bluuebunny/crossref_metadata_2025 huggingface dataset:
Science and Modernity
Authors: Gaukroger Stephen
Published: February 2007

This introductory chapter sets out the basic ideas that motivate the book. First, science in the West from the early modern era onwards has developed in a very distinctive way that distinguishes it from earlier forms of scientific activity, which had traditionally exhibited a pattern of slow, irregular, intermittent growth that alternated with substantial periods of stagnation. Second, the emergence of a scientific culture reveals that the distinctive features of scientific culture are not sui generis, something to be elucidated merely through reflection on the supposed nature of science. Rather, they have arisen as a result of specific and contingent challenges that have emerged since the 17th century, challenges which are generated in an intellectual culture that goes beyond developments internal to particular scientific programmes. Third, this distinctiveness of Western scientific practice and its cultural and cognitive standing derives in large part from the legitimatory aspirations that it takes on in the course of the 17th century.
Augustinian Synthesis to Aristotelian Amalgam
Authors: Gaukroger Stephen
Published: February 2007

In the 13th century, natural philosophy changed status from an enterprise of marginal significance into one that formed the principal point of entry into the understanding of the world and our place in it. This was effected through the introduction of Aristotelianism into the University of Paris at the beginning of the 13th century where, in its new role as a philosophical foundation for systematic theology, natural philosophy became the single point of entry into natural knowledge of the natural and supernatural realms. The compatibility of Aristotelian natural philosophy was never wholly resolved, however, and matters came to a head at the beginning of the 16th century on the question of the immortality of the soul, where Aristotelian natural philosophy and Christian teaching were in conflict. In many ways, this conflict, which centred around the work of Pomponazzi, provided a model for the later Copernicanism disputes.
Renaissance Natural Philosophies
Authors: Gaukroger Stephen
Published: February 2007

There were three competing movements in 16th-century natural philosophy. Platonism was revived in the 15th century and Ficino and Patrizi attempted, unsuccessfully, to provide an alternative to Aristotelianism. The renaissance naturalism of the 16th century aimed to secure autonomy for natural philosophy by presenting an increasingly radicalized naturalistic picture of the natural realm. Late scholastic textbook writers, from the late 16th to the early 17th centuries, attempted, unsuccessfully, to reform and systematize Christianized Aristotelianism to meet the new demands placed on it by developments in natural philosophy.
Reconstructing Natural Philosophy
Authors: Gaukroger Stephen
Published: February 2007

Many of the perceived failures of Aristotelian natural philosophy in the late 16th and early 17th centuries were put down to his conception of method. In fact, both defenders of Aristotle and his critics took his method of presentation for a method of discovery, the former trying to establish how it could act as a method of discovery, and the latter replacing it with something new. Bacon attempted to provide a radical alternative to Aristotelianism, though in some respects, it was locked into the same programme as Aristotle. Of more immediate significance were disputes over the hypothetical standing of Copernicanism, disputes in which Kepler and Galileo were major players.
Experimental Natural Philosophy
Authors: Gaukroger Stephen
Published: February 2007

This chapter deals with experimental philosophy, as represented in Gilbert on magnetism, Hobbes on the air pump, and Newton on the production of the spectrum. It is shown that experimental philosophy differs from mechanism in quite radical ways. In particular, it has explanatory success but in apparently very localized domains, and it construes causation not in terms of underlying causes but in terms of causes acting at the same level. Its difference from mechanism is manifest in the contrast between Descartes' and Newton's accounts of the production of the spectrum: Descartes provides a fully geometrical account of the separation of coloured rays, but then shifts into a different register, a qualitative and speculative one in attempting to provide a micro-corpuscularian account of the physical basis of colour production; Newton manages to account for the spectrum without leaving the phenomenal geometricized level, eschewing any recourse to ‘underlying’ causes.
The Quantitative Transformation of Natural Philosophy
Authors: Gaukroger Stephen
Published: February 2007

This chapter looks at attempts to quantify natural phenomena and, in particular, forces. Early efforts along these lines — notably by Galileo and Descartes — tried to extrapolate from statics to dynamics, whereas later in the century kinematics, as pioneered by Galileo, was taken as the model by Huygens and Newton. Newton, building on Hooke's suggestion that planetary orbits were not a given and unquestionable feature of the cosmos, was able to show how such orbits were generated and clarify the dynamics needed to account for the processes involved. In this way, mechanics, traditionally excluded from natural philosophy in the Aristotelian sense, is transformed not only into a natural-philosophical discipline, but into what was in many respects the natural-philosophical discipline par excellence.
An ensemble approach to microarray data-based gene prioritization after missing value imputation
Authors: Hua Dong , Lai Yinglei
Published: February 2007

Motivation: Microarrays have been widely used to discover novel disease related genes. Some types of microarray, such as cDNA arrays, usually contain a considerable portion of missing values. When missing value imputation and gene prioritization are sequentially conducted, it is necessary to consider the distribution space of prioritization scores due to the existence of missing values. We propose an ensemble approach to address this issue. A bootstrap procedure enables us to generate a resample multivariate distribution of the prioritization scores and then to obtain the expected prioritization scores.

