bluuebunny/crossref_metadata_2025 huggingface dataset:
Limited Utility of a Rapid Quantitative Enzyme-Linked Fluorescent Assay for the D-Dimer in the Diagnosis of Overt Disseminated Intravascular Coagulation
Authors: Sharma Prashant , Saxena Renu
Published: March 2010

The role of quantitative D-dimer assay in screening for and diagnosing overt disseminated intravascular coagulation (DIC), conventionally diagnosed by the International Society of Thrombosis and Haemostasis’ (ISTH) score, was evaluated. Of patients with clinical conditions associated with overt DIC, 142 with ISTH scores ≥5 (compatible with overt DIC) and 61 with ISTH scores <5 (suggestive of nonovert DIC) underwent the quantitative D-dimer assay. Accuracy indices, receiver operating characteristic (ROC) curve—derived cutoffs, and areas under curve were compared. Mean D-dimer level in overt DIC was 4147.2 ± 2707 ng/mL. In nonovert DIC, it was 1678.9 ± 1888.3 ng/mL. Both were higher than healthy controls (229.6 ± 129.9 ng/mL). An optimized cutoff (2040 ng/mL) had relatively low sensitivity (75.4%) and specificity (73.8%). Extensive overlap between groups at this cutoff reduced diagnostic utility. Lowered cutoffs increased sensitivity (eg, 91.5% at 1000 ng/mL) but diminished specificity (59%), limiting use of screening. In conclusion, the quantitative D-dimer as a stand-alone assay has a limited role in diagnosis of overt DIC.
Developmental pathways for first language acquisition of Mandarin nominal expressions: Comparing monolingual with simultaneous Mandarin—English bilingual children
Authors: Chang-Smith Meiyun
Published: March 2010

This comparative study explores the first language acquisition of Mandarin nominal expressions by monolingual and simultaneous Mandarin—English bilingual children, with the aim of contributing new data relevant to the autonomous vs. interdependent debate in bilingual first language acquisition. More specifically, it focuses on the developmental sequences of complex definite and indefinite nominal expressions in the forms of [demonstrative + numeral + classifier + noun] and [numeral + classifier + noun] respectively, comparing both qualitatively and quantitatively the developmental pathways and time progression observed in corpora derived from two longitudinal studies. The bilingual corpus analyzed consists of an extensive daily record of utterances from age 10 months to 33 months, while the monolingual corpus is derived from a set of eight video recorded sessions spanning the age range from 20 months to 26 months. The outcomes provide support for the Autonomous Development Hypothesis, to the extent that the developmental pathway of Mandarin nominal expressions as elaborated in the bilingual child’s case is found to be highly comparable with that of the monolingual counterpart and that up to the end of the observation period no apparent transfers from English nominal syntax to Mandarin were observed.
BAMFLA: Issues, methods and directions
Authors: Li Wei
Published: March 2010

This introduction to the special issue of Bilingual and Multilingual First Language Acquisition (BAMFLA) of Chinese children outlines theoretical concerns and methodological issues, as well as future directions of this fast developing research area.
The phonological development of a trilingual child: Facts and factors
Authors: Yang Hsueh-Yin , Zhu Hua
Published: March 2010

This article investigates the early phonological development of a trilingual child who is acquiring Spanish, Mandarin and Taiwanese simultaneously. By examining the natural speech data recorded between the age of 1;3 and 2;0, the article reports the age of emergence and stabilization of the vowels and consonants, speech accuracy and phonological error patterns in each language. The data show that by the age of two the child is able to produce most of the vowels in the three languages. However, there are cross-linguistic differences in the rate of acquisition of consonants and speech accuracy: the child’s Spanish consonant inventory develops faster than the other two languages, while the child has statistically significantly higher speech accuracy in Taiwanese than in Spanish, which is in turn higher than that in Mandarin. There is also evidence of interaction or interference between the languages, e.g. the existence of unusual error patterns. These facts are interpreted in the context of phonological saliency of the three phonological systems and language input.
Children’s play after anaesthesia and surgery: background factors and associations to behaviour during anaesthetic induction
Authors: Proczkowska-Björklund Marie , Gustafsson Per A. , Svedin Carl Göran
Published: March 2010

