bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of twin-arginine signal peptides
Authors: Bendtsen Jannick Dyrløv , Nielsen Henrik , Widdick David , Palmer Tracy , Brunak Søren
Published: July 2005

Background

Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Sec-dependent translocation pathway. To complement other methods for classical signal peptide prediction we here present a publicly available method, TatP, for prediction of bacterial Tat signal peptides.

Results

We have retrieved sequence data for Tat substrates in order to train a computational method for discrimination of Sec and Tat signal peptides. The TatP method is able to positively classify 91% of 35 known Tat signal peptides and 84% of the annotated cleavage sites of these Tat signal peptides were correctly predicted. This method generates far less false positive predictions on various datasets than using simple pattern matching. Moreover, on the same datasets TatP generates less false positive predictions than a complementary rule based prediction method.

Conclusion

The method developed here is able to discriminate Tat signal peptides from cytoplasmic proteins carrying a similar motif, as well as from Sec signal peptides, with high accuracy. The method allows filtering of input sequences based on Perl syntax regular expressions, whereas hydrophobicity discrimination of Tat- and Sec-signal peptides is carried out by an artificial neural network. A potential cleavage site of the predicted Tat signal peptide is also reported. The TatP prediction server is available as a public web server at http://www.cbs.dtu.dk/services/TatP/.
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)
Authors: Zeeberg Barry R , Qin Haiying , Narasimhan Sudarshan , Sunshine Margot , Cao Hong , Kane David W , Reimers Mark , Stephens Robert M , Bryant David , Burt Stanley K , Elnekave Eldad , Hari Danielle M , Wynn Thomas A , Cunningham-Rundles Charlotte , Stewart Donn M , Nelson David , Weinstein John N
Published: July 2005

Background

We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interpretation of the results from a single microarray (or other high-throughput experimental platform), using a graphical user interface. Although that version can be used to examine the results from a number of microarrays one at a time, that is a rather tedious task, and original GoMiner includes no apparatus for obtaining a global picture of results from an experiment that consists of multiple microarrays. We wanted to provide a computational resource that automates the analysis of multiple microarrays and then integrates the results across all of them in useful exportable output files and visualizations.

Results

We now introduce a new tool, High-Throughput GoMiner, that has those capabilities and a number of others: It (i) efficiently performs the computationally-intensive task of automated batch processing of an arbitrary number of microarrays, (ii) produces a human-or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories, (iii) integrates the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories, (iv) provides a fast form of 'false discovery rate' multiple comparisons calculation, and (v) provides annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

Conclusion

High-Throughput GoMiner achieves the desired goal of providing a computational resource that automates the analysis of multiple microarrays and integrates results across all of the microarrays. For illustration, we show an application of this new tool to the interpretation of altered gene expression patterns in Common Variable Immune Deficiency (CVID). High-Throughput GoMiner will be useful in a wide range of applications, including the study of time-courses, evaluation of multiple drug treatments, comparison of multiple gene knock-outs or knock-downs, and screening of large numbers of chemical derivatives generated from a promising lead compound.
Are antifibrinolytic drugs equivalent in reducing blood loss and transfusion in cardiac surgery? A meta-analysis of randomized head-to-head trials
Authors: Carless Paul A , Moxey Annette J , Stokes Barrie J , Henry David A
Published: July 2005

Background

Aprotinin has been shown to be effective in reducing peri-operative blood loss and the need for re-operation due to continued bleeding in cardiac surgery. The lysine analogues tranexamic acid (TXA) and epsilon aminocaproic acid (EACA) are cheaper, but it is not known if they are as effective as aprotinin.

Methods

Studies were identified by searching electronic databases and bibliographies of published articles. Data from head-to-head trials were pooled using a conventional (Cochrane) meta-analytic approach and a Bayesian approach which estimated the posterior probability of TXA and EACA being equivalent to aprotinin; we used as a non-inferiority boundary a 20% increase in the rates of transfusion or re-operation because of bleeding.

Results

Peri-operative blood loss was significantly greater with TXA and EACA than with aprotinin: weighted mean differences were 106 mls (95% CI 37 to 227 mls) and 185 mls (95% CI 134 to 235 mls) respectively. The pooled relative risks (RR) of receiving an allogeneic red blood cell (RBC) transfusion with TXA and EACA, compared with aprotinin, were 1.08 (95% CI 0.88 to 1.32) and 1.14 (95% CI 0.84 to 1.55) respectively. The equivalent Bayesian posterior mean relative risks were 1.15 (95% Bayesian Credible Interval [BCI] 0.90 to 1.68) and 1.21 (95% BCI 0.79 to 1.82) respectively. For transfusion, using a 20% non-inferiority boundary, the posterior probabilities of TXA and EACA being non-inferior to aprotinin were 0.82 and 0.76 respectively. For re-operation the Cochrane RR for TXA vs. aprotinin was 0.98 (95% CI 0.51 to 1.88), compared with a posterior mean Bayesian RR of 0.63 (95% BCI 0.16 to 1.46). The posterior probability of TXA being non-inferior to aprotinin was 0.92, but this was sensitive to the inclusion of one small trial.