Results: We used a published microarray two-sample data set to illustrate our approach. We focused on the following issues after missing value imputation: (i) concordance of gene prioritization and (ii) control of true and false positives. We compared our approach with the traditional non-ensemble approach to missing value imputation. We also evaluated the performance of non-imputation approach when the theoretical test distribution was available. The results showed that the ensemble imputation approach provided clearly improved performances in the concordance of gene prioritization and the control of true/false positives, especially when sample sizes were about 5–10 per group and missing rates were about 10–20%, which was a common situation for cDNA microarray studies.

Availability: The Matlab codes are freely available at http://home.gwu.edu/~ylai/research/Missing.

Contact:  ylai@gwu.edu
CGHcall: calling aberrations for array CGH tumor profiles
Authors: van de Wiel Mark A. , Kim Kyung In , Vosse Sjoerd J. , van Wieringen Wessel N. , Wilting Saskia M. , Ylstra Bauke
Published: February 2007

Summary: CGHcall achieves high calling accuracy for array CGH data by effective use of breakpoint information from segmentation and by inclusion of several biological concepts that are ignored by existing algorithms. The algorithm is validated for simulated and verified real array CGH data. By incorporating more than three classes, CGHcall improves detection of single copy gains and amplifications. Moreover, it allows effective inclusion of chromosome arm information.

Availability: An R-package (GUI), a manual and an example data set are available at http://www.few.vu.nl/~mavdwiel/CGHcall.html.

Contact:  mark.vdwiel@vumc.nl

Supplementary information: Supplementary data are available at Bioinformatics online.
5‐Fluorouracil Ointment for the Treatment of Otitis Media With Effusion
Authors: Kanemaru Shin‐ichi , Nakamura Tatsuo , Yamashita Masaru , Magrfov Akhmar , Omori Koichi , Ito Juichi
Published: February 2007

Objectives/Hypothesis: Our aim was to evaluate the combined effect of 5‐fluorouracil (5‐FU) and myringotomy for the treatment of otitis media with effusion (OME). OME is usually treated with medication, myringotomy, or insertion of a ventilation tube (VT). Except for VT insertion, however, treatment effects are short‐lived. VT insertion has numerous sequelae: increased susceptibility to infection, large perforation of the tympanic membrane, cholesteatoma, and eventual hearing deterioration. We estimated the depressant action of 5‐FU on normal cell proliferation in vitro. In addition, clinically, we assessed whether 5‐FU has the potential to prolong the effect of myringotomy.

Study Design: An in vitro study and a clinical study were conducted.

Materials and Methods: In study I, fibroblasts harvested from the peritoneum of three green fluorescent protein transgenic mice were cultured with different doses of 5‐FU. After 2 weeks, their proliferation rates were compared. In study II, patients (54 males, 47 females) were selected randomly from a group of patients with intractable OME. Myringotomy with or without a single dose of 5‐FU ointment (approximately 0.10–0.30 mg) was performed in group I (n = 64) and group II (n = 37), respectively. The natural closure rates of the tympanic membrane were assessed in both groups.

Results: In vitro, 5‐FU inhibited the growth of fibroblasts in a dose‐dependent manner. The average time to tympanic membrane closure was 20.5 days in group I and 8.1 days in group II. No adverse events were observed in either group.

Conclusions: Topical application of 5‐FU ointment is useful in prolonging the effect of myringotomy. 5‐FU ointment therapy is easy, safe, and cost‐effective and may be of wide application.
Smaragdicoccus niigatensis gen. nov., sp. nov., a novel member of the suborder Corynebacterineae
Authors: Adachi Kyoko , Katsuta Atsuko , Matsuda Satoru , Peng Xue , Misawa Norihiko , Shizuri Yoshikazu , Kroppenstedt Reiner M. , Yokota Akira , Kasai Hiroaki
Published: February 2007

A polyphasic taxonomic approach was applied to determine the taxonomic position of a hydrocarbon-degrading actinomycete, strain Hou_blueT, which was isolated from soil samples collected from an oil spring in Niigata, Japan. The results of 16S rRNA and gyrB gene sequence comparisons indicated that strain Hou_blueT represented a novel lineage in the suborder Corynebacterineae. Colonies were malachite green-like in colour on 1/10 trypticase soy agar and the cell morphology was coccoid in all growth phases. The cell-wall diamino acid and sugar indicated chemotype IV and variation A1γ. The sugars of the peptidoglycan were glycolated. The polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and some unspecified glycolipids. The organism contained two novel cyclic forms of menaquinone, smaragdiquinone A-8(H4, ω-cycl) and smaragdiquinone B-8(H4, dicycl). The major fatty acids were cis-9-18 : 1 (34.46 %) and 16 : 0 (25.1 %). Small amounts of 10-methyl-branched fatty acids were also present (10-methyl-17 : 0, 0.17 %), but not tuberculostearic acid (10-methyl-18 : 0), which has been shown to be present in all nocardiae. Gas-chromatographic analysis of the mycolic acid revealed a carbon-chain length of C43–C49. The DNA G+C content was 63.7 mol%. On the basis of phenotypic and phylogenetic distinctness, the organism is proposed to represent a novel genus and species, Smaragdicoccus niigatensis gen. nov., sp. nov., with the type strain Hou_blueT (=MBIC 06267T=DSM 44881T).
Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK
Authors: Chelo Ivo M. , Zé-Zé Líbia , Tenreiro Rogério
Published: February 2007