Children can experience anaesthetic induction as fearful and frightening and this can lead to postoperative behaviour changes and symptoms of high anxiety. A fearful experience can also lead to avoidant reactions due to raised negative emotions in situations similar to that, which evoked the fear. To analyse children’s reactions after anaesthesia to anaesthetic play equipment, 49 children (three—six years old) were video-filmed during play with anaesthetic equipment 14 days after anaesthesia and surgery. The risk that the child avoided playing with anaesthetic equipment was increased if the child took the premedication unwillingly and if the child was younger. The risk for not telling about the experience was increased if the child took the premedication unwillingly and if the child showed signs of shyness. The risk for telling mostly unspecific memories increased if the child was younger and if the child showed signs of shyness. Avoidant reactions could bee seen in 50 percent of the children. It is important to be aware of the characteristics of a vulnerable child (age, shyness) and to meet the child without raising negative emotions in any part of the anaesthetic process, in order to avoid negative reactions in future encounters.
What a Mess
Authors: White Michele
Published: March 2010

eBay promises to engage everyone while asserting its organizational logic and configuring people. eBay encourages members to identify as traditionally gendered and heterosexual by employing personalization and Web 2.0 conventions. Members tend to follow eBay’s directives and self-present with such culturally approved identities as binary gendered individuals and heterosexual couples. These identities, including the over 1000 portrayals of heterosexual couples and chaotic homes that I analyze using the humanities methods of close visual, textual and theoretical analysis are worth studying because they are derived from significant identifications with objects, consumerism and the company, and compromised by the messy aspects of collecting and the purportedly defiling features of used objects. Members’ depictions of disordered homes negatively code individuals, render the eBay site and auctions as less desirable and suggest the association of the company with goodness and heteronormative purity is fraudulent. The clutter and disorganization of other Web 2.0 sites also troubles traditional identity positions and organizational logics. Further research into the ways norming occurs in these settings is imperative because narratives about internet empowerment make it difficult to identify how regulation and personalization work together.
User Authority Through Mediated Interaction
Authors: Laughey Dan
Published: March 2010

This article will attempt to outline the most significant implications posed by eBay to traditional relationships between producers and consumers. In several respects, eBay provides greater seller—buyer interactivity and inclusiveness than any other marketplace. The new forms of mediated interaction opened up by eBay seem to accommodate greater scope for what I call ‘user authority’ than have ever existed previously. This article will apply theories of productive consumption, consumer authority and mediated interactions to an empirical study of eBay-in-use, drawing on the author’s autobiographical experiences alongside those of a network of sellers of antique and collectable items.
Consuming Professions
Authors: Hardey Michael
Published: March 2010

By the middle of the 20th century the medical profession had established itself as the archetypical profession. The relationship between doctor and patient was variously regarded as ‘special’, ‘outside’ or otherwise at a distance from other consumer experiences. Since then, the status of doctors has changed and information about health and illness has moved from the confines of the consulting room to the World Wide Web. This article considers the recent development of Web 2.0 resources that are constructed around user-generated content about identified health practitioners and services. Web sites where users can both read and write comments about health practitioners and services reflect the broader consumer content industry commonly associated with sites such as Amazon and TripAdvisor. In this article, user reviews about health care are contextualized along two dimensions: first, the relationship with differently oriented health care systems; and second, the engagement with Web 2.0 characteristics and challenges to established consumer information sources. Examples are provided from a number of user-review sites and the implications of their growing popularity are discussed. It is concluded that we are witnessing the beginning of a new phase of the doctor—consumer/patient relationship.
‘Love it. Buy it. Sell it’
Authors: Denegri-Knott Janice , Molesworth Mike
Published: March 2010

Our work adds to existing research on eBay by presenting it as a space where consumers’ imaginations are stimulated and where their psychological work to manufacture ever new wants and desires allows for a reflection of consumer tastes and practices. To do so, we conceptualize eBay as a digital virtual space that allows consumers to browse at length through a plethora of goods, test preferences and potentially reflect on the significance of objects and daydreams pursued.

Conceptually, we draw a synthesis between desire and imagination-laden narratives within consumer research with Rob Shield’s analytic of the digital virtual and its relationship to the real and ideal. From that reading we attribute eBay with a liminoid texture that helps us account for the social dramas that some of its users, such as famed science fiction writer William Gibson, may experience. We argue that whilst eBay does not provoke the initial breach, its enormous, global, ever changing catalogue of goods, produces a crisis that invites the user to engage in redressive action. That analysis has two moments, one focusing on the eBay experience as a form of flânerie, and then, how visual and written information gathered from searching eBay can be used to craft daydreams relative to a desired good. Specifically, we consider concrete consumer practices through which consumers feed and actualize more substantive daydreams of an improved life, including bookmarking, bidding and winning (owning) desired items. We conclude that eBay’s significance as a seductive site to consume (in) lies in its ability to allow for the continuous construction of latent wants while providing consumers with the tools to react to these wants in various ways.
University students’ attitudes about learning in small groups after frequent participation
Authors: Hillyard Cinnamon , Gillespie Diane , Littig Peter
Published: March 2010