Conclusion

The available data are conflicting regarding the equivalence of lysine analogues and aprotinin in reducing peri-operative bleeding, transfusion and the need for re-operation. Decisions are sensitive to the choice of clinical outcome and non-inferiority boundary. The data are an uncertain basis for replacing aprotinin with the cheaper lysine analogues in clinical practice. Progress has been hampered by small trials and failure to study clinically relevant outcomes.
Efficacy of the epidural blood patch for the treatment of post lumbar puncture headache BLOPP: A randomised, observer-blind, controlled clinical trial [ISRCTN 71598245]
Authors: Oedit R , van Kooten F , Bakker SLM , Dippel DWJ
Published: July 2005

Background

Post dural punction headache (PDPH) occurs in 10% to 40% of the patients who had a lumbar puncture. Its symptoms can be severe and incapacitating. The epidural blood patch is widely accepted as the treatment of choice for postdural puncture headache. Uncontrolled studies report rapid recovery after patching in 90% to 100% of treated patients. However, sufficient evidence from randomised, controlled clinical trials is lacking.

Methods

BLOPP (blood patch for post dural puncture headache) is a randomised, single centre, observer-blind clinical trial. Patients with PDPH for at least 24 hours and at most 7 days after lumbar puncture will be randomised to treatment with an epidural blood patch (EDBP) or to conventional treatment, i.e. 24 hours bed rest and ample fluid intake. PDPH 24 hours after treatment, classified on a 4-point scale (no, mild, moderate, severe) is the primary outcome. The secondary outcome is the presence of PDPH 7 days after treatment. We estimated that a sample size of 2 × 20 patients would provide us with a power of 80% to detect a relative reduction in number of patients with persisting PDPH after 24 hours of 50% at the usual significance level α = 5%, taking into account that in approximately 10% of the patients the PDPH will have resolved spontaneously after one day.

Discussion

The EDBP is accepted as the treatment of choice for PDPH although randomised, controlled data is scarce. Our randomised, observer-blind clinical trial enables us to compare the efficacy of two clinically practiced methods of PDPH treatment; EDBP versus conventional treatment, as they are applied in clinical practise.
Familial breast cancer: characteristics and outcome of BRCA 1–2 positive and negative cases
Authors: Veronesi Andrea , Giacomi Clelia de , Magri Maria D , Lombardi Davide , Zanetti Martina , Scuderi Cristina , Dolcetti Riccardo , Viel Alessandra , Crivellari Diana , Bidoli Ettore , Boiocchi Mauro
Published: July 2005

Background

The clinical and pathological characteristics and the clinical course of patients with breast cancer and BRCA 1–2 mutation are poorly known.

Methods

From 1997, patients with breast cancer and a family history of breast or ovarian cancer were offered BRCA testing. The clinical and pathological features of patients with known BRCA status were retrospectively assessed and comparisons were made between cancers arising in BRCA positive and BRCA wild type (WT) patients respectively. Type of treatment, pattern of relapse, event (local relapse, contralateral breast cancer, metastases) free and overall survival were also compared in the two groups. Out of the 210 patients tested, 125 had been treated and followed-up at our Institution and were evaluated in this study.

Results

BRCA positive patients tended to be more often premenopausal (79% vs 65%) and to have positive lymphnodes (63% vs 49%), poorly differentiated tumours (76% vs 40% – p = 0.002 at univariate analysis, not significant at multivariate analysis) and negative estrogen receptors (43% vs 29%). Treatment was not different in the two groups. In the 86 BRCA-WT patients, the first event was a local relapse in 3 (3%), metachronous contralateral breast cancer in 7 (8%) and distant metastases in 16 (19%). In the 39 BRCA positive patients, the corresponding figures were 3 (8%), 8 (21%) and 3 (8%). There was no difference in event free survival, with a median of 180 months in both groups of patients. At 20 years, projected survival was 85% for BRCA positive patients and 55% for BRCA-WT, but this difference was not statistically significant.

Conclusion

Although BRCA positive patients have more frequently negative prognostic factors, their prognosis appears to be equal to or better than in patients with BRCA-WT.
Normative data of bone Mineral Density in healthy population of Tehran, Iran: A Cross sectional study
Authors: Larijani Bagher , Hossein-Nezhad Arash , Mojtahedi Alireza , Pajouhi Mohammad , Bastanhagh Mohammad H , Soltani Akbar , Mirfezi Seyed-Zahra , Dashti Roya
Published: July 2005

Background

Osteoporosis is a major problem and is a hidden epidemic disease in the world. Early diagnosis by measurement of Bone Mineral Density (BMD) and treatment can prevent and reduce disease complications, especially fractures. As there is no comprehensive study in Iran, this study designed to assess BMD discrepancy in 20–69 yr Tehran population as well as prevalence of osteoporosis and osteopenia.

Methods

553 people (34% men, 66%women) from 50 Blocks in Tehran randomly selected. The assessment of BMD in spine and femur region performed through DXA method. All subjects clinically examined and their BMIs determined.