The phylogenetic structure of the Leuconostoc–Oenococcus–Weissella clade was evaluated by comparison of 16S rRNA gene, dnaA, gyrB, rpoC and dnaK sequence analysis. Phylogenies obtained with the different genes were in overall good agreement and a well-supported, almost fully resolved phylogenetic tree was obtained when the combined data were analysed in a Bayesian approach. A rapid basal diversification of the three genera is suggested. Evolutionary rates of the 16S rRNA gene in these genera seem to be different and specifically related to the evolution of this group, revealing the importance of this sequence in the constitution of the present taxonomy, but preventing its straightforward use in phylogenetic inference.
Pedobacter panaciterrae sp. nov., isolated from soil in South Korea
Authors: Yoon Min-Ho , Ten Leonid N. , Im Wan-Taek , Lee Sung-Taik
Published: February 2007

A Gram-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 042T, was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was positive for catalase and oxidase, but negative for gelatinase and production of indole and H2S. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were summed feature 4 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH; 35.7 %), iso-C15 : 0 (24.3 %) and iso-C17 : 0 3-OH (11.6 %). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 042T fell within the radiation of the cluster comprising Pedobacter species. On the basis of 16S rRNA gene sequence similarities, the phylogenetically closest recognized species of the genus Pedobacter to strain Gsoil 042T included Pedobacter heparinus DSM 2366T (98.1 %), Pedobacter africanus DSM 12126T (97.8 %) and Pedobacter caeni LMG 22862T (97.2 %). The 16S rRNA gene sequence similarity with other recognized species of the genus Pedobacter was less than 96.1 %. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness between strain Gsoil 042T and its phylogenetically closest neighbours was less than 43 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 042T should be classified as representing a novel species in the genus Pedobacter, for which the name Pedobacter panaciterrae sp. nov. is proposed. The type strain is Gsoil 042T (=KCTC 12594T=LMG 23400T).
Halomonas indalinina sp. nov., a moderately halophilic bacterium isolated from a solar saltern in Cabo de Gata, Almería, southern Spain
Authors: Cabrera Antonio , Aguilera Margarita , Fuentes Susana , Incerti Claudia , Russell Nick J. , Ramos-Cormenzana Alberto , Monteoliva-Sánchez Mercedes
Published: February 2007

A moderately halophilic bacterium, strain CG2.1T, isolated from a solar saltern at Cabo de Gata, a wildlife reserve located in the province of Almería, southern Spain, was subjected to a polyphasic taxonomic study. This organism was an aerobic, motile, Gram-negative rod that produced orange-pigmented colonies. Strain CG2.1Twas able to grow at salinities of 3–25 % (w/v) and at temperatures of 15–40 °C. The pH range for growth was 5–9. Strain CG2.1Twas a heterotroph capable of utilizing various carbohydrates as carbon sources. The organism reduced nitrate and showed phenylalanine deaminase activity. The major fatty acids were C18 : 1ω7c, C16 : 0and C19 : 0cycloω8c. The DNA G+C content was 60.9 mol%. On the basis of the phenotypic and phylogenetic data, strain CG2.1Tappeared to be a member of the genusHalomonasand clustered closely withHalomonas marisflavi(97.1 % 16S rRNA gene sequence similarity). However, the level of DNA–DNA relatedness between the novel isolate and the most closely relatedHalomonasspecies was low. On the basis of these data, strain CG2.1Trepresents a novel member of the genusHalomonas, for which the nameHalomonas indalininais proposed. The type strain is CG2.1T(=CECT 5902T=LMG 23625T).
Multiple sequence alignment: In pursuit of homologous DNA positions
Authors: Kumar Sudhir , Filipski Alan
Published: February 2007

DNA sequence alignment is a prerequisite to virtually all comparative genomic analyses, including the identification of conserved sequence motifs, estimation of evolutionary divergence between sequences, and inference of historical relationships among genes and species. While it is mere common sense that inaccuracies in multiple sequence alignments can have detrimental effects on downstream analyses, it is important to know the extent to which the inferences drawn from these alignments are robust to errors and biases inherent in all sequence alignments. A survey of investigations into strengths and weaknesses of sequence alignments reveals, as expected, that alignment quality is generally poor for two distantly related sequences and can often be improved by adding additional sequences as stepping stones between distantly related species. Errors in sequence alignment are also found to have a significant negative effect on subsequent inference of sequence divergence, phylogenetic trees, and conserved motifs. However, our understanding of alignment biases remains rudimentary, and sequence alignment procedures continue to be used somewhat like benign formatting operations to make sequences equal in length. Because of the central role these alignments now play in our endeavors to establish the tree of life and to identify important parts of genomes through evolutionary functional genomics, we see a need for increased community effort to investigate influences of alignment bias on the accuracy of large-scale comparative genomics.
Large-scale identification of novel transcripts in the human genome
Authors: Peters Brock A. , St. Croix Brad , Sjöblom Tobias , Cummins Jordan M. , Silliman Natalie , Ptak Janine , Saha Saurabh , Kinzler Kenneth W. , Hatzis Christos , Velculescu Victor E.
Published: February 2007

Although the sequencing of the human genome has been completed, the number and identity of genes contained within it remains to be fully determined. We used LongSAGE to analyze 660,357 human transcripts from human brain mRNA and identified expression of 17,409 known genes and >15,000 different transcripts that were not annotated in genome databases. Analysis of a subset of these unannotated transcripts suggests that 85% were differentially expressed in various tissue types and that fewer than 20% would have been detected by ab initio gene predictions. These studies suggest that the human genome contains on the order of twice as many transcribed regions as are currently annotated and that experimental approaches will be required to fully elucidate the novel genes corresponding to these transcripts.
High-resolution copy number analysis of paraffin-embedded archival tissue using SNP BeadArrays
Authors: Oosting Jan , Lips Esther H. , van Eijk Ronald , Eilers Paul H.C. , Szuhai Károly , Wijmenga Cisca , Morreau Hans , van Wezel Tom
Published: February 2007

