bluuebunny/crossref_metadata_2025 huggingface dataset:
Psychosocial Functioning Problems Over Time Among High-Risk Youths
Authors: Dembo Richard , Wareham Jennifer , Poythress Norman , Meyers Kathleen , Schmeidler James
Published: February 2008

The authors report the results of latent class analyses and latent class transition analyses of antisocial behavior risk factors among 137 youths participating in a juvenile diversion program. The study examined the youths' latent classifications using baseline and 1-year follow-up measures of family, peer, education, and mental health risk factors. Latent class transition analyses were conducted to determine the stability and change of latent class membership across two time points. For both baseline and follow-up measures, latent class analyses suggested that two latent classes were most appropriate for characterizing the youths using the four domains of risk factors. One class reflected youths reporting few problems in any risk area; the second class reflected youths reporting problems in many of the risk domains. The latent class transition analyses indicated that about two thirds of the youths experienced similar problems over time. The results emphasize the heterogeneity of this study's sample. Policy implications and intervention service needs are discussed.
Exploring the Impact of Changes in Group Composition on Trends in Specialization
Authors: Armstrong Todd A.
Published: February 2008

Stander and colleagues, in 1989, noted that change in specialization may be caused by two distinct but potentially complementary processes: (a) a change in group composition, where change in specialization is the product of the attrition of offenders who vary systematically in their tendency to specialize; and (b) a change in the tendency to specialize among persistent offenders. Results of the current study support earlier work finding change in the tendency to specialize among persistent offenders. Results also show that those who desist do differ in their tendency to specialize in drug and miscellaneous offenses, thereby suggesting that attrition will influence trends in specialization for these offense types. Post hoc analyses indicate that the relative influence of changes in group composition on trends in specialization is minor.
The Effect of Urban Neighborhood Disorder on Evaluations of the Police and Courts
Authors: Sprott Jane B. , Doob Anthony N.
Published: February 2008

Are people dissatisfied with the courts as well as the police when they perceive high levels of disorder in their neighborhoods? Consistent with previous research, this study, using a representative sample of Canadian adults, demonstrates that people are significantly more negative about the police when they perceive high levels of disorder. They are not, however, more negative toward the courts when confronted with these social problems. It is possible that they have heard the police rhetoric—namely, that the police form the “thin blue line” between order and chaos. Although the public holds the police and the courts responsible for increasing rates of crime, victimization, and fear, they do not see the courts as being responsible for neighborhood disorder, which they see as being the sole responsibility of the police.
The Impact of Residential and Nonresidential Drug Treatment on Recidivism Among Drug-Involved Probationers
Authors: Krebs Christopher P. , Strom Kevin J. , Koetse Willem H. , Lattimore Pamela K.
Published: February 2008

A variety of approaches for addressing drug use and drug-related crime among the nearly 5 million offenders on community supervision in the United States has been tried and evaluated, but questions remain about which policies or programs are most effective. The authors use a large data set to assess the impact of residential and nonresidential drug treatment on recidivism. Propensity score matching is used to establish equivalent treatment and comparison groups and to enable comparisons of treatment type. Survival analysis is used to determine the extent to which each treatment modality and numerous covariates were associated with time until recidivism. Compared to those receiving no treatment, those receiving nonresidential treatment took longer to fail or recidivate. However, those receiving residential treatment did not differ from those who received no treatment in time to failure. In the treatment-only model, nonresidential treatment participants took longer to fail than their matched residential treatment counterparts.
Open-Bay and Single-Family Room Neonatal Intensive Care Units
Authors: Shepley Mardelle McCuskey , Harris Debra D. , White Robert
Published: February 2008

The purpose of this study is to explore the implications of neonatal intensive care unit (NICU) single-family rooms (SFRs) relative to open-bay arrangements. A recent trend in the design of NICUs has been to increase the number of private patient rooms for neonates and their families. Several factors have contributed to the popularity of SFRs, including compliance with the Health Insurance Portability and Accountability Act, which mandates the need to provide patient privacy. Surveys of NICU medical staff ( N = 75) explored the preferences and experiences of individuals providing care in two facilities, an SFR NICU and a combination unit with open-bay infant stations and SFRs. The results of this study indicate that SFR NICU design may increase staff satisfaction and reduce staff stress.
Undertaking an Art Survey to Compare Patient Versus Student Art Preferences
Authors: Nanda Upali , Eisen Sarajane L. , Baladandayuthapani Veerabhadran
Published: February 2008

There is a growing body of evidence on using art as a positive distraction to improve health outcomes. However, there is little research on art for patient rooms, patients' stated art preferences, and how these compare with the art preferences of those with an art or design background. This article addresses the issue and describes the findings of an art survey containing both best-selling art images and images considered appropriate for health care. Sixty-seven hospital patients, 75 interior design students, and 50 building science/architecture students were surveyed. Images were rated on emotional response (how does this picture make you feel) and selection (would you put this picture in your room). Significant differences across the three populations were found for art preferences along the two rating scales and correspondence between emotional impact and selection of artwork. In addition, level of design exposure and gender were also seen to have an effect.
The Political Consequences of Assassination
Authors: Iqbal Zaryab , Zorn Christopher
Published: February 2008

