bluuebunny/crossref_metadata_2025_split huggingface dataset:
10 Catechizing, Education, and Reading Practices
Authors: Holmes Andrew R. 
Published: February 2007

Abstract
This chapter begins by outlining how catechizing and visitation was conducted, and the impact evangelicalism had upon pastoral efficiency in the Synod of Ulster. Section two examines the provision of education through Sunday and day schools, noting the symbiotic relationship between the supply of opportunities for education on the part of voluntary societies and the demands of the laity. The chapter concludes by examining in general terms the reading practices of Presbyterians, what and how they read, and the impact evangelicalism had upon the demand for, and supply of, certain types of reading material.
8 Conclusion: Legitimizing Democracy and Democratizing Legitimacy
Authors: Deveaux Monique 
Published: February 2007

AbstractIn this concluding chapter, the main arguments of the book are briefly recapped and extended. Democratic legitimacy is defended as a core norm for plural, liberal democratic societies, one which should also guide deliberations about contested cultural practices. This chapter also makes the case for expanding the scope of what we understand as (legitimating) democratic activity, so as to include not only formal, institutionalized democratic practices and spaces, but also informal, everyday expressions of democratic agency. Such a shift should enable us to better see and foster women’s capacities and opportunities to resist, affirm, transform, and reinvent their cultural traditions and arrangements, which speak directly to the issue of the legitimacy of those traditions.
The Aims of Enquiry
Authors: Gaukroger Stephen 
Published: February 2007

AbstractThis chapter builds on the previous two to offer a more integrated account of the intersections between questions of truth, justification, objectivity, and legitimacy. The origins of philosophy in Plato's Socratic dialogues are represented as a struggle between sophism and philosopher, where the difference lies in a commitment to uncovering the truth. This concern can be traced through to the early modern period, but the 17th century witnessed a shift from notions of truth to notions of objectivity and impartiality as a guide for natural philosophical enquiry.
Corpuscularianism and the Rise of Mechanism
Authors: Gaukroger Stephen 
Published: February 2007

AbstractFrom the early 17th century onwards, the dominant natural philosophy was mechanism: the view that all explanations must ultimately take the form of a reduction to a very economical range of features at the micro-corpuscularian level, e.g., in the paradigm case, size, speed, and direction of motion. Gassendi and Beeckman offered very different routes to mechanism: Gassendi's was a legitimatory programme that focuses on matter theory, whereas Beeckman's approach comes directly out of mechanics, which it attempted to transform into natural philosophy by fleshing it out in micro-corpuscularian terms. The crucial stage in mechanism comes with the rise of concerted attempts to integrate mechanics and matter theory into a consistent whole, at the same time offering the mechanism so devised as a complete theory of the cosmos, and it is the approaches of Hobbes, whose closest affinities are with Gassendi, and Descartes, whose closest affinities are with Beeckman, that bring out most clearly what is at issue here.
OMWSA: detection of DNA repeats using moving window spectral analysis
Authors: Du Liping , Zhou Hongxia , Yan Hong 
Published: February 2007

AbstractSummary: Repetitive DNA sequences play paramount biological roles, such as gene variation and regulatory functions on gene expressions. Until now, detection of various kinds of DNA repeats accurately is still an open problem. In this article, we propose a new method and a visualization tool for detecting DNA repeats in a 2D plane of location and frequency by using optimized moving window spectral analysis. The spectrogram can display the general distribution of repetitive sequences while showing the repeat period, length and location without any prior knowledge. Experimental results demonstrate that our method is accurate and robust even under the condition of excessive mutating and interleaving.Availability: Available on http://www.hy8.com/~tec/sw01/omwsa01.zip.Contact: h.yan@cityu.edu.hkSupplementary information: Supplementary data are available at Bioinformatics online.
PROMALS: towards accurate multiple sequence alignments of distantly related proteins
Authors: Pei Jimin , Grishin Nick V. 
Published: February 2007