High-density SNP microarrays provide insight into the genomic events that occur in diseases like cancer through their capability to measure both LOH and genomic copy numbers. Where currently available methods are restricted to the use of fresh frozen tissue, we now describe the design and validation of copy number measurements using the Illumina BeadArray platform and the application of this technique to formalin-fixed, paraffin-embedded (FFPE) tissue. In fresh frozen tissue from a set of colorectal tumors with numerous chromosomal aberrations, our method measures copy number patterns that are comparable to values from established platforms, like Affymetrix GeneChip and BAC array-CGH. Moreover, paired comparisons of fresh frozen and FFPE tissues showed nearly identical patterns of genomic change. We conclude that this method enables the use of paraffin-embedded material for research into both LOH and numerical chromosomal abnormalities. These findings make the large pathological archives available for genomic analysis, which could be especially relevant for hereditary disease where fresh material from affected relatives is rarely available.
Refinement and expansion of signaling pathways: The osmotic response network in yeast
Authors: Gat-Viks Irit , Shamir Ron
Published: February 2007

The analysis of large-scale genome-wide experiments carries the promise of dramatically broadening our understanding on biological networks. The challenge of systematic integration of experimental results with established biological knowledge on a pathway is still unanswered. Here we present a methodology that attempts to answer this challenge when investigating signaling pathways. We formalize existing qualitative knowledge as a probabilistic model that depicts known interactions between molecules (genes, proteins, etc.) as a network and known regulatory relations as logics. We present algorithms that analyze experimental results (e.g., transcription profiles) vis-à-vis the model and propose improvements to the model based on the fit to the experimental data. These algorithms refine the relations between model components, as well as expand the model to include new components that are regulated by components of the original network. Using our methodology, we have modeled together the knowledge on four established signaling pathways related to osmotic shock response inSaccharomyces cerevisiae. Using over 100 published transcription profiles, our refinement methodology revealed three cross talks in the network. The expansion procedure identified with high confidence large groups of genes that are coregulated by transcription factors from the original network via a common logic. The results reveal a novel delicate repressive effect of the HOG pathway on many transcriptional target genes and suggest an unexpected alternative functional mode of the MAP kinase Hog1. These results demonstrate that, by integrated analysis of data and of well-defined knowledge, one can generate concrete biological hypotheses about signaling cascades and their downstream regulatory programs.
Quantitative GUS Activity Assay of Plant Extracts
Authors: Blázquez Miguel
Published: February 2007

INTRODUCTION

The activity of ß-glucuronidase (GUS) can be accurately determined in extracts of plant tissue using 4-methylumbelliferyl ß-D-glucuronide (4-MUG) as a substrate. Upon hydrolysis by GUS, the fluorochrome 4-methyl umbelliferone (4-MU) is produced. Using excitation at 365 nm and measuring emission at 455 nm, the amount of 4-MU produced can be quantified. Under these conditions, background fluorescence from the substrate is negligible, especially if the appropriate filter is selected.
Usefulness of Inhospital Change in B‐Type Natriuretic Peptide Levels in Predicting Long‐Term Outcome in Elderly Patients Admitted for Decompensated Heart Failure
Authors: Cournot Maxime , Leprince Philippe , Sylvain Destrac , Ferrières Jean
Published: February 2007

The usefulness of repeated measures of B‐type natriuretic peptide (BNP) in elderly subjects with decompensated heart failure to improve risk stratification remains poorly known. This prospective cohort study included 61 consecutive patients older than 70 years (mean age, 82.7 years) hospitalized for decompensated heart failure. Clinical, radiologic, biologic, and echographic data were collected at admission and at discharge. The median BNP level at admission was 1136 pg/mL and the mean change during the hospitalization was −32%. Cardiac death or readmission were best predicted by the change in BNP levels, with the poorest prognosis in patients who did not achieve a decrease of at least 40% (hazard ratio, 4.03; 95% confidence interval, 1.50–10.84 in multivariate analysis). Admission of an elderly patient for decompensated heart failure is a daily situation in clinical practice, in which 2 BNP measurements seem to provide reliable information on long‐term prognosis.
Latitudinal gradients in onset date, onset temperature and duration of spawning of roach
Authors: Lappalainen J. , Tarkan A. S.
Published: February 2007

Onset date, onset temperature and duration of spawning of roach Rutilus rutilus were related to latitude (40–66° N) and altitude (−1–825 m) based on data from the literature over the whole geographic distribution of roach. Onset date was positively and duration was negatively correlated with latitude, while no correlation was found between onset temperature and latitude. No significant correlations were found between any of the analysed variables of spawning and altitude, probably because most of the analysed populations were below 300 m altitude.
Swimming alters responses to hypoxia in the Adriatic sturgeon Acipenser naccarii
Authors: McKenzie D. J. , Steffensen J. F. , Korsmeyer K. , Whiteley N. M. , Bronzi P. , Taylor E. W.
Published: February 2007