Results

The average spinal BMD score in men were more than in women. The peak bone mass of spine bone both in men and women occurred during 20–29 yr and reduction began from the age of 40. At the age of 60 to 69, loose of bone density was 19.6% in lumbar spine and 18.5% in femur of women and also 7.9% in lumbar spine and 14.6% in femur of men. Prevalence of osteoporosis in this age group in lumbar spine and femur was 32.4% and 5.9% in women and 9.4% and 3.1% in men respectively.

Conclusion

In all age groups, peak bone mass was lower than European or American population, whereas the rate of bone loss was as much as the some population and actually this process justifies the prevalence of osteoporosis and osteopenia in Tehran population.
Efficient assembly of de novohuman artificial chromosomes from large genomic loci
Authors: Basu Joydeep , Compitello George , Stromberg Gregory , Willard Huntington F , Van Bokkelen Gil
Published: July 2005

Background

Human Artificial Chromosomes (HACs) are potentially useful vectors for gene transfer studies and for functional annotation of the genome because of their suitability for cloning, manipulating and transferring large segments of the genome. However, development of HACs for the transfer of large genomic loci into mammalian cells has been limited by difficulties in manipulating high-molecular weight DNA, as well as by the low overall frequencies of de novo HAC formation. Indeed, to date, only a small number of large (>100 kb) genomic loci have been reported to be successfully packaged into de novo HACs.

Results

We have developed novel methodologies to enable efficient assembly of HAC vectors containing any genomic locus of interest. We report here the creation of a novel, bimolecular system based on bacterial artificial chromosomes (BACs) for the construction of HACs incorporating any defined genomic region. We have utilized this vector system to rapidly design, construct and validate multiple de novo HACs containing large (100–200 kb) genomic loci including therapeutically significant genes for human growth hormone (HGH), polycystic kidney disease (PKD1) and ß-globin. We report significant differences in the ability of different genomic loci to support de novo HAC formation, suggesting possible effects of cis-acting genomic elements. Finally, as a proof of principle, we have observed sustained ß-globin gene expression from HACs incorporating the entire 200 kb ß-globin genomic locus for over 90 days in the absence of selection.

Conclusion

Taken together, these results are significant for the development of HAC vector technology, as they enable high-throughput assembly and functional validation of HACs containing any large genomic locus. We have evaluated the impact of different genomic loci on the frequency of HAC formation and identified segments of genomic DNA that appear to facilitate de novo HAC formation. These genomic loci may be useful for identifying discrete functional elements that may be incorporated into future generations of HAC vectors.
Action ethical dilemmas in surgery: an interview study of practicing surgeons
Authors: Torjuul Kirsti , Nordam Ann , Sørlie Venke
Published: July 2005

Background

The aim of this study was to describe the kinds of ethical dilemmas surgeons face during practice.

Methods

Five male and five female surgeons at a University hospital in Norway were interviewed as part of a comprehensive investigation into the narratives of physicians and nurses about ethically difficult situations in surgical units. The transcribed interview texts were subjected to a phenomenological-hermeneutic interpretation.

Results

No gender differences were found in the kinds of ethical dilemmas identified among male and female surgeons. The main finding was that surgeons experienced ethical dilemmas in deciding the right treatment in different situations. The dilemmas included starting or withholding treatment, continuing or withdrawing treatment, overtreatment, respecting the patients and meeting patients' expectations. The main focus in the narratives was on ethical dilemmas concerning the patients' well-being, treatment and care. The surgeons narrated about whether they should act according to their own convictions or according to the opinions of principal colleagues or colleagues from other departments. Handling incompetent colleagues was also seen as an ethical dilemma. Prioritization of limited resources and following social laws and regulations represented ethical dilemmas when they contradicted what the surgeons considered was in the patients' best interests.

Conclusion

The surgeons seemed confident in their professional role although the many ethical dilemmas they experienced in trying to meet the expectations of patients, colleagues and society also made them professionally and personally vulnerable.
Structural genomics of human proteins – target selection and generation of a public catalogue of expression clones
Authors: Büssow Konrad , Scheich Christoph , Sievert Volker , Harttig Ulrich , Schultz Jörg , Simon Bernd , Bork Peer , Lehrach Hans , Heinemann Udo
Published: July 2005

Background

The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics initiative, targets human proteins for structure determination. It has implemented high throughput procedures for all steps from cloning to structure calculation. This article describes the selection of human target proteins for structure analysis, our high throughput cloning strategy, and the expression of human proteins in Escherichia coli host cells.

Results and Conclusion

Protein expression and sequence data of 1414 E. coli expression clones representing 537 different proteins are presented. 139 human proteins (18%) could be expressed and purified in soluble form and with the expected size. All E. coli expression clones are publicly available to facilitate further functional characterisation of this set of human proteins.
Lysis with Saponin improves detection of the response through CD203c and CD63 in the basophil activation test after crosslinking of the high affinity IgE receptor FcεRI
Authors: Hoffmann Hans Jürgen , Bøgebjerg Mette , Nielsen Lars Peter , Dahl Ronald
Published: July 2005

Background

The basophil activation test (BAT), in which translocation of markers to the surface of blood basophils is measured in response to allergen by flow cytometry, is a rapid assay that is gaining popularity. Two markers are currently being evaluated for the BAT; CD63 and the lineage-specific CD203c. In a recent report, detection of CD203c after lysis with Saponin was shown to be superior to detection of CD63 after lysis with formic acid. We wanted to compare a) lysis with formic acid and lysis with Saponin, b) the response through CD203c and CD63, and c) the definition 10% activated cells above background with the probability binning metric T(χ) > 4, on sets of data generated with blood basophils stimulated with varying concentrations of anti-FcεRI antibody.