AbstractMotivation: Accurate multiple sequence alignments are essential in protein structure modeling, functional prediction and efficient planning of experiments. Although the alignment problem has attracted considerable attention, preparation of high-quality alignments for distantly related sequences remains a difficult task.Results: We developed PROMALS, a multiple alignment method that shows promising results for protein homologs with sequence identity below 10%, aligning close to half of the amino acid residues correctly on average. This is about three times more accurate than traditional pairwise sequence alignment methods. PROMALS algorithm derives its strength from several sources: (i) sequence database searches to retrieve additional homologs; (ii) accurate secondary structure prediction; (iii) a hidden Markov model that uses a novel combined scoring of amino acids and secondary structures; (iv) probabilistic consistency-based scoring applied to progressive alignment of profiles. Compared to the best alignment methods that do not use secondary structure prediction and database searches (e.g. MUMMALS, ProbCons and MAFFT), PROMALS is up to 30% more accurate, with improvement being most prominent for highly divergent homologs. Compared to SPEM and HHalign, which also employ database searches and secondary structure prediction, PROMALS shows an accuracy improvement of several percent.Availability: The PROMALS web server is available at: http://prodata.swmed.edu/promals/Contact: jpei@chop.swmed.eduSupplementary information: Supplementary data are available at Bioinformatics online.
A simulation test bed for hypotheses of genome evolution
Authors: Beiko Robert G. , Charlebois Robert L. 
Published: February 2007

AbstractMotivation: Microbial genomes undergo evolutionary processes such as gene family expansion and contraction, variable rates and patterns of sequence substitution and lateral genetic transfer. Simulation tools are essential for both the generation of data under different evolutionary models and the validation of analytical methods on such data. However, meaningful investigation of phenomena such as lateral genetic transfer requires the simultaneous consideration of many underlying evolutionary processes.Results: We have developed EvolSimulator, a software package that combines non-stationary sequence and gene family evolution together with models of lateral genetic transfer, within a customizable birth–death model of speciation and extinction. Here, we examine simulated data sets generated with EvolSimulator using existing statistical techniques from the evolutionary literature, showing in detail each component of the simulation strategy.Availability: Source code, manual and other information are freely available at www.bioinformatics.org.au/evolsimContact: beiko@cs.dal.caSupplementary information: Supplementary data are available at Bioinformatics online.
CopyCat : cophylogenetic analysis tool
Authors: Meier-Kolthoff Jan P. , Auch Alexander F. , Huson Daniel H. , Göker Markus 
Published: February 2007

AbstractSummary: We have developed the software CopyCat which provides an easy and fast access to cophylogenetic analyses. It incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies. CopyCat offers various features, such as the creation of customized host–parasite association data and the computation of phylogenetic host/parasite trees based on the NCBI taxonomy.Availability: CopyCat and its manual are freely available at http://www-ab.informatik.uni-tuebingen.de/software/copycat.Contact: auch@informatik.uni-tuebingen.deSupplementary information: Results of the real-world example can be found at http://www-ab.informatik.uni-tuebingen.de/software/copycat or Bioinformatics online.
Ontology development for biological systems: immunology
Authors: Diehl Alexander D. , Lee Jamie A. , Scheuermann Richard H. , Blake Judith A. 
Published: February 2007

AbstractSummary: We recently implemented improvements to the representation of immunology content of the biological process branch of the Gene Ontology (GO). The aims of the revision were to provide a comprehensive representation of immunological processes and to improve the organization of immunology related terms in the GO to match current concepts in the field of immunology. With these improvements, the GO will better reflect current understanding in the field of immunology and thus prove to be a more valuable resource for knowledge representation in gene annotation and analysis in the areas of immunology related to genomics and bioinformatics.Availability: http://www.geneontology.orgContact: adiehl@informatics.jax.org
Mechanisms of cardiac protection from ischemia/reperfusion injury: a role for caveolae and caveolin‐1
Authors: Patel Hemal H. , Tsutsumi Yasuo M. , Head Brian P. , Niesman Ingrid R. , Jennings Michelle , Horikawa Yousuke , Huang Diane , Moreno Ana L. , Patel Piyush M. , Insel Paul A. , Roth David M. 
Published: February 2007