This study examined the frequency of small groups in university students’ coursework and how that related to their general attitudes toward learning in groups and their views about different aspects of group work. We administered a survey to 208 students in an upper-division interdisciplinary arts and sciences program. Students reported that they had been in multiple groups, of different duration and types, both in their current program and in courses at their lower-division institutions. A regression analysis uncovered strong relationships between students’ past and present group experiences, peers, and instructor clarity about group purpose. The findings suggest that successful group work is no longer a matter of instructor effort but requires campus initiatives and interdepartmental coordination if students are to understand and experience the benefits of learning in small groups.
Distinguishing the learning approaches adopted by undergraduates in their use of online resources
Authors: Knight Jasper
Published: March 2010

This article reports a study which sought to evaluate the different learning strategies adopted by students when accessing virtual learning environment (VLE)-hosted resources because, if student achievement corresponds to the learning strategy that is adopted whilst accessing VLE resources, directed tasks can be put in place that will encourage students to adopt the learning strategy that is most closely associated with this higher achievement. The different approaches adopted by undergraduates ( n = 46) in their use of online learning resources for a single second-year module are evaluated by analysing their record of accessing these resources at three time-points during the module, and their performance in coursework and exams. From these longitudinal data, three learning approaches are identified (two surface and one deep). It is found that students who adopted a deep learning approach, in which online resources were accessed consistently throughout the module, performed markedly higher than surface learners who focused their online activity at the beginning or end of the module’s duration. Implications for teaching strategies are discussed.
Assessing autonomous learning in research methods courses: Implementing the student-driven research project
Authors: Vandiver Donna M. , Walsh Jeffrey A.
Published: March 2010

As empirical assessments of teaching strategies increase in many disciplines and across many different courses, a paucity of such assessment seems to exist in courses devoted to social science research methods. This lack of assessment and evaluation impedes progress in developing successful teaching pedagogy. The teaching— learning issue addressed here incorporates active learning teaching strategies with autonomous student learning. The strategy was implemented in research methods courses with inherently complex material not conducive to passive teaching and learning strategies. This work implemented a pre/post-test assessment of undergraduate students in a research methods course who participated in a semester-long tiered-assignment research project. Findings suggest that students’ learning preferences increased over the semester for each type inquired; students felt, upon completion of the semester, that they could conduct a research project if asked to do so; their interest in research methods and appreciation for the subject increased over the semester; and they enjoyed learning about their peers’ behavior.
The more the merrier? The effect of group size on effectiveness in SME funding campaigns
Authors: Wincent Joakim , Örtqvist Daniel , Eriksson Jessica , Autio Erkko
Published: March 2010

To overcome resource shortages, companies can subscribe to groups that, in competition with other groups, seek to obtain external funding for the joint development of innovations. In this context, the authors argue smaller groups are better equipped to be successful in external funding campaigns. Based on five-year panel data from a sample of 53 Swedish groups of small and medium-sized companies, the authors find support for a claim suggesting that due to the adverse effect of group size on governance and internal cohesion, the costs associated with group size will outweigh benefits, which reduce the ability to compete for external funding. Consistent with their expectations, the authors find that the adverse effect of group size on fundraising effectiveness is mitigated by internal and external governance devices including the presence of external directors on the group board and interlocking board memberships, and by a bottom-up group formation process.
An influenza outbreak in a regional residential facility
Authors: Hurley James C , Flockhart Susan
Published: March 2010

Influenza is a highly contagious infection with the potential for outbreaks in residential facilities despite seemingly adequate vaccination levels among residents. The management of an influenza A outbreak in a residential facility for cognitively impaired residents of an Australian regional health service is described. Twenty-five of the residents of a 60-bed standalone facility were affected, with one fatality resulting. As virological confirmation of the outbreak was received late on a Friday, the initiation of antiviral treatment and prophylaxis occurred out of hours. The unanticipated consequences of this out-of-hours management are discussed. The management of an influenza outbreak in a dementiaspecific residential facility requires a specific infection control response which anticipates the ethical issues relating to the care of the cognitively impaired.
Analysis of the impact of a new electro-chemical activation system for potable water disinfection on the Legionella pneumophila isolation rate in a Spanish hospital
Authors: Rivera J.M. , Granizo J.J. , Aguilar L. , Giménez M.J. , Aguiar J.M. , Mozota J. , Vos-Arenilla A. , Prieto J.
Published: March 2010