Methods

Blood from volunteers was incubated with serial logarithmic dilutions of anti-FcεRI and subsequently with antibodies to CD203c PE and CD63 FITC. Sets of samples set up in parallel were lysed with either Saponin based Whole Blood Lysing reagent or with formic acid based Immunoprep/Q-prep. Samples were acquired on a FACS Calibur, but were compensated and analysed offline. Responders were defined as persons who had 10% or more activated basophils above background, or a T(χ) > 4, for two consecutive dilutions of anti-FcεRI antibody.

Results

More basophils (median 1164 vs. median 397) and better discrimination of upregulated CD203c and CD63 amongst responders were obtained after lysis with Saponin than after lysis with formic acid. We suggest that CD203c may be a more sensitive marker for the BAT than CD63, as 6/11 responders were found with CD203c, compared with 3/11 with CD63. Most responders (7/11) were identified with probability binning.

Conclusion

A combination of lysis with Saponin and the markers CD203c and CD63 computed by probability binning may be the most sensitive method of detecting activation of basophils after stimulation through FcεRI.
Colocalization of endogenous TNF with a functional intracellular splice form of human TNF receptor type 2
Authors: Scherübl Christoph , Schneider-Brachert Wulf , Schütze Stephan , Hehlgans Thomas , Männel Daniela N
Published: July 2005

Background

Tumor necrosis factor (TNF) is a pleiotropic cytokine involved in a broad spectrum of inflammatory and immune responses including proliferation, differentiation, and cell death. The biological effects of TNF are mediated via two cell surface TNF receptors: p55TNFR (TNFR1; CD120a) and p75TNFR (TNFR2; CD120b). Soluble forms of these two receptors consisting of the extracellular domains are proteolytically cleaved from the membrane and act as inhibitors. A novel p75TNFR isoform generated by the use of an additional transcriptional start site has been described and was termed hicp75TNFR. We focused on the characterization of this new isoform as this protein may be involved in chronic inflammatory processes.

Methods

Cell lines were retroviraly transduced with hp75TNFR isoforms. Subcellular localization and colocalization studies with TNF were performed using fluorescence microscopy including exhaustive photon reassignment software, flow cytometry, and receptosome isolation by magnetic means. Biochemical properties of the hicp75TNFR were determined by affinity chromatography, ELISA, and western blot techniques.

Results

We describe the localization and activation of a differentially spliced and mainly intracellularly expressed isoform of human p75TNFR, termed hicp75TNFR. Expression studies with hicp75TNFR cDNA in different cell types showed the resulting protein mostly retained in the trans-Golgi network and in endosomes and colocalizes with endogenous TNF. Surface expressed hicp75TNFR behaves like hp75TNFR demonstrating susceptibility for TACE-induced shedding and NFκB activation after TNF binding.

Conclusion

Our data demonstrate that intracellular hicp75TNFR is not accessible for exogenously provided TNF but colocalizes with endogenously produced TNF. These findings suggest a possible intracellular activation mechanism of hicp75TNFR by endogenous TNF. Subsequent NFκB activation might induce anti-apoptotic mechanisms to protect TNF-producing cells from cytotoxic effects of TNF. In addition, the intracellular and not TACE-accessible splice form of the hp75TNFR could serve as a pool of preformed, functional hp75TNFR.
Vasculature deprivation – induced osteonecrosis of the rat femoral head as a model for therapeutic trials
Authors: Bejar Jacob , Peled Eli , Boss Jochanan H
Published: July 2005

Experimental Osteonecrosis

The authors' experience with experimentally produced femoral capital osteonecrosis in rats is reviewed: incising the periosteum at the base of the neck of the femur and cutting the ligamentum teres leads to coagulation necrosis of the epiphysis. The necrotic debris is substituted by fibrous tissue concomitantly with resorption of the dead soft and hard tissues by macrophages and osteoclasts, respectively. Progressively, the formerly necrotic epiphysis is repopulated by hematopoietic-fatty tissue, and replaced by architecturally abnormal and biomechanically weak bone. The femoral heads lose their smooth-surfaced hemispherical shape in the wake of the load transfer through the hip joint such that, together with regressive changes of the joint cartilage and inflammatory-hyperplastic changes of the articular membrane, an osteoarthritis-like disorder ensues.

Therapeutic Choices

Diverse therapeutic options are studied to satisfy the different opinions concerning the significance of diverse etiological and pathogenic mechanisms: 1. Exposure to hyperbaric oxygen. 2. Exposure to hyperbaric oxygen and non-weight bearing on the operated hip. 3. Medication with enoxaparin. 4. Reduction of intraosseous hypertension, putting to use a procedure aimed at core decompression, namely drilling a channel through the femoral head. 5. Medication with vascular endothelial growth factor with a view to accelerating revascularization. 6. Medication with zoledronic acid to decrease osteoclastic productivity such that the remodeling of the femoral head is slowed.