ABSTRACTCaveolae, small invaginations in the plasma membrane, contain caveolins (Cav) that scaffold signaling molecules including the tyrosine kinase Src. We tested the hypothesis that cardiac protection involves a caveolin‐dependent mechanism. We usedin vitroandin vivomodels of ischemia‐reperfusion injury, electron microscopy (EM), transgenic mice, and biochemical assays to address this hypothesis. We found that Cav‐1 mRNA and protein were expressed in mouse adult cardiac myocytes (ACM). The volatile anesthetic, isoflurane, protected ACM from hypoxia‐induced cell death and increased sarcolemmal caveolae. Hearts of wild‐type (WT) mice showed rapid phosphorylation of Src and Cav‐1 after isoflurane and ischemic preconditioning. The Src inhibitor PP2 reduced phosphorylation of Src (Y416) and Cav‐1 in the heart and abolished isoflurane‐induced cardiac protection in WT mice. Infarct size (percent area at risk) was reduced by isoflurane in WT (30.5±4vs.44.2±3,n=7,P<0.05) but not Cav‐1−/−mice (46.6±5vs.41.7±3,n=7). Cav‐1−/−mice exposed to isoflurane showed significant alterations in Src phosphorylation and recruitment of C‐terminal Src kinase, a negative regulator of Src, when compared to WT mice. The results indicate that isoflurane modifies cardiac myocyte sarcolemmal membrane structure and composition and that activation of Src and phosphorylation of Cav‐1 contribute to cardiac protection. Accordingly, therapies targeted to post‐translational modification of Src and Cav‐1 may provide a novel approach for such protection.—Patel, H. H., Tsutsumi, Y. M., Head, B. P., Niesman, I. R., Jennings, M., Horikawa, Y. Huang, D., Moreno, A. L., Patel, P. M., Insel, P. A., Roth, D. M. Mechanisms of cardiac protection from ischemia/reperfusion injury: a role for caveolae and caveolin‐1.FASEB J.21, 1565–1574 (2007)
Laser Eustachian Tuboplasty: Two‐Year Results
Authors: Poe Dennis S. , Grimmer J. Fredrik , Metson Ralph 
Published: February 2007

AbstractObjective/Hypothesis: Laser eustachian tuboplasty (LETP) combined with appropriate medical management will eliminate the chronic presence of middle ear effusions in selected patients.Methods: The study population consisted of 13 adults with otitis media with effusion (OME). Patients underwent slow‐motion video endoscopy to identify the location and extent of surgical resection. A diode or argon laser was used to vaporize areas of hypertrophic mucosa and submucosa along the cartilaginous eustachian tube. Patients were evaluated at 6, 12, and 24 months. Successful outcome was defined as absence of OME. Patients with evidence of reflux disease or allergic rhinitis were treated with medical therapy before surgery and throughout the follow‐up period as indicated.Results: LETP combined with medical management eliminated OME in 36% (4 of 11) of patients at 6 months, 40% (4 of 10) at 1 year, and 38% (3 of 8) at 2 years. Failure of LETP correlated with presence of laryngopharyngeal reflux (P = .01) or allergic disease (P = .05) for the results at 1 year but not at 2 years.Conclusions: LETP combined with appropriate medical management may be an effective treatment in select patients with chronic persistent eustachian tube dysfunction. A controlled trial with a larger number of subjects will be necessary to determine the efficacy of LETP and identify those factors predictive of successful outcome.
Protein Expression of the Tumor Suppressors p16INK4A and p53 and Disease Progression in Recurrent Respiratory Papillomatosis
Authors: Pham Truc T. , Ongkeko Weg M. , An Yi , Yi Eunhee S. 
Published: February 2007

AbstractBackground: Recurrent respiratory papillomatosis (RRP) is a benign condition that rarely metastasizes as invasive squamous cell carcinoma. Although this disease is associated with human papillomavirus, the role of this virus in tumorigenesis is unclear.Objectives: The aim of this study is to assess the involvement of the tumor suppressors P16INK4A and p53 in RRP tumor progression.Design: Immunohistochemistry of p16INK4A and p53 was performed on biopsies of recurrent squamous papillomas and invasive lesions in nine patients.Results: Twenty biopsies were graded as papillomas (RP), three as papillomas with high‐grade dysplasia/carcinoma in situ (HGD/CIS), and two as invasive squamous cell carcinoma (SCCA). Forty‐five percent of RP and 60% of HGD/CIS/SCCA expressed p16INK4A. Fifty percent of RP and 100% of HGD/CIS/SCCA expressed p53. The difference in the frequency of p53‐positive staining between HGD/CIS and SCCA (100% of tissues examined) and RP (50% of tissues examined) approached statistical significance. Neither p16INK4A nor p53 was predictive of invasive transformation.Conclusions: Expression of p16INK4A, which is a surrogate for the tumor suppressor retinoblastoma (Rb), did not immediately lead to invasive disease. There is no correlation between disease severity of RRP and level of p16INK4A.
Extracranial Head and Neck Schwannomas: A Clinical Analysis of 33 Patients
Authors: Zhang Hao , Cai Changping , Wang Shili , Liu Huiru , Ye Yanfen , Chen Xueming 
Published: February 2007