When the Adriatic sturgeon Acipenser naccarii was exposed to progressive hypoxia under static conditions, it exhibited a linear decline in O2 uptake, behaving as an ‘oxyconformer’. When, however, it was allowed to swim at a low sustained speed, it could regulate O2 uptake down to a mean ±s.e. critical (Pcrit) of 4·9 ± 0·5 kPa (n= 6). At moderate levels of hypoxia, static fish exhibited significant reductions in arterial blood O2 content, and increases in plasma lactate, which were not observed in swimming animals.
NF‐κB activation in development and progression of cancer
Authors: Inoue Jun‐ichiro , Gohda Jin , Akiyama Taishin , Semba Kentaro
Published: February 2007

Nuclear factor‐κΒ (NF‐κB) binds specifically to NF‐κB‐binding sites (κB sites, 5′‐GGGRNNYYCC‐3′; R, purine; Y, pyrimidine; N, any nucleotide) present in enhancer regions of various genes. Binding of various cytokines, growth factors and pathogen‐associated molecular patterns to specific receptors activates NF‐κB and expression of genes that play critical roles in inflammation, innate and acquired immunity, bone remodeling and generation of skin appendices. Activation of NF‐κB is also involved in cancer development and progression. NF‐κB is activated in cells that become malignant tumors and in cells that are recruited to and constitute the tumor microenvironment. In the latter scenario, the TLR‐TRAF6‐NF‐kB pathways seem to play major roles, and NF‐κB activation results in production of cytokines, which in turn induce NF‐κB activation in premalignant cells, leading to expression of genes involved abnormal growth and malignancy. Furthermore, NF‐κB activation is involved in bone metastasis. Osteoclasts, whose generation requires the RANK‐TRAF6‐NF‐κB pathways, release various growth factors stored in bone, which results in creation of microenvironment suitable for proliferation and colonization of cancer cells. Therefore, NF‐κB and molecules involved its activation, such as TRAF6, are attractive targets for therapeutic strategies against cancer. (Cancer Sci 2007; 98: 268–274)
Proto‐oncogene, Pim‐3 with serine/threonine kinase activity, is aberrantly expressed in human colon cancer cells and can prevent Bad‐mediated apoptosis
Authors: Popivanova Boryana Konstantinova , Li Ying‐Yi , Zheng Huachuan , Omura Kenji , Fujii Chifumi , Tsuneyama Koichi , Mukaida Naofumi
Published: February 2007

We previously observed that Pim‐3 with serine/threonine kinase activity, was aberrantly expressed in malignant lesions of endoderm‐derived organs, liver and pancreas. Because Pim‐3 protein was not detected in normal colon mucosal tissues, we evaluated Pim‐3 expression in malignant lesions of human colon, another endoderm‐derived organ. Pim‐3 was detected immunohistochemically in well‐differentiated (43/68 cases) and moderately differentiated (23/41 cases) but not poorly differentiated colon adenocarcinomas (0/5 cases). Moreover, Pim‐3 proteins were detected in adenoma (35/40 cases) and normal mucosa (26/111 cases), which are adjacent to adenocarcinoma. Pim‐3 was constitutively expressed in SW480 cells and the transfection with Pim‐3 short hairpin RNA promoted apoptosis. In the same cell line, a pro‐apoptotic molecule, Bad, was phosphorylated at Ser112 and Ser136 sites of phosphorylation that are representative of its inactive form. Ser112 but not Ser136 phosphorylation in this cell line was abrogated by Pim‐3 knockdown. Furthermore, in human colon cancer tissues, Pim‐3 co‐localized with Bad in all cases (9/9) and with phospho‐Ser112Bad in most cases (6/9). These observations suggest that Pim‐3 can inactivate Bad by phosphorylating its Ser112 in human colon cancer cells and thus may prevent apoptosis and promote progression of human colon cancer. (Cancer Sci 2007; 98: 321–328)
Anthrax outbreak among Grevy's zebra (Equus grevyi) in Samburu, Kenya
Authors: Muoria Paul K. , Muruthi Philip , Kariuki Waititu K. , Hassan Boru A. , Mijele Dominic , Oguge Nicholas O.
Published: February 2007

An anthrax outbreak occurred in the Wamba area of southern Samburu, Kenya, between December 2005 and March 2006. The outbreak affected equids including the endangered Grevy's zebras (Equus grevyi), plain zebras (Equis Burchelli) and donkeys (Equus asinus). Most of the deaths were localized in Nkaroni area just west of Wamba town. The diagnosis of anthrax was rapidly confirmed by bacteriological methods. The relevant government departments, including the Kenya Wildlife Service and Veterinary Department, and other stakeholders were promptly informed. Fifty‐three Grevy's zebra and 26 plains zebras died from anthrax. An equal number (eighteen) of adult male and female Grevy's zebras succumbed to the disease. The outbreak affected immature and mature individuals equally. The dead plain zebras included fifteen adult females, two adult males and nine immature individuals. The Veterinary Department responded by vaccinating livestock while Kenya Wildlife Service vaccinated 620 Grevy's zebras within southern Samburu. Examination of sites at which carcasses of animals which succumbed to the disease were burnt, revealed that unsupervised burning did not eliminate anthrax spores in 42% of the cases (n = 14). There is an urgent need to incorporate strategic wildlife disease monitoring in the struggle to save Grevy's zebras and other endangered species.
Characterization of Xenopus egg membrane microdomains containing uroplakin Ib/III complex: roles of their molecular interactions for subcellular localization and signal transduction
Authors: Mahbub Hasan A.K.M. , Ou Zhize , Sakakibara Keiichi , Hirahara Shino , Iwasaki Tetsushi , Sato Ken‐ichi , Fukami Yasuo
Published: February 2007