Glucocorticoid-related osteonecrosisappears to be apoptosis-related, thus differing from the vessel-deprivation-induced tissue coagulation found in idiopathic osteonecrosis. The quantities of TNF-α, RANK-ligand and osteoprotegerin are raised in glucocorticoid-treated osteoblasts so that the differentiation of osteoclasts is blocked. Moreover, the osteoblasts and osteocytes of the femoral cortex mostly undergo apoptosis after a lengthy period of glucocorticoid medication.
Inhibition of Tat activity by the HEXIM1 protein
Authors: Fraldi Alessandro , Varrone Francesca , Napolitano Giuliana , Michels Annemieke A , Majello Barbara , Bensaude Olivier , Lania Luigi
Published: July 2005

Background

The positive transcription elongation factor b (P-TEFb) composed by CDK9/CyclinT1 subunits is a dedicated co-factor of HIV transcriptional transactivator Tat protein. Transcription driven by the long terminal repeat (LTR) of HIV involves formation of a quaternary complex between P-TEFb, Tat and the TAR element. This recruitment is necessary to enhance the processivity of RNA Pol II from the HIV-1 5' LTR promoter. The activity of P-TEFb is regulated in vivo and in vitro by the HEXIM1/7SK snRNA ribonucleic-protein complex.

Results

Here we report that Tat transactivation is effectively inhibited by co-expression of HEXIM1 or its paralog HEXIM2. HEXIM1 expression specifically represses transcription mediated by the direct activation of P-TEFb through artificial recruitment of GAL4-CycT1. Using appropriate HEXIM1 mutants we determined that effective Tat-inhibition entails the 7SK snRNA basic recognition motif as well as the C-terminus region required for interaction with cyclin T1. Enhanced expression of HEXIM1 protein modestly affects P-TEFb activity, suggesting that HEXIM1-mediated repression of Tat activity is not due to a global inhibition of cellular transcription.

Conclusion

These results point to a pivotal role of P-TEFb for Tat's optimal transcription activity and suggest that cellular proteins that regulate P-TEFb activity might exert profound effects on Tat function in vivo.
Saline Systems: A research journal bridging gene systems and ecosystems
Authors: DasSarma Shiladitya
Published: July 2005

Saline Systems addresses the publication needs of scientists conducting basic and applied research on coastal and inland saline environments and their flora and fauna. The journal covers research at all levels, from individual genes to whole genomes and entire ecosystems. Rapid progress in the molecular biology and microbial ecology of halotolerant and halophilic organisms and the sensitivity of many saline environments warrants an online journal with fast turnaround times. Many saline environments are threatened and the need for an Open Access journal to address the dissemination and sharing of knowledge on their conservation and management is compelling. Saline Systems provides an interdisciplinary forum for scientists working within all of the relevant fields.
A hundred years of Dunaliella research: 1905–2005
Authors: Oren Aharon
Published: July 2005

A hundred years have passed since the description of the genus Dunaliella, the unicellular green alga which is responsible for most of the primary production in hypersaline environments worldwide. The present paper provides an historical survey of research on Dunaliella, from the early work in the 19th century to the thorough taxonomic studies by Teodoresco, Hamburger, Lerche and others from the beginnig of the 20th century onwards. It attempts to trace the origin of some of the most important breakthroughs that have contributed to our present understanding of this alga that plays such a key role in many hypersaline environments.
Effect of salinity stress on the life history variables of Branchipus schaefferi Fisher, 1834 (Crustacea: Anostraca)
Authors: Sarma SSS , Beladjal Lynda , Nandini S , Cerón-Martínez Gerardo , Tavera-Briseño Karina
Published: July 2005

Background

Freshwater anostracans inhabit ephemeral water bodies in which as the water level decreases due to evaporation the salt concentration increases. Thus, for most anostracans salinity becomes the major stress factor.

Results

We tested five concentrations of NaCl (0 to 8 g/l) on the life table demography of Branchipus schaefferi fed Chlorella (alga). Age-specific survivorship curves of male and female B. schaefferi showed nearly a similar pattern in that increased salt concentration resulted in decreased survivorship. The age-specific reproduction (mx) of females showed several peaks of cyst production at 0 and 1 g/l salinity while in treatments containing salt at 4 or 8 g/l, there were fewer peaks. Average lifespan, life expectancy at birth, gross and net reproductive rates, generation time and the rate of population increase were all significantly influenced by the salt concentration in the medium. The highest value of net reproductive rate (970 cysts/female) was in treatments containing 0 g/l of salt, while the lowest was 13 cysts/female at 8 g/l. The rate of population increase (r) varied from 0.52 to 0.32 per day depending on the salt concentration in the medium.