In a field study comparing isolation rates pre- and post-installation of an electro-chemical activation system for Legionella pneumophila disinfection of potable hot water in a Spanish hospital, a total of 250 tap samples pre-installation and 113 post-installation were collected. Chlorine levels were higher ( p < 0.001) post-installation (0.55 ± 0.41 vs. 1.19 ± 0.44 ppm). Of 38.0% (138/363) samples positive for L. pneumophila, 111 (80.4%) were serogroups 2—14. Post-installation, the isolation rate was lower (46.8% vs. 18.6%; p < 0.001, odds ratio (OR) 0.26, 95% confidence interval (CI) 0.15—0.44) due to significant ( p < 0.001; OR 0.25, 95% CI 0.14—0.45) reduction in L. pneumophila serogroups 2—14 from 38.4% to 13.3%. Post-installation, isolation rates were lower in spring (44.4% vs. 0.0%; p < 0.001), summer (80.0% vs. 25.0%; p = 0.003) and autumn (72.0% vs. 28.9%; p = 0.018), but not in winter (18.5% vs. 11.8%; p = 0.688). The seasonal wave constructed with pre-installation data significantly decreased post-installation by decreasing isolation rates in summer and autumn to rates similar to those found in winter pre-installation.
The use of an e-learning infection prevention programme in the pre-registration nursing curriculum
Authors: Pellowe C. , Adams J. , Elliott S. , Murrell K. , Cox D.
Published: March 2010

The infection prevention e-learning project initiated by the NHS University was launched in September 2005 and is now administered by the NHS Core Learning Unit. It was intended to be the definitive infection prevention programme for all NHS staff both clinical and non-clinical; however, a higher education institution saw its potential for use in the pre-registration nursing programme and trialled it in the Common Foundation Programme (CFP). This article describes the use of the programme in the CFP and an evaluation of the students’ experience of e-learning.
Influence of tin and bismuth on machinability of lead free 6000 series aluminium alloys
Authors: Timelli G. , Bonollo F.
Published: March 2010

The present paper presents the microstructural characteristics of an extruded AA6012A-T6 (AlMgSiBiSn) alloy and the microstructural changes occurring during turning operations, analysing the mechanism involved in chip breaking. An experimental investigation has been conducted to determine the effects of different cutting speed and feedrate on the machinability of the alloy. The machinability of the AA6012A-T6 alloy, where Pb is substituted by Bi and Sn, has then been compared to the standard AA6012-T6 (AlMgSiPb) and AA6082-T6 (AlSiMg) alloys. The results indicate that the extensive plastic deformation induces a preferred orientation of the grain structure and secondary phases along the shear plane, and a local increase in the alloy temperature. Low melting point compounds, such as the Sn and Bi bearing particles, transform into a soft or liquid state, changing their initial compact shape to assume a needle-like morphology. The β-Mg2Si and α-Al(FeMn)Si particles are not influenced by the working temperature and keep their initial shape. The AA6082-T6 alloy shows a very poor machinability, with long and continuous strips, while the AA6012A-T6 alloy reveals a good chip formation with small and discontinuous C shaped chips, similar to the AA6012-T6 (AlMgSiPb) alloy. In particular, a feedrate higher than 0·2 mm rev−1 provides short and suitable chips, independently of cutting speed.
Phase field method
Authors: Qin R. S. , Bhadeshia H. K.
Published: March 2010

In an ideal scenario, a phase field model is able to compute quantitative aspects of the evolution of microstructure without explicit intervention. The method is particularly appealing because it provides a visual impression of the development of structure, one which often matches observations. The essence of the technique is that phases and the interfaces between the phases are all incorporated into a grand functional for the free energy of a heterogeneous system, using an order parameter which can be translated into what is perceived as a phase or an interface in ordinary jargon. There are, however, assumptions which are inconsistent with practical experience and it is important to realise the limitations of the method. The purpose of this review is to introduce the essence of the method, and to describe, in the context of materials science, the advantages and pitfalls associated with the technique.
Reinforcing effect of carbon nanotubes on PEEK composite filled with carbon fibre
Authors: Li J. , Zhang L. Q.
Published: March 2010