A single‐transmembrane protein uroplakin III (UPIII) and its tetraspanin binding‐partner uroplakin Ib (UPIb) are members of the UP proteins that were originally identified in mammalian urothelium. In Xenopus laevis eggs, these proteins: xUPIII and xUPIb, are components of the cholesterol‐enriched membrane microdomains or “rafts” and involved in the sperm–egg membrane interaction and subsequent egg activation signaling via Src tyrosine kinase at fertilization. Here, we investigate whether the xUPIII‐xUPIb complex is in close proximity to CD9, a tetraspanin that has been implicated in the sperm–egg fusion in the mouse and GM1, a ganglioside typically enriched in egg rafts. Preparation of the egg membrane microdomains using different non‐ionic detergents (Brij 98 and Triton X‐100), chemical cross‐linking, co‐immunoprecipitation, in vitro kinase assay and in vitro fertilization experiments demonstrated that GM1, but not CD9, is in association with the xUPIII‐xUPIb complex and contributes to the sperm‐dependent egg activation. Transfection experiments using HEK293 cells demonstrated that xUPIII and xUPIb localized efficiently to the cholesterol‐dependent membrane microdomains when they were co‐expressed, whereas co‐expression of xUPIII and CD9, instead of xUPIb, did not show this effect. Furthermore, xUPIII and xUPIb were shown to suppress kinase activity of the wild type, but not a constitutively active form of, Xenopus Src protein co‐expressed in HEK293 cells. These results provide novel insight into the molecular architecture of the egg membrane microdomains containing xUPIII, xUPIb and Src, which may contribute to the understanding of sperm–egg interaction and signaling during Xenopus fertilization.
Hierarchy of Atg proteins in pre‐autophagosomal structure organization
Authors: Suzuki Kuninori , Kubota Yuka , Sekito Takayuki , Ohsumi Yoshinori
Published: February 2007

Autophagy is a bulk degradation process that is conserved in eukaryotic cells and functions in the turnover of cytoplasmic materials and organelles. When eukaryotic cells face nutrient starvation, the autophagosome, a double‐membraned organelle, is generated from the pre‐autophagosomal structure (PAS). In the yeast Saccharomyces cerevisiae, 16 ATG (autophagy‐related) genes are essential for autophagosome formation. Most of the Atg proteins are involved in the PAS, leading to autophagosome production. However, the mechanism of PAS organization remains to be elucidated. Here, we performed a systematic and quantitative analysis by fluorescence microscopy to develop a hierarchy map of Atg proteins involved in PAS organization. This analysis suggests that Atg17p is the most basic protein in PAS organization: when it is specifically targeted to the plasma membrane, other Atg proteins are recruited to that location, suggesting that Atg17p acts as a scaffold protein to organize Atg proteins to the PAS.
Historical problems of travel for women geologists
Authors: Burek Cynthia V. , Kölbl‐Ebert Martina
Published: February 2007

From unsuitable clothes to lack of chaperones, from harassment to lack of proper funding, throughout history women geologists have encountered difficulties travelling to their field locations or working in the field, whether these locations were close by or abroad. Most early female geologists were able to avoid many difficulties because they were protected through working locally, where their high social standing was known and respected, or because they worked in a team with husband, father or brother. However, the problem was to grow in the second half of the nineteenth century, when women started to appear as students and professionally trained geologists. This feature explores the difficulties of female geologists undertaking fieldwork from the late nineteenth to the mid‐twentieth century.
Effect of light curing type on cytotoxicity of dentine‐bonding agents
Authors: Ergün G. , Eğilmez F. , Üçtaşli M. B. , Yilmaz Ş.
Published: February 2007

Aim  To compare the cytotoxic effects of dentine‐bonding agents (DBAs) polymerized with two different curing units at 24 h and 72 h on L‐929 cells.

Methodology  Disc‐shaped test samples of light‐activated DBAs were prepared according to manufacturers’ instructions and cured with either conventional quartz tungsten halogen or light‐emitting diode light curing units (LCUs). After curing, the samples were transferred into a culture medium for 24 h. Eluates were obtained and pipetted onto L‐929 mouse fibroblast cultures (3 × 104 cells per well), incubated for evaluation after 24 and 72 h. After both incubation periods, measurements were performed by an dimethylthiazol diphenyltetrazolium assay. The degree of cytotoxicity for each sample was determined according to the reference value represented by the cells with a control (culture without sample). Statistical significance was determined by a three‐way analysis of variance followed by the Mann–Whitney U‐test.

Results  No significant three‐factor interaction occurred amongst LCUs, DBAs and time factors (P = 0.955). LCUs and DBAs had a significant two‐factor interaction (P < 0.001). In general, the test materials cured with the light‐emitting diode LCU demonstrated higher cell survival rates when compared with the those cured with the quartz tungsten halogen.