Conclusion

The low survival and offspring production of B. schaefferi at higher salinity levels suggests that this species is unlikely to colonize inland saline water bodies. Therefore, the temporary ponds in which it is found, proper conservative measures must be taken to protect this species.
Connectionist Models and Their Properties
Authors: Feldman J.A. , Ballard D.H.
Published: July 2005

Much of the progress in the fields constituting cognitive science has been based upon the use of explicit information processing models, almost exclusively patterned after conventional serial computers. An extension of these ideas to massively parallel, connectionist models appears to offer a number of advantages. After a preliminary discussion, this paper introduces a general connectionist model and considers how it might be used in cognitive science. Among the issues addressed are: stability and noise‐sensitivity, distributed decision‐making, time and sequence problems, and the representation of complex concepts.
Intensional Concepts in Propositional Semantic Networks*
Authors: Maida Anthony S. , Shapiro Stuart C.
Published: July 2005

An integrated statement is made concerning the semantic status of nodes in a propositional semantic network, claiming that such nodes represent only intensions. Within the network, the only reference to extensionality is via a mechanism to assert that two intensions have the same extension in same world. This framework is employed in three application problems to illustrate the nature of its solutions.

The formalism used here utilizes only assertional information and no structural, or definitional, information. This restriction corresponds to many of the psychologically motivated network models. Some of the psychological implications of network processes called node merging and node splitting are discussed. Additionally, it is pointed out that both our networks and the psychologically based networks are prone to memory confusions about knowing unless augmented by domain‐specific inference processes, or by structural information.
Routine Computing Tasks: Planning as Understanding
Authors: Mannes Suzanne M. , Kintsch Walter
Published: July 2005

A system called NETWORK is described which implements the construction‐integration model of Kintsch (1988) in a routine computing‐task domain. This system builds a plan of action on‐line for a given task from a set of plan elements. These plan elements are simple overlearned production rules that are put together by NETWORK to produce plans for novel tasks. This approach is contrasted with other types of planners as NETWORK is shown to plan solutions to a variety of tasks. Discussions focussing on the use of long‐term memory, case‐based reasoning, and planning and acting are presented.

NETWORK takes as input a task description, uses this information to select related knowledge from its long‐term memory, and constructs a network representation of the task. This network is then integrated through a spreading‐activation procedure where irrelevant items in the network become deactivated, and things that appear related sustain each other's higher activation. Subsequently, a decision process chooses a plan element for firing, depending upon its level of activation with those more highly activated being considered for action first. When a plan element is found that can fire, its outcomes are added to the state of the world. The process repeats until a selection of plan elements is produced to complete the task.
A Computational Theory of Learning Causal Relationships
Authors: Pazzani Michael
Published: July 2005

I present a cognitive model of the human ability to acquire causal relationships. I report on experimental evidence demonstrating that human learners acquire accurate causal relationships more rapidly when training examples are consistent with a general theory of causality. This article describes a learning process that uses a general theory of causality as background knowledge. The learning process, which I call theory‐driven learning (TDL), hypothesizes causal relationships consistent both with observed data and the general theory of causality. TDL accounts for data on both the rate at which human learners acquire causal relationships, and the types of causal relationships they acquire. Experiments with TDL demonstrate the advantage of TDL for acquiring causal relationships over similarity‐based approaches to learning: Fewer examples are required to learn an accurate relationship.
The Role of Explanations and Plan Recognition in the Learning of Theatrical Scripts
Authors: Noice Helga
Published: July 2005

It is generally assumed that a professional actor learns a role by committing the words to memory line by line or sentence by sentence. However, a pilot study indicated that this is not so. The research reported here is concerned with specifying the mental processes that professional actors employ in the course of learning theatrical scripts. Twenty‐eight professional actors and 28 novices were assigned either to a gist or a rote condition. The former was designed to reveal the strategies actually used by actors to learn lengthy texts. The latter was designed to require subjects to learn text by repetition with as little contribution from semantic analysis as possible with meaningful material. All subjects were given identical six‐page scenes from a realistic play. Two measures were used: elaborated recall and summarization. Analysis of elaborated recall protocols show that actors construct far more elaborations than novices, and that the great majority of these elaborations concern how the assigned character actively affects or is affected by another character. Results indicate that actors approach the learning of complex material by adopting the assigned character's perspective, and by actively asking questions in order to infer that character's plan.

Summarization results indicate that actors and novices construct different mental representations of the same text. Actors were more likely to summarize the scene as an unfolding process rather than a fixed entity. Also, they tended to ignore the temporal ordering of the text, implying the operation of a plan structure during encoding and retrieval. Furthermore, both expertise and a strategy based on elaboration appeared to encourage the drawing of inferences. This is shown by an increase in the number of subjects (as a function either of strategy or expertise) who included the unstated but implied resolution of the scene in their summaries.
Catalytic Linear Grooving of Graphite Surface Layers by Pt, Ru, and PtRu Nanoparticles
Authors: Takasu Yoshio , Konishi Shunsuke , Miyoshi Ryo , Nukii Keisuke , Matsuse Takehiro , Sugimoto Wataru , Murakami Yasushi
Published: July 2005

