) method is an efficient tool for the analysis of gene expression data and competitive with bi-clustering techniques.Contact: ulrich.wagner@fgcz.ethz.chSupplementary information: Supplementary data and an executable demo program of the MAP implementation are freely available at http://www.fgcz.ch/publications/map
Exploring sequence-structure relationships in the tyrosine kinome space: functional classification of the binding specificity mechanisms for cancer therapeutics
Authors: Verkhivker Gennady M. 
Published: May 2007

AbstractMotivation: Evolutionary and structural conservation patterns shared by more than 500 of identified protein kinases have led to complex sequence-structure relationships of cross-reactivity for kinase inhibitors. Understanding the molecular basis of binding specificity for protein kinases family, which is the central problem in discovery of cancer therapeutics, remains challenging as the inhibitor selectivity is not readily interpreted from chemical proteomics studies, neither it is easily discernable directly from sequence or structure information. We present an integrated view of sequence-structure-binding relationships in the tyrosine kinome space in which evolutionary analysis of the kinases binding sites is combined with computational proteomics profiling of the inhibitor–protein interactions. This approach provides a functional classification of the binding specificity mechanisms for cancer agents targeting protein tyrosine kinases.Results: The proposed functional classification of the kinase binding specificities explores mechanisms in which structural plasticity of the tyrosine kinases and sequence variation of the binding-site residues are linked with conformational preferences of the inhibitors in achieving effective drug binding. The molecular basis of binding specificity for tyrosine kinases may be largely driven by conformational adaptability of the inhibitors to an ensemble of structurally different conformational states of the enzyme, rather than being determined by their phylogenetic proximity in the kinome space or differences in the interactions with the variable binding-site residues. This approach provides a fruitful functional linkage between structural bioinformatics analysis and disease by unraveling the molecular basis of kinase selectivity for the prominent kinase drugs (Imatinib, Dasatinib and Erlotinib) which is consistent with structural and proteomics experiments.Contact: verk@ku.edu or gverkhiv@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online.
READING WALTER BENJAMIN'S CONCEPT OF THE RUIN IN VICTOR HUGO'S
NOTRE-DAME DE PARIS
Authors: Stephens Bradley 
Published: May 2007

Abstract

Walter Benjamin's readings of modernity are repeatedly strained by the tension he identifies between demystification and the drive towards the mythic. How are we to awaken from ‘ideological dream-states’ and engage with an indeterminate reality without positing the unity of an integrated whole to begin with? I suggest that Hugo's
Notre-Dame de Paris
yields a compelling perspective on this dilemma. Hugo never denies the lure of myths in his novel, simply their possibility, recognising that they remain as irresistible as they are incredible. He energises the opposition between artifice and actuality, proposing that man can only oscillate between both the ideal and the real, even though he cannot overcome their incompatibility. This dynamic is observed upon Notre-Dame herself. Her hybrid edifice bears the mark of bygone values, yet as such stands as a monument to the transformative sweep of time. In turn, Hugo teases yet simultaneously refuses any absolute narrative viewpoint, stressing both the limitations of language and his own subjectivity. What makes this reading less an exercise of intellectual indulgence than a matter of critical urgency is Benjamin's widely overlooked attraction towards Hugo as a modernist writer. Indeed, the novel deploys two key tools of Benjamin's thinking: allegory, to expose meaning as arbitrary, and the ruin, which preserves the image of a history that is no more. I explore Hugo's representation of both novel and cathedral as realms of contrast, not integration, so as to make a productive return to the dilemmas Benjamin encounters.
EXHIBITING PAIN: SOPHIE CALLE'S
DOULEUR EXQUISE
Authors: Jordan Shirley Ann 
Published: May 2007