The main objective of the present paper is to develop high wear resistance carbon fibre reinforced polyether ether ketone composite with addition of multiwall carbon nanotubes. These compounds were well mixed in a batch mixer, and compounded polymers were fabricated into sheets of known thickness by compression moulding. Samples were tested for wear resistance with respect to different concentration of fillers. The wear resistance properties of these samples depend on filler aspect ratio. Wear resistance of composite with 20 wt- of carbon fibre increases when multiwall carbon nanotubewas introduced. The worn surface features have been examined using scanning electron microscope. Photomicrographs of the worn surfaces revealed higher wear resistance with the addition of carbon nanotube. Also better interfacial adhesion between carbon and vinyl ester in carbon reinforced vinyl ester composite was observed.
FOXO3A as a key molecule for all-trans retinoic acid–induced granulocytic differentiation and apoptosis in acute promyelocytic leukemia
Authors: Sakoe Yasuhiko , Sakoe Kumi , Kirito Keita , Ozawa Keiya , Komatsu Norio
Published: March 2010

All-trans retinoic acid (ATRA) induces granulocytic differentiation and apoptosis in acute promyelocytic leukemia (APL) cells, although the detailed mechanisms are not fully understood. We investigated ATRA-induced cellular responses mediated by the transcription factor FOXO3A in APL cells. FOXO3A was constitutively phosphorylated and localized in the cytoplasm in both APL-derived NB4 cells and primary APL cells. Upon treating the cells with ATRA, FOXO3A phosphorylation was reduced and FOXO3A translocated into the nucleus. In addition, the expression of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL), a target molecule for FOXO3A, was increased at the transcriptional and protein levels. As expected, transfection of a short hairpin RNA (shRNA) oligonucleotide specific for FOXO3A significantly inhibited ATRA-induced granulocytic differentiation and apoptosis in NB4 cells. In NB4-derived ATRA-resistant NB4/RA cells, neither FOXO3A nuclear localization nor subsequent TRAIL induction was observed after ATRA treatment. Furthermore, forced expression of active FOXO3A in the nucleus induced TRAIL production and apoptosis in NB4/RA cells. We conclude that activation of FOXO3A is an essential event for ATRA-induced cellular responses in NB4 cells. FOXO3A is a promising target for therapeutic approaches to overcome ATRA resistance in APL.
A novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting relative thermostability of protein mutants
Authors: Li Yunqi , Middaugh C Russell , Fang Jianwen
Published: March 2010

Background

The ability to design thermostable proteins is theoretically important and practically useful. Robust and accurate algorithms, however, remain elusive. One critical problem is the lack of reliable methods to estimate the relative thermostability of possible mutants.

Results

We report a novel scoring function for discriminating hyperthermophilic and mesophilic proteins with application to predicting the relative thermostability of protein mutants. The scoring function was developed based on an elaborate analysis of a set of features calculated or predicted from 540 pairs of hyperthermophilic and mesophilic protein ortholog sequences. It was constructed by a linear combination of ten important features identified by a feature ranking procedure based on the random forest classification algorithm. The weights of these features in the scoring function were fitted by a hill-climbing algorithm. This scoring function has shown an excellent ability to discriminate hyperthermophilic from mesophilic sequences. The prediction accuracies reached 98.9% and 97.3% in discriminating orthologous pairs in training and the holdout testing datasets, respectively. Moreover, the scoring function can distinguish non-homologous sequences with an accuracy of 88.4%. Additional blind tests using two datasets of experimentally investigated mutations demonstrated that the scoring function can be used to predict the relative thermostability of proteins and their mutants at very high accuracies (92.9% and 94.4%). We also developed an amino acid substitution preference matrix between mesophilic and hyperthermophilic proteins, which may be useful in designing more thermostable proteins.

Conclusions

We have presented a novel scoring function which can distinguish not only HP/MP ortholog pairs, but also non-homologous pairs at high accuracies. Most importantly, it can be used to accurately predict the relative stability of proteins and their mutants, as demonstrated in two blind tests. In addition, the residue substitution preference matrix assembled in this study may reflect the thermal adaptation induced substitution biases. A web server implementing the scoring function and the dataset used in this study are freely available at http://www.abl.ku.edu/thermorank/.
Role of casein kinase 1 in the glucose sensor-mediated signaling pathway in yeast
Authors: Pasula Satish , Chakraborty Samujjwal , Choi Jae H , Kim Jeong-Ho
Published: March 2010

Background

In yeast, glucose-dependent degradation of the Mth1 protein, a corepressor of the glucose transporter gene (HXT) repressor Rgt1, is a crucial event enabling expression of several HXT. This event occurs through a signaling pathway that involves the Rgt2 and Snf3 glucose sensors and yeast casein kinase 1 and 2 (Yck1/2). In this study, we examined whether the glucose sensors directly couple with Yck1/2 to convert glucose binding into an intracellular signal that leads to the degradation of Mth1.