Platinum, Ru, and Pt0.5Ru0.5 nanoparticles prepared from respective metal complexes have been found to form grooves, i.e., nanochannels, on cleavage planes of HOPG at 900 °C under a gas mixture stream of hydrogen and nitrogen. The mutual orientation of these grooves observed by HRSEM and AFM was 30 or 60 degrees.
Improved Thermal Stability of LiCoO2 by Cyclotriphosphazene Additives in Lithium-ion Batteries
Authors: Zhang Qing , Noguchi Hideyuki , Wang Hongyu , Yoshio Masaki , Otsuki Masashi , Ogino Takao
Published: July 2005

Fluorinated cyclotriphosphazene is selected as a novel flame-retarding additive in the electrolyte for lithium-ion batteries. The effect of the phosphazenes on the thermal stability of LiCoO2 cathode has been investigated by the thermal analyses on charged LiCoO2 electrodes in the presence of the electrolyte with or without the additives. Possible mechanism for the influence of the additive on the thermal stability of LiCoO2 has been proposed.
Synthetic Studies of Norzoanthamine. Preparation of the Diene-yne-diene Precursor of an ABC-ring Fragment
Authors: Irifune Taiji , Ohashi Tomohiro , Ichino Takao , Sakai Emi , Suenaga Kiyotake , Uemura Daisuke
Published: July 2005

The diene-yne-diene precursor of the ABC-ring fragment of norzoanthamine, a bioactive alkaloid from the colonial zoanthid Zoanthus sp., was prepared.
Fabrication of Silver Probes for Localized Plasmon Excitation in Near-field Raman Spectroscopy
Authors: Saito Yuika , Murakami Takashi , Inouye Yasushi , Kawata Satoshi
Published: July 2005

We present a new method for preparing a silver probe for tip-enhanced near-field Raman spectroscopy. In this method, the probe is coated with silver colloids by a simple chemical reaction known as a mirror reaction. Silver particles ≈40 nm in diameter, which is ideal for localized surface plasmon excitation in the visible wavelength range, are formed at the tip apex with high reproducibility. Futhermore, tip-enhanced Raman spectra of single-walled carbon nanotubes were measured by using the probe.
Synthesis and Properties of Conjugated Copolymer Having Alternate Structure of Diphenylanthracene and Allene
Authors: Hiroki Kazuaki , Kijima Masashi
Published: July 2005

A conjugated copolymer having an alternate structure of 9,10-diphenylanthracene and 1,3-diphenylallene was synthesized by the Suzuki–Miyaura cross-coupling reaction with 9,10-dibororanylanthracene and 1,3-bis(4-bromophenyl)-1,3-diphenylallene. The diphenylanthracene moiety worked as an absorptive and emissive center unit in the polymer. The twisted allene moiety not only controlled conjugation length of the polymer but also suppressed formation of excimers, which realized intense pure blue fluorescence with high quantum efficiency (Φf ≈ 1.0) in CHCl3 solution.
A modified technique to bypass the maxillary artery to supraclinoid internal carotid artery by using radial artery graft: an anatomical study
Authors: Arbağ Hamdi , Ustun Mehmet Erkan , Buyukmumcu Mustafa , Cicekcibasi Aynur Emine , Ulku Cagatay Han
Published: July 2005

Objective: This study aims to examine the use of a radial artery graft for bypass of the maxillary artery (MA) to the supraclinoid internal carotid artery (ICA) in treating ICA occlusions.

Study design and setting: This method was carried out on five adult cadaver sides. The MA was reached 1–2 cm inferior to the crista infratemporalis, following a frontotemporal craniotomy and a zygomatic arch osteotomy. Extradurally 2–3 cm lateral to the foramen rotundum, a hole was drilled in the sphenoid bone with a 4 mm tipped drill. A radial artery graft was passed through the hole to the inside of the dura. Before giving the infraorbital artery branch, the MA was dissected from the surrounding tissue and transected. The proximal end of the graft was anastomosed end-to-end with the MA and the distal end of the graft end-to-side with the supraclinoid ICA.

Results: The mean calibre of the MA was 2.6 ± 0.3 mm. The mean calibre of the proximal end of the radial artery graft was 2.5 ± 0.25 mm and the distal end was 2.35 ± 0.2 mm. The mean length of the radial artery graft was 4.0 ± 0.5cm.

Conclusion: This study suggested that the cases with ICA occlusion, which require high blood flow, may be treated as an alternative to current bypass methods requiring long vein grafts.
The aetiology of chronic cough: a review of current theories for the otorhinolaryngologist
Authors: O’Hara J , Jones N S
Published: July 2005

Most studies agree that post-nasal drip syndrome (PNDS), asthma, gastroesophageal reflux disease (GORD), and laryngopharyngeal reflux (LPR) are the commonest causes of chronic cough in the immunocompetent, non-smoking patient who is not taking an angiotensin-converting enzyme inhibitor. No diagnostic test has been found to define those who are said to have PNDS other than a response to a first-generation antihistamine. Examining the available evidence suggests that mechanical stimulation of the pharynx by mucus is not an adequate theory for the production of cough. Inflammatory mediators in the lower airways are raised in PNDS, cough variant asthma and GORD, and the theory that an inflammatory process is affecting 'one airway' is a plausible one. Nasal disease is more likely to result in cough from the co-existing involvement of the lower airways through an as yet undefined pathway, and eosinophil and mast cell mediation appear a likely mechanism.
Mucocutaneous leishmaniasis presenting as facial cellulitis
Authors: Clayton Rima , Grabczynska Sophie
Published: July 2005