AbstractObjective: To study the clinical features, diagnosis, and management of the extracranial head and neck schwannomas.Study Design: Retrospective study.Methods: The clinical data of 33 patients with schwannoma of the head and neck from 1996 to 2006 were studied retrospectively.Results: Extracranial head and neck schwannomas usually presented as solitary and well‐demarcated lesions with insidious course. Although benign, the lesion can cause secondary symptoms, such as nasal obstruction, dysphasia, and hoarseness, relevant to location of the lesion. Fine needle aspiration cytology, computed tomography scans, and magnetic resonance imaging may provide limited implications in the diagnosis of schwannomas, whereas postoperative pathologic examination establishes the final diagnosis.Conclusions: Complete surgical excisions with appropriate approaches have proven to be efficient and successful in the treatment of head and neck schwannomas.
War, Politics, and Voice: The Vocal Fold Paralysis of George Orwell
Authors: Sulica Lucian 
Published: February 2007

AbstractBackground: In 1936, like many individuals who felt the menace of fascism, George Orwell traveled to Spain to lend his support to the cause of the Republic, battling a right‐wing coup. Spain, during its Civil War, was an eye‐opening experience for him, yielding insights that allowed, and even compelled him to write Animal Farm and 1984. Spain was also a close brush with death. In May of 1937, in a trench on a windswept ridge near Huesca, Orwell was shot through the neck by a sniper, leaving him with a paralyzed vocal fold.Design: A thorough review of firsthand accounts of Orwell's injury and subsequent care was made. These are presented in the context of current knowledge of ballistics, penetrating neck trauma, and vocal fold paralysis.Results and Conclusion: Orwell survived largely because of the nature of his wounding with a high‐velocity jacketed military round. His recovery followed a course in many ways typical for patients with vocal fold paralysis. His writings leave us a unique and extraordinary account of the experience of being shot, of the medical care of the day, of the handicap of paralytic dysphonia, and of survival and heroism under extraordinary circumstances.
Effect of Surgical Treatment on Lymphoproliferation in Advanced Supraglottic Laryngeal Cancer
Authors: Conti‐Freitas Luiz Carlos , Foss‐Freitas Maria Cristina , Mamede Rui Celso Martins , Foss Norma Tiraboschi 
Published: February 2007

AbstractObjectives: The capacity of cell immunity to act against tumor cells has been presented as a decisive influence in the prognosis of patients with cancer. The aim of this study was to evaluate lymphoproliferation in nonadherent peripheral blood cell cultures of patients with advanced supraglottic laryngeal cancer.Study Design: Fourteen patients with advanced supraglottic laryngeal cancer were studied prospectively. Lymphoproliferation was quantified by adding 3H‐thymidine and measured in counts/minute using liquid scintillation spectrometry. Based on the ratio between stimulated and baseline cultures, the proliferation index was calculated before and 236 ± 18 days after the surgery.Results: Lymphoproliferation was lower in patients than in healthy controls (P = .01) in the preoperative as well as in the late postoperative period (P = .006 and P = .02, respectively). However, there was no change from preoperative to late postoperative.Conclusion: Pre‐ and postoperative results show that patients with advanced supraglottic laryngeal cancer present lymphoproliferation diminished before the surgery, and in the late postoperative period, there was no recovery of immune capacity evaluated by lymphoproliferation measurement.
Distress in Spouses and Patients After Treatment for Head and Neck Cancer
Authors: Verdonck‐de Leeuw Irma M. , Eerenstein Simone E. , Van der Linden Mecheline H. , Kuik Dirk J. , de Bree Remco , Leemans C. Rene 
Published: February 2007