Results

High levels of glucose induce degradation of Mth1 through the Rgt2/Snf3 glucose signaling pathway. Fluorescence microscopy analysis indicates that, under glucose-limited conditions, GFP-Mth1 is localized in the nucleus and does not shuttle between the nucleus and cytoplasm. If glucose-induced degradation is prevented due to disruption of the Rgt2/Snf3 pathway, GFP-Mth1 accumulates in the nucleus. When engineered to be localized to the cytoplasm, GFP-Mth1 is degraded regardless of the presence of glucose or the glucose sensors. In addition, removal of Grr1 from the nucleus prevents degradation of GFP-Mth1. These results suggest that glucose-induced, glucose sensor-dependent Mth1 degradation occurs in the nucleus. We also show that, like Yck2, Yck1 is localized to the plasma membrane via C-terminal palmitoylation mediated by the palmitoyl transferase Akr1. However, glucose-dependent degradation of Mth1 is not impaired in the absence of Akr1, suggesting that a direct interaction between the glucose sensors and Yck1/2 is not required for Mth1 degradation.

Conclusion

Glucose-induced, glucose sensor-regulated degradation of Mth1 occurs in the nucleus and does not require direct interaction of the glucose sensors with Yck1/2.
Molecular profiling of the developing mouse axial skeleton: a role for Tgfbr2 in the development of the intervertebral disc
Authors: Sohn Philip , Cox Megan , Chen Dongquan , Serra Rosa
Published: March 2010

Background

Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-β superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing mouse tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-β has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-β action in these specialized joints is not known. One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing mouse IVD and to begin to understand the mechanism of TGF-β action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing mouse vertebrae and IVD. We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice as well as in sclerotome cultures treated with TGF-β or BMP4.

Results

Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/database searches resulting in a list of genes that can be used as markers of IVD. Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We also generated lists of genes regulated by TGF-β or BMP4 in cultured sclerotome. As expected, treatment with BMP4 resulted in up-regulation of cartilage marker genes including Acan, Sox 5, Sox6, and Sox9. In contrast, treatment with TGF-β1 did not regulate expression of cartilage markers but instead resulted in up-regulation of many IVD markers including Fmod and Adamtsl2.

Conclusions

We propose TGF-β has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-β that warrant further investigation as regulators of IVD development.
The role of phenotypic plasticity on the proteome differences between two sympatric marine snail ecotypes adapted to distinct micro-habitats
Authors: Martínez-Fernández Mónica , de la Cadena María Páez , Rolán-Alvarez Emilio
Published: March 2010

Background

The role of phenotypic plasticity is increasingly being recognized in the field of evolutionary studies. In this paper we look at the role of genetic determinationversusplastic response by comparing the protein expression profiles between two sympatric ecotypes adapted to different shore levels and habitats using two-dimensional protein maps.

Results

We compared qualitative and quantitative differences in protein expression between pools of both ecotypes from different environments (field and laboratory conditions). The results suggested that ecotype differences may affect about 7% of the proteome in agreement with previous studies, and moreover these differences are basically insensitive to environmental changes. Thus, observed differences between wild ecotypes can be mainly attributed to genetic factors rather than phenotypic plasticity.

Conclusions

These results confirm the mechanism of adaptation already proposed in this species and a minor role of phenotypic plasticity in this ecological speciation process. In addition, this study provides a number of interesting protein spots potentially involved in adaptation, and therefore candidates for a future identification.
New insights into the evolution of subtilisin-like serine protease genes in Pezizomycotina
Authors: Li Juan , Yu Li , Yang Jinkui , Dong Linqian , Tian Baoyu , Yu Zefen , Liang Lianming , Zhang Ying , Wang Xu , Zhang Keqin
Published: March 2010

Background

Subtilisin-like serine proteases play an important role in pathogenic fungi during the penetration and colonization of their hosts. In this study, we perform an evolutionary analysis of the subtilisin-like serine protease genes of subphylum Pezizomycotina to find if there are similar pathogenic mechanisms among the pathogenic fungi with different life styles, which utilize subtilisin-like serine proteases as virulence factors. Within Pezizomycotina, nematode-trapping fungi are unique because they capture soil nematodes using specialized trapping devices. Increasing evidence suggests subtilisin-like serine proteases from nematode-trapping fungi are involved in the penetration and digestion of nematode cuticles. Here we also conduct positive selection analysis on the subtilisin-like serine protease genes from nematode-trapping fungi.