We report a case of mucocutaneous leishmaniasis caused by Leishmania viannia braziliensis. Despite several courses of both oral and intravenous antibiotics no improvement was seen. This case highlights the importance of taking a thorough history, including details of recent travel, and considering rarer causes when no improvement with antibiotics is seen. Our patient was infected with a particularly virulent strain and destruction of the mucous membranes is not uncommon. Rapid diagnosis and treatment are therefore crucial.
Acute otitis media in children - there are guidelines but are they followed?
Authors: Woolley S L , Smith D R K
Published: July 2005

Aims: To determine whether guidelines relating to the diagnosis and treatment of acute otitis media (AOM) in children are followed in a tertiary paediatric emergency department (ED).

Methods: A literature search was undertaken to identify national and international guidelines relating to the diagnosis and management of AOM in children. The guidelines were assessed for their applicability to UK practice. A retrospective case note audit was undertaken. Children presenting to the ED with a discharge diagnosis of AOM over a two month period were identified from the ED computer discharge system. The notes were analysed for compliance with the identified guidelines.

Results: 50 children were identified (age range three months to 11 years). Eighty-six per cent of children received antibiotics. Fifty-two per cent of children had documented signs of AOM. Twenty-five of these children received antibiotics (22 in accordance with guidelines, three not in accordance with guidelines, antibiotic not documented in one case). Thirty-nine per cent of children received antibiotics inappropriately. In all cases, the antibiotic dosage was below the dose recommended in all guidelines.

Conclusion: There is poor compliance with national (and international) guidelines for the management of AOM in this ED. National guidelines must be introduced into the department by direct teaching at senior house officer and middle grade level, a re-audit must be carried out and regular reviews of the notes of patients diagnosed with AOM must be undertaken to ensure compliance with guidelines is maintained.
With a Little Help from My Friends (and Substitutes): Social Referents and Influence in Psychological Contract Fulfillment
Authors: Ho Violet T. , Levesque Laurie L.
Published: July 2005

This study investigated employees’ choice of social referents and the impact of social influence on their beliefs of psychological contract fulfillment. Using data from a field study conducted with 99 employees in a research organization, we found that one’s referent choice varied with the domain of promise evaluated. When evaluating the organization’s fulfillment of organization-wide promises, employees’ referents were primarily coworkers with whom they had close direct ties, namely, friends and advice givers. On the other hand, when evaluating the fulfillment of job-related promises, employees’ referents were mainly fellow workers who could substitute for them and people with whom they had multiple relationships.

The effects of social influence also varied with the domain of promise evaluated. For organization-wide promises, employees’ fulfillment evaluations were similar to those of their friends. However, for job-related promises, their fulfillment evaluations were dissimilar to those of coworkers who played the dual roles of friends and substitutes.

This study advances psychological contracts research by demonstrating that third parties to the psychological contract can influence fulfillment evaluations. In turn, the effect of such influence is contingent on the domain of promises being evaluated and the nature of the networks. We discuss implications for research in psychological contracts, social networks and influence, and referent choice.
Antecedents and Performance Implications of Contracting for Knowledge Workers: Evidence from Information Technology Services
Authors: Mayer Kyle J. , Nickerson Jack A.
Published: July 2005

This paper develops a theory that predicts why firms organize their knowledge workers as employees versus independent contractors and predicts the performance implications of this choice. It then empirically examines this organizational choice—which our theory predicts will be driven by contracting difficulties arising from expropriation concerns, measurement costs, and interdependence—and its implications for profitability for 190 information technology service projects. Using a two-stage switching regression model, our analysis shows that projects aligned according to our theory are on average more profitable than misaligned projects and that firm capability impacts organizational choice but not profitability.
Improvisation and Innovative Performance in Teams
Authors: Vera Dusya , Crossan Mary
Published: July 2005

This paper builds on the principles and insights from improvisational theater to unpack the nature of collective improvisation and to consider what it takes to do it well and to innovate. Furthermore, we discuss the role of training in enhancing the incidence and effectiveness of improvisation. We propose that two common misconceptions about improvisation have hindered managers’ understanding of how to develop the improvisational skill. First, the spontaneous facet of improvisation tends to be overemphasized, and second, there is a general assumption that improvisation always leads to positive performance. Our goal is to clear up the conceptual confusion about improvisation by laying out the various aspects of preparation that are required for effective improvisation. In our theoretical model, we delineate how the improvisational theater principles of “practice,” “collaboration,” “agree, accept, and add,” “be present in the moment,” and “draw on reincorporation and ready-mades” can be used to understand what it takes to improvise well in work teams and to create a context favoring these efforts. Our findings support a contingent view of the impact of improvisation on innovative performance. Improvisation is not inherently good or bad; however, improvisation has a positive effect on team innovation when combined with team and contextual moderating factors. We also provide initial evidence suggesting that the improvisational skill can be learned by organizational members through training. Our results shed light on the opportunities provided by training in improvisation and on the challenges of creating behavioral change going beyond the individual to the team and, ultimately, to the organization.