Conclusions  Differential toxic effects of the DBAs cured with the quartz tungsten halogen or the light‐emitting diode on the fibroblast cells may prove to be very important when suitable DBAs or LCUs are used for operative restorations.
Valuing of altruism and honesty in nursing students: a two‐decade replication study
Authors: Johnson Martin , Haigh Carol , Yates‐Bolton Natalie
Published: February 2007

Title. Valuing of altruism and honesty in nursing students: a two‐decade replication study

Aim.  This paper reports a study investigating changes in the self‐reported values of nursing students over the period 1983–2005 in the light of changes in student demography.

Background.  Nurses’ values have been studied by both qualitative and survey methods over half a century. Generally idealism and altruism are said to wane as a result of professional socialisation, whilst honesty has been rarely examined.

Method.  Building on an instrument designed by William Scott, further items were developed which addressed value orientations in a nursing context. Using a Likert scale and demographic items, a 1983 survey of three schools of nursing in England was repeated with a comparable population of students in 2005.

Findings.  Student valuing of altruism and honesty has changed in important ways in the intervening decades. Nursing students are now generally less altruistic (P = 0·01) but value honesty with patients a great deal more (P = 0·01) than their counterparts in 1983.

Conclusion.  The current situation, with older students having more domestic responsibilities and some students needing to have extra jobs besides their nursing course, seems to have led them to adopt a pragmatic approach. However, there are encouraging changes in the valuing of honesty with patients, which reflect in part students’ increased maturity and changed social attitudes to healthcare professional paternalism.
A qualitative examination of changing practice in Canadian neonatal intensive care units
Authors: Stevens Bonnie , Lee Shoo K. , Law Madelyn P. , Yamada Janet ,   Canadian Neonatal Network EPIC Study Group
Published: February 2007

Objective  The goal was to explore the perspectives of health care professionals on factors that influence change to policies, protocols and practices in the Neonatal Intensive Care Unit (NICU) with regard to nosocomial infection and chronic lung disease.

Study design  An exploratory descriptive design using semi‐structured individual and focus group interviews was used. Individual interviews (n = 76) and focus group sessions (n = 14 with a total of 78 participants) were conducted for a total of 154 health professional participants.

Methods  Mayring’s qualitative content analysis approach was used to analyse the data. All interviews were audio‐taped, transcribed and analysed using inductive reasoning. The data were then organized into categories that reflected emerging themes.

Results  Seven categories that influenced practice change were derived from the data including staffing issues, consistency in practice, the approval process, a multidisciplinary approach to care, frequency and consistency of communication, rationale for change and the feedback process. These categories were further delineated into three emerging themes related to human resources, organizational structure and communications. Pettigrew’s conceptual framework provided a lens to view the results in relation to the process of change.

Conclusions  This study has helped to further our understanding of individual and organizational factors that facilitate and hinder changes in clinical practice in the NICU. These factors will be used as a starting point for organizational change to enhance infant outcomes in the NICU.
Fluorescence relaxation in 3D from diffraction‐limited sources of PAGFP or sinks of EGFP created by multiphoton photoconversion
Authors: CALVERT P. D. , PEET J. A. , BRAGIN A. , SCHIESSER W. E. , PUGH E. N.
Published: February 2007

The relaxation of fluorescence from diffraction‐limited sources of photoactivatable green fluorescent protein (PAGFP) or sinks of photobleached enhanced GFP (EGFP) created by multiphoton photo‐conversion was measured in solutions of varied viscosity (η), and in live, spherical Chinese hamster ovary (CHO) cells. Fluorescence relaxation was monitored with the probing laser fixed, or rapidly scanning along a line bisected by the photoconversion site. Novel solutions to several problems that hamper the study of PAGFP diffusion after multiphoton photoconversion are presented. A theoretical model of 3D diffusion in a sphere from a source in the shape of the measured multiphoton point‐spread function was applied to the fluorescence data to estimate the apparent diffusion coefficient, Dap. The model incorporates two novel features that make it of broad utility. First, the model includes the no‐flux boundary condition imposed by cell plasma membranes, allowing assessment of potential impact of this boundary on estimates of Dap. Second, the model uses an inhomogeneous source term that, for the first time, allows analysis of diffusion from sources produced by multiphoton photoconversion pulses of varying duration. For diffusion in aqueous solution, indistinguishable linear relationships between Dap and η−1 were obtained for the two proteins: for PAGFP, Daq= 89 ± 2.4 μm2 s−1 (mean ± 95% confidence interval), and for EGFP Daq= 91 ± 1.8 μm2 s−1. In CHO cells, the application of the model yielded Dap= 20 ± 3 μm2 s−1 (PAGFP) and 19 ± 2 μm2 s−1 (EGFP). Furthermore, the model quantitatively predicted the decline in baseline fluorescence that accompanied repeated photobleaching cycles in CHO cells expressing EGFP, supporting the hypothesis of fluorophore depletion as an alternative to the oft invoked ‘bound fraction’ explanation of the deviation of the terminal fluorescence recovery from its pre‐bleach baseline level. Nonetheless for their identical diffusive properties, advantages of PAGFP over EGFP were found, including an intrinsically higher signal/noise ratio with 488‐nm excitation, and the requirement for ∼1/200th the cumulative light energy to produce data of comparable signal/noise.
Glutathione conjugates in the vacuole are degraded by γ‐glutamyl transpeptidase GGT3 in Arabidopsis
Authors: Ohkama‐Ohtsu Naoko , Zhao Ping , Xiang Chengbin , Oliver David J.
Published: February 2007