Results

Phylogenetic analysis of 189 subtilisin-like serine protease genes from Pezizomycotina suggests five strongly-supported monophyletic clades. The subtilisin-like serine protease genes previously identified or presumed as endocellular proteases were clustered into one clade and diverged the earliest in the phylogeny. In addition, the cuticle-degrading protease genes from entomopathogenic and nematode-parasitic fungi were clustered together, indicating that they might have overlapping pathogenic mechanisms against insects and nematodes. Our experimental bioassays supported this conclusion. Interestingly, although they both function as cuticle-degrading proteases, the subtilisin-like serine protease genes from nematode-trapping fungi and nematode-parasitic fungi were not grouped together in the phylogenetic tree. Our evolutionary analysis revealed evidence for positive selection on the subtilisin-like serine protease genes of the nematode-trapping fungi.

Conclusions

Our study provides new insights into the evolution of subtilisin-like serine protease genes in Pezizomycotina. Pezizomycotina subtilisins most likely evolved from endocellular to extracellular proteases. The entomopathogenic and nematode-parasitic fungi likely share similar properties in parasitism. In addition, our data provided better understanding about the duplications and subsequent functional divergence of subtilisin-like serine protease genes in Pezizomycotina. The evidence of positive selection detected in the subtilisin-like serine protease genes of nematode-trapping fungi in the present study suggests that the subtilisin-like serine proteases may have played important roles during the evolution of pathogenicity of nematode-trapping fungi against nematodes.
Transcriptome profiling of a Sinorhizobium meliloti fadD mutant reveals the role of rhizobactin 1021 biosynthesis and regulation genes in the control of swarming
Authors: Nogales Joaquina , Domínguez-Ferreras Ana , Amaya-Gómez Carol V , van Dillewijn Pieter , Cuéllar Virginia , Sanjuán Juan , Olivares José , Soto María J
Published: March 2010

Background

Swarming is a multicellular phenomenom characterized by the coordinated and rapid movement of bacteria across semisolid surfaces. In Sinorhizobium meliloti this type of motility has been described in a fadD mutant. To gain insights into the mechanisms underlying the process of swarming in rhizobia, we compared the transcriptome of a S. meliloti fadD mutant grown under swarming inducing conditions (semisolid medium) to those of cells grown under non-swarming conditions (broth and solid medium).

Results

More than a thousand genes were identified as differentially expressed in response to growth on agar surfaces including genes for several metabolic activities, iron uptake, chemotaxis, motility and stress-related genes. Under swarming-specific conditions, the most remarkable response was the up-regulation of iron-related genes. We demonstrate that the pSymA plasmid and specifically genes required for the biosynthesis of the siderophore rhizobactin 1021 are essential for swarming of a S. meliloti wild-type strain but not in a fadD mutant. Moreover, high iron conditions inhibit swarming of the wild-type strain but not in mutants lacking either the iron limitation response regulator RirA or FadD.

Conclusions

The present work represents the first transcriptomic study of rhizobium growth on surfaces including swarming inducing conditions. The results have revealed major changes in the physiology of S. meliloti cells grown on a surface relative to liquid cultures. Moreover, analysis of genes responding to swarming inducing conditions led to the demonstration that iron and genes involved in rhizobactin 1021 synthesis play a role in the surface motility shown by S. meliloti which can be circumvented in a fadD mutant. This work opens a way to the identification of new traits and regulatory networks involved in swarming by rhizobia.
The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization
Authors: Tam Patrick PC , Barrette-Ng Isabelle H , Simon Dawn M , Tam Michael WC , Ang Amanda L , Muench Douglas G
Published: March 2010

Background

Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD) is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants.

Results

The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1) RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus.

Conclusions

The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to date. This, along with the amino acid variability observed within their PUM-HDs, suggests that these proteins may be involved in a wide range of post-transcriptional regulatory events that are important in providing plants with the ability to respond rapidly to changes in environmental conditions and throughout development.
Hip fracture types in men and women change differently with age
Authors: Tanner David A , Kloseck Marita , Crilly Richard G , Chesworth Bert , Gilliland Jason
Published: March 2010

Background

Hip fractures are expensive and a frequent cause of morbidity and mortality in the elderly. In most studies hip fractures have been viewed as a unitary fracture but recently the two main types of fracture (intertrochanteric and subcapital) have been viewed as two fractures with a different etiology and requiring a different approach to prevention. The relative proportion of intertrochanteric fractures increases with age in women. In previous studies no particular pattern in men has been noted. In this study, we explored changes in the relative proportion of the two fracture types with age in the two genders.