AbstractBackground: The objective of this study is to obtain insight into distress in spouses and patients treated for head and neck cancer.Methods: Forty‐one patient–spouse pairs completed the Hospital Anxiety and Depression Scale (HADS). Inclusion criteria included curative treatment for head and neck cancer. Exclusion criteria were visiting the clinic without a spouse, bad news at the routine follow‐up examination, diseases causing cognitive dysfunction, and poor understanding of the Dutch language. Next to the HADS, the assessment protocol included age, gender, health status, coping strategy, time since cancer treatment, tumor stage and site, treatment modality, functional and social impairment, and caregiving burden.Results: A clinical level of distress was noted in 20% of the spouses and in 27% of the patients. Distress in spouses was related to the presence of a feeding tube in patients, a passive coping style, less vitality, and a disrupted daily life schedule resulting from caregiving. Distress in patients was related to the presence of a feeding tube, speech and swallowing problems, less social contacts, a passive style of coping, and nonexpression of emotions.Conclusion: Distress is often present in spouses and patients treated for head and neck cancer. Routine screening for psychologic distress is recommended.
Effects of Halofuginone on Fibrosis Formation Secondary to Experimentally Induced Subglottic Trauma
Authors: Ertuğrul E. Eylem , Cincik Hakan , Dogru Salim , Cekin Engin , Berber Ufuk , Gungor Atila , Poyrazoğlu I. Ethem 
Published: February 2007

AbstractObjective: The aim of the study was to assess the antifibrotic effect of systemically applied halofuginone after subglottic injury.Materials and Methods: After standardized trauma to subglottic area, rats were divided into two groups: a study group that received treatment and a control group that did not. The rats were treated with 0.1 mg/kg/day intraperitoneal halofuginone injection for 30 days. The larynx specimens were examined histopathologically under light microscope for epithelization, inflammation, necrosis, and fibrosis.Results: The fibrosis indexes of the treated group were significantly less than those of the control group (P < .01).Conclusions: Systemically applied halofuginone hydrobromide decreases fibrosis/scar tissue formation secondary to experimentally induced acute subglottic trauma.
Reduction and S-Carboxymethylation of Proteins: Microscale Method
Authors: Simpson Richard J. 
Published: February 2007

INTRODUCTIONReduction and alkylation of microscale amounts of protein (10-50 μg) require special attention. Classical methods for desalting and dialysis should be avoided due to large sample losses. Adding a small quantity of detergent to the protein solution during all manipulations can also reduce protein loss. This protocol describes a procedure for reduction and S-carboxymethylation of low-microgram amounts of protein. Samples are reduced and alkylated in small volumes (<200 μl) in the presence of detergent and desalted (and concentrated) by RP-HPLC in yields of >90%.
Subcellular Localization of GUS- and GFP-Tagged Proteins in Onion Epidermal Cells
Authors: von Arnim Albrecht 
Published: February 2007

INTRODUCTIONRecombinant tags (i.e., reporter proteins) offer an excellent alternative to antibodies for determining the subcellular localization of proteins. The most user-friendly tags are the ß-glucuronidase (GUS) reporter enzyme from Escherichia coli and fluorescent proteins derived primarily from the green fluorescent protein (GFP) of the jellyfish Aequorea victoria. GUS is useful primarily as a tag to address nuclear localization, whereas GFP is more versatile. Moreover, GFP is detectable directly in living cells, whereas GUS is only detected indirectly by staining of fixed tissue. This may lead to artifacts or it may obscure problems with protein solubility. In this protocol, protein localization is routinely assayed after particle-mediated transient transformation of onion epidermal cells. With this method it can be determined rapidly whether a given fusion protein is active, and preliminary targeting data can be obtained.
Transgene Expression in Regenerated Roots: Figure 1.
Authors: Malamy Jocelyn 
Published: February 2007

INTRODUCTIONThis procedure, which uses a root transformation protocol, provides a rapid method for assessing gene expression in Arabidopsis roots. It is useful for testing promoter:reporter gene constructs, for expressing genes, the overexpression of which is lethal in whole plants, and for transforming the roots of plants that are recalcitrant to conventional transformation techniques. The protocol has been used successfully with Ws, No-0, and RLD ecotypes.
Transient Expression in Protoplasts
Authors: Katagiri Fumiaki 
Published: February 2007

INTRODUCTIONThe study of transient gene expression provides a useful complement to the study of stably transformed plants. Transient assays offer a quick method of testing the effects of genes, using either phenotypic, molecular, or biochemical readouts. Transient assays based on Agrobacterium-mediated transformation of leaf explants have been described for other plant species, but it is not known how well these assays work in Arabidopsis. Alternatives include transient expression in protoplasts or in regenerating roots. The latter is especially suitable for investigating root-specific gene function.