Abstract

This article focuses on the relationship between the subjective and the collective in the work of project artist Sophie Calle through a ‘virtual visit’ to her mixed-media installation
Douleur exquise
(1984–2003). Through detailed analysis of the intricate systems of narrative in and between the installation's three parts, it assesses the contribution of Calle's project to two phenomena which are of central importance to cultural production in France and beyond at the start of the twenty-first century. The first is a fascination with
l'intime
and with punctures or shifts in the public/private boundary, and the article explores how
Douleur exquise
develops Calle's customary handling of autofictional tensions and the exposure of self and other. The second is our obsessive memorial imperative, a cultural development to which Calle has not yet formally been linked. The article argues that Calle's installation demonstrates an anthropological interest in cultural constructions of suffering, mourning practices and memorial artefacts. Finally, it suggests that
Douleur exquise
self-consciously invites us to respond to it as a new kind of monument, one appropriate to process-driven project art. This, the article defines as a ‘soft monument’.
First Report of Damping-Off and Leaf Spot Caused by Cylindrocladium scoparium on Different Accessions of Bottlebrush Cuttings in Italy
Authors: Polizzi G. , Vitale A. , Aiello D. , Dimartino M. A. , Parlavecchio G. 
Published: May 2007

In May of 2006, approximately 10,000 cuttings of bottlebrushes (Callistemon cvs. Laevis, Hannah Ray, Kings Park Special, Masotti Mini Red, and Rose Opal with either C. viminalis (Soland. ex Gaertn.) Cheel. [excluded] or C. citrinus (Curtis) Skeels as one parent) grown in a nursery in eastern Sicily (Italy) exhibited severe disease symptoms including damping-off, leaf spots, and collar and root rot. Initially, the infections were detected on approximately 30% of the cuttings, but by late September 2006, 70% of the plants had symptoms. A Cylindrocladium sp. was consistently isolated from the diseased portions of plants onto potato dextrose agar. To determine the species, single-conidial isolates of the fungus were cultured on carnation leaf agar (CLA) for 7 days at 25°C with 12 h of light/dark conditions. Only the mycelia and spores growing on the carnation leaves were examined with a light microscope, and the isolates were identified as Cylindrocladium scoparium Morgan (teleomorph Calonectria morganii Crous, Alfenas & M.J. Wingf.) on the basis of their pyriform to broadly ellipsoidal terminal vesicles, conidiophore branching pattern, and conidia (1). In addition, the ability of the colonies to mate with South African tester strains of C. scoparium (2,3) confirmed the identification. Koch's postulates were fulfilled by inoculating 10 cuttings for each bottlebrush accession with a spore suspension (105 conidia per ml) of one isolate of the pathogen (DISTEF-GCs7) obtained from 14-day-old single-spore colonies grown on CLA at 24°C under fluorescent cool white lights with 12 h of light/dark. Following inoculation, all plants were maintained in plastic bags in a growth chamber at 25 ± 1°C and 90 to 95% relative humidity. The same number of cuttings was used as a control. Damping-off, crown root rot, and leaf spots symptoms identical to those observed in the nursery appeared within 5 to 20 days. No symptoms were detected on the control plants. C. scoparium was reisolated from the artificially infected tissues. The isolate, used in the pathogenicity proof, was deposited at the Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures (Accession No. CBS 120930). The presence of C. scoparium was detected for the first time in Italy on mastic tree in 2005 (3). To our knowledge, this is the first report of C. scoparium on bottlebrush in Italy and it represents the first information about the susceptibility of these Callistemon cultivar accessions to the fungus and confirms the spread of the pathogen in Sicilian ornamental nurseries. References: (1) P. W. Crous. Taxonomy and Pathology of Cylindrocladium (Calonectria) and Allied Genera. The American Phytopathological Society, St. Paul MN, 2002. (2) P. W. Crous and M. J. Wingfield. Mycotaxon 51:341, 1994. (3) G. Polizzi et al. Plant Dis. 90:1110, 2006.
First Report of Phytoplasmas Associated with the Degeneration Syndrome of Artichoke in Catalonia (Spain)
Authors: Batlle A. , Sabaté J. , Laviña A. 
Published: May 2007