γ‐Glutamyl transpeptidase (GGT) is the enzyme responsible for breaking the γ‐glutamyl bond between Glu and Cys in glutathione (GSH). We are using this gene family to study GSH degradation in plants. There are four putative GGT genes in Arabidopsis, and one of them, GGT3 (At4g29210), is analyzed in this study. GGT3 is localized to the vacuole based on organelle‐targeting programs, subcellular distribution of GFP fusion proteins during transient expression in onion (Allium cepa) epidermal tissues, and its ability to metabolize vacuolar substrates in Arabidopsis plants. While Northern blots and promoter:GUS expression patterns have suggested that GGT3 is transcribed at relatively high levels in all parts of the plant, a comparison of enzyme activities in different organs of wild‐type and a ggt3 knockout mutant showed that GGT3 was a major contributor to total GGT activity in roots, but a relatively minor contributor in other tissues. Wild‐type Arabidopsis plants treated with monobromobimane (mBB) form a fluorescent GSH–mBB conjugate that is moved into the vacuole and then metabolized to Cys‐Gly–mBB and Cys–mBB in that order. The first step is catalyzed by GGT3, and GSH–mBB metabolism is completely blocked in the roots of ggt3 knockout plants. In ggt3 leaves, some GSH–mBB metabolism still proceeds using the apoplastic GGT1. This identifies GGT3 as catalyzing the obligate initial step in GSH conjugate metabolism, and suggests that it has an important role in protecting plants from some xenobiotic chemicals.
Contrasting genetic diversity with phenotypic diversity in coloration and size in Xantho poressa (Brachyura: Xanthidae), with new results on its ecology
Authors: Reuschel Silke , Schubart Christoph D.
Published: February 2007

The ecology of Xantho poressa (Olivi, 1792) (Brachyura) was studied during field trips to the Mediterranean Sea, the Black Sea and the Spanish Atlantic Ocean. Our results reveal that X. poressa lives from the intertidal to the shallow subtidal zone, and inhabits relatively protected rocky shores, often with pebble underground, from juvenile to adult stages. A mark–recapture experiment revealed a high population density in this habitat. All stages, but predominantly juveniles, show a variability of colour patterns, which allow the crabs to blend in with the rocky substratum, thereby hiding from predators as passive defence. Adulthood can be reached with a carapace length smaller than 6 mm. The morphometric analysis of the species revealed allometric growth in carapace shape. Variability in overall size could be observed at different collecting sites. Neither the colour morphs nor the size differences could be attributed to differences of Cytochrome Oxidase subunit I mitochondrial DNA sequences, suggesting that ecological rather than genetic patterns are responsible for the different phenotypes.
Widening the gene pool of cultivated lentils through introgression of alien chromatin from wild Lens subspecies
Authors: Gupta D. , Sharma S. K.
Published: February 2007

Wild Lens species/subspecies are a potential source for increasing genetic diversity in cultivated lentil. Four intraspecific crosses were attempted between cultivated and wild lentils. Viable hybrids were produced between L. culinaris ssp. culinaris × L. culinaris ssp. orientalis and L. culinaris ssp. culinaris × L. culinaris ssp. odomensis. Normal meiosis and pollen fertility were observed in the first set of crosses, whereas chromosomal abnormalities and reduced pollen fertility were observed in the second set of crosses. These crosses were also studied for some quantitative traits. The range, mean and coefficient of variation were calculated in parents, F1, F2 and BC1 generations to determine the extent of variability generated in the cultivated lentil through introgression of genes from wild lentil. The cultivated lentil × L. culinaris ssp. orientalis crosses showed substantially higher variability for all the traits than crosses involving cultivated lentil ×L. culinaris ssp. odomensis. The results of the present study indicated that these wild subspecies can be exploited for breeding purposes and their variation can easily be utilized to widen the genetic base of the cultivated lentil.
Downregulated P1 promoter‐driven hepatocyte nuclear factor‐4α expression in human colorectal carcinoma is a new prognostic factor against liver metastasis
Authors: Oshima Tomoko , Kawasaki Takashi , Ohashi Riuko , Hasegawa Go , Jiang Shuying , Umezu Hajime , Aoyagi Yutaka , Iwanari Hiroko , Tanaka Toshiya , Hamakubo Takao , Kodama Tatsuhiko , Naito Makoto
Published: February 2007

Liver metastases are the most critical prognostic factors for patients with colorectal carcinomas (CRC). It has been reported that the dysregulation of hepatocyte nuclear factor‐4α (HNF4α) expression is linked to the development of CRC, gastric cancer and hepatocellular carcinoma. The purpose of the present paper was to examine the P1 and P2 promoter‐driven HNF4α (P1 and P2) expression in surgically resected CRC. Immunohistochemically, P1, P2, MUC1 and CD10 expression were evaluated in 63 cases of primary CRC. Positive staining with P1, P2, MUC1 and CD10 antibodies were observed in 37 (59%), 63 (100%), 42 (67%) and 27 (43%) cases, respectively. Loss or decreased P1 expression was observed with respect to the depth of the tumor invasion. The frequency of P1‐positive expression in Dukes' C and D tumors was significantly lower than that in Dukes' A and B tumors. There was a relationship between the loss of P1 expression and metachronous liver metastases, and the survival rate of the P1‐negative patients without liver metastasis at the time of the primary CRC resection tended to be worse than that of the P1‐positive patients. These findings suggest that downregulation of P1 expression is involved in tumor metastasis and a worse prognosis.