Methods

Patients of 50 years and older, with a diagnosis of hip fracture, discharged from two local acute care hospitals over a 5 year period (n = 2150) were analyzed as a function of age and gender to explore the relative proportions of intertrochanteric and subcapital fractures, and the change in relative proportion in the two genders with age.

Results

Overall, for the genders combined, the proportion of intertrochanteric fractures increases with age (p = .007). In women this increase is significant (p < .001), but in men the opposite pattern is observed, with the proportion of intertrochanteric fractures falling significantly with age (p = .025).

Conclusions

The pattern of hip fractures is different in men and women with aging. It is likely that the pattern difference reflects differences in type and rate of bone loss in the genders, but it is conjectured that the changing rate and pattern of falling with increasing age may also be important. The two main hip fracture types should be considered distinct and different and be studied separately in studies of cause and prevention.
Telling partners about chlamydia: how acceptable are the new technologies?
Authors: Hopkins Carol A , Temple-Smith Meredith J , Fairley Christopher K , Pavlin Natasha L , Tomnay Jane E , Parker Rhian M , Bowden Frank J , Russell Darren B , Hocking Jane S , Chen Marcus Y
Published: March 2010

Background

Partner notification is accepted as a vital component in the control of chlamydia. However, in reality, many sexual partners of individuals diagnosed with chlamydia are never informed of their risk. The newer technologies of email and SMS have been used as a means of improving partner notification rates. This study explored the use and acceptability of different partner notification methods to help inform the development of strategies and resources to increase the number of partners notified.

Methods

Semi-structured telephone interviews were conducted with 40 people who were recently diagnosed with chlamydia from three sexual health centres and two general practices across three Australian jurisdictions.

Results

Most participants chose to contact their partners either in person (56%) or by phone (44%). Only 17% chose email or SMS. Participants viewed face-to-face as the "gold standard" in partner notification because it demonstrated caring, respect and courage. Telephone contact, while considered insensitive by some, was often valued because it was quick, convenient and less confronting. Email was often seen as less personal while SMS was generally considered the least acceptable method for telling partners. There was also concern that emails and SMS could be misunderstood, not taken seriously or shown to others. Despite these, email and SMS were seen to be appropriate and useful in some circumstances. Letters, both from the patients or from their doctor, were viewed more favourably but were seldom used.

Conclusion

These findings suggest that many people diagnosed with chlamydia are reluctant to use the new technologies for partner notification, except in specific circumstances, and our efforts in developing partner notification resources may best be focused on giving patients the skills and confidence for personal interaction.
Pancreatic adenocarcinoma exerts systemic effects on the peripheral blood myeloid and plasmacytoid dendritic cells: an indicator of disease severity?
Authors: Tjomsland Vegard , Sandström Per , Spångeus Anna , Messmer Davorka , Emilsson Johan , Falkmer Ursula , Falkmer Sture , Magnusson Karl-Eric , Borch Kurt , Larsson Marie
Published: March 2010

Background

Dendritic cells (DCs) isolated from tumor bearing animals or from individuals with solid tumors display functional abnormalities and the DC impairment has emerged as one mechanism for tumor evasion from the control of the immune system. Ductal pancreatic adenocarcinoma (PDAC), the most common pancreatic cancer, is recognized as a very aggressive cancer type with a mortality that almost matches the rate of incidence.

Methods

We examined the systemic influence ductal pancreatic adenocarcinoma (PDAC) exerted on levels of peripheral blood DCs and inflammatory mediators in comparison to the effects exerted by other pancreatic tumors, chronic pancreatitis, and age-matched controls.

Results

All groups examined, including PDAC, had decreased levels of myeloid DCs (MDC) and plasmacytoid DCs (PDC) and enhanced apoptosis in these cells as compared to controls. We found elevated levels of PGE2 and CXCL8 in subjects with PDAC, and chronic pancreatitis. Levels of these inflammatory factors were in part restored in PDAC after tumor resection, whereas the levels of DCs were impaired in the majority of these patients ~12 weeks after tumor removal. Our results prove that solid pancreatic tumors, including PDAC, systemically affect blood DCs. The impairments do not seem to be tumor-specific, since similar results were obtained in subjects with chronic pancreatitis. Furthermore, we found that PDAC patients with a survival over 2 years had significant higher levels of blood DCs compared to patients with less than one year survival.

Conclusions

Our findings points to the involvement of inflammation in the destruction of the blood MDCs and PDCs. Furthermore, the preservation of the blood DCs compartment in PDAC patients seems to benefit their ability to control the disease and survival.