Spain is the second largest producer of artichoke (Cynara scolymus L.) in the world with 230,000 tons produced annually. The region of Catalonia, located in northeast Spain, has 3,500 ha dedicated to this crop. Low yield and degeneration anomalies are widespread problems in the Mediterranean area. The degeneration syndrome results in curled leaves and late development of capitulum. The association of this syndrome with different viruses such as Artichoke degeneration virus (ADV), Artichoke latent virus (ALV), Broad bean wilt virus (BBWV), Cucumber mosaic virus (CMV), and many others was not conclusive. Other studies indicated that this phenomenon could be related to a regression of the cultivar toward the species of origin, the wild cardoon (C. cardunculus L. var. sylvestris). The distribution of degenerated plants in the principal artichoke-growing areas of Catalonia together with the presence of plants with normal and degenerated tissues in the same plant suggested the presence of phytoplasmas. Samples from 30 symptomatic and 30 asymptomatic plants of cv. Blanca de Tudela were collected in February of 2006 from different areas of Catalonia and analyzed by PCR amplification of phytoplasma DNA. DNA for PCR analyses was prepared from leaf petioles and midribs according to the Ahrens and Seemüller procedure (1). Nested-PCR was carried out with rRNA primer pairs P1/P7 and fU5/rU3 (2,3). Alternatively, nested-PCR, with primers Tuf 1 f/r in the first step and Tuf AY f/r in the second, amplifying a DNA fragment of the elongation gene Tu of the phytoplasmas belonging to Aster yellows and stolbur groups was conducted (4). Results showed a high correlation between presence of symptoms and phytoplasma detection. Phytoplasmas were detected in 100% of the symptomatic plants (30 of 30) and only in one of the asymptomatic plants. The restriction fragment length profiles of Tuf AY amplicons with HpaII showed two different patterns, the most important belonging to the aster yellows (16SrI) group phytoplasma and the other to the stolbur (16SrXII) group phytoplasma. To our knowledge, this is the first time that phytoplasmas have been detected in artichoke and associated with degeneration of this crop. References: (1) U. Ahrens and E. Seemüller. Phytopathology 82:828, 1992. (2) S. Deng and C. Hiruki. J. Microbiol. Methods 14:53, 1991. (3) K. H. Lorenz et al. Phytopathology 85:771, 1995. (4) B. Schneider et al. Microbiology 143:3381, 1997.
Immunogold labelling of tumour cells during NK/target cell interactions
Authors: ZANYK M. J. , BANERJEE D. , HEARN S. A. 
Published: May 2007

Using a system of immunocolloidal gold labelling, we have monitored the expression and distribution of transferrin receptors (TfRs) within the K562 cell line, during NK/target cell interactions. An indirect method of immunolabelling was used to effectively immunolabel tumour cells without disrupting the natural effectontarget interactions. Successful localization of TfRs demonstrates the potential of the described technique for discerning antigenic distribution of other cell:cell interactions.Immunolabelling has also provided a useful method for demonstrating receptor down‐regulation within NK target cells, as a proposed cause of reduced receptor expression by TPA‐treated cells. Following 30 and 60 min incubation periods with TPA, approximately 15 and 30%, respectively, of the gold/antibody complexes were relocated from the surface membrane to an intracellular location within endocytotic vesicles. The demonstration of receptor down‐regulation is important as a proposed cause of TPA‐induced tumour cell resistance to NK‐mediated cytolysis.
Cytological grading of breast carcinoma—a feasible proposition?
Authors: HUNT C. M. , ELLIS I. O. , ELSTON C. W. , LOCKER A. , PEARSON D. , BLAMEY R. W. 
Published: May 2007

Fine needle aspiration cytology (FNAC) of the breast is widely used in the diagnosis of breast carcinoma. In some centres this is sometimes the only diagnostic procedure performed prior to definitive treatment. A grading system based on cytology would be helpful in the selection of patients for appropriate therapy. The aim of this study, therefore, was to devise such a system for grading breast carcinoma based on cytological features alone.The features assessed were the degree of cell clustering, nuclear pleomorphism, nuclear diameter, the presence of multiple, easily visible nucleoli and necrosis. Cytological features were compared to the histological grade of the tumours following excision. Discriminant analysis showed that the features with the closest correlation with histological grade were nuclear diameter, nuclear pleomorphism and the presence of nucleoli. A scoring system based on these three parameters enabled the classification of tumours into high and low cytological grades which showed a close correlation with histological grade.