The assassination of a political leader is among the highest-profile acts of political violence, and conventional wisdom holds that such events often have substantial political, social, and economic effects on states. We investigate the extent to which the assassination of a head of state affects political stability through an analysis of all assassinations of heads of state between 1952 and 1997. We examine the political consequences of assassination by assessing the levels of political unrest, instability, and civil war in states that experience the assassination of their head of state. Our findings support the existence of an interactive relationship among assassination, leadership succession, and political turmoil: in particular, we find that assassinations' effects on political instability are greatest in systems in which the process of leadership succession is informal and unregulated.
Effects of the Proton Pump Inhibitor Lansoprazole on the Pharmacokinetics and Pharmacodynamics of Prasugrel and Clopidogrel
Authors: Small David S. , Farid Nagy A. , Payne Christopher D. , Weerakkody Govinda J. , Li Ying G. , Brandt John T. , Salazar Daniel E. , Winters Kenneth J.
Published: February 2008

Prasugrel and clopidogrel, thienopyridine prodrugs, are each metabolized to an active metabolite that inhibits the platelet P2Y12 ADP receptor. In this open‐label, 4‐period crossover study, the effects of the proton pump inhibitor lansoprazole on the pharmacokinetics and pharmacodynamics of prasugrel and clopidogrel were assessed in healthy subjects given single doses of prasugrel 60 mg and clopidogrel 300 mg with and without concurrent lansoprazole 30 mg qd. Cmax and AUC0‐tlast of prasugrel's active metabolite, R‐138727, and clopidogrel's inactive carboxylic acid metabolite, SR26334, were assessed. Inhibition of platelet aggregation (IPA) was measured by turbidimetric aggregometry 4 to 24 hours after each treatment. Lansoprazole (1) decreased R‐138727 AUC0‐tlast and Cmax by 13% and 29%, respectively, but did not affect IPA after the prasugrel dose, and (2) did not affect SR62334 exposure but tended to lower IPA after a clopidogrel dose. A retrospective tertile analysis showed in subjects with high IPA after a clopidogrel dose alone that lansoprazole decreased IPA, whereas IPA was unaffected in these same subjects after a prasugrel dose. The overall data suggest that a prasugrel dose adjustment is not likely warranted in an individual taking prasugrel with a proton pump inhibitor such as lansoprazole.
The Mere Presence of Opposite-Sex Others on Judgments of Sexual and Romantic Desirability: Opposite Effects for Men and Women
Authors: Hill Sarah E. , Buss David M.
Published: February 2008

Men's and women's mate preferences impose on each a unique set of adaptive problems that must be solved when judging the desirability of prospective mates. One potentially revealing source of information about an individual's desirability as a romantic partner is contained in the decisions made by same-sex others. The present studies predicted that men's and women's desirability assessments would be affected in opposite ways when target persons were depicted with members of the target's opposite sex. Study 1 (N = 847) documented that women rated men more desirable when shown surrounded by women than when shown alone or with other men (a desirability enhancement effect ). In sharp contrast, men rated women less desirable when shown surrounded by men than when shown alone or with women (a desirability diminution effect) . Study 2 (N = 627) demonstrated similar sexually divergent effects for estimates of the desirability of same-sex competitors.
The Self-Protective Altruist: Terror Management and the Ambivalent Nature of Prosocial Behavior
Authors: Hirschberger Gilad , Ein-Dor Tsachi , Almakias Shaul
Published: February 2008

Three studies examined the hypothesis that mortality salience (MS) will increase prosocial behaviors when the prosocial cause promotes terror management processes. However, when the prosocial cause interferes with these processes, MS will reduce prosocial behavior. In Study 1, following a MS procedure, participants indicated their willingness to donate money to charity or to donate to an organ donation organization. In Study 2, a research assistant randomly distributed fliers with reminders of death or back pain, and another research assistant solicited participants' assistance from either a charitable fund booth or an organ donation booth. Study 3 examined the impact of MS on helping a wheelchair-bound confederate or a walking confederate. The results indicated that MS increased charitable donations and increased help to a walking confederate. However, MS significantly decreased organ donation card signings and decreased help to a wheelchair-bound confederate. The discussion examines the tension between personal fear and worldview validation.
A Tale of Two Industries
Authors: Hodges Nancy Nelson , Karpova Elena
Published: February 2008

This qualitative study explores recent textile and apparel industry dynamics from the point of view of the news media to understand how such dynamics are presented to the general public. North Carolina, having been home to many jobs in these industries, was used as a case study. Data were a total of 600 articles from two of the state's primary newspapers spanning the period from 1998 to 2003. Content of these articles was analyzed via a hermeneutic, interpretative framework to develop a thematic interpretation of the image of the two industries provided by the news media. Several themes were tied together through three broad topical areas—industry changes, strategic initiatives, and the impact of loss—and provide a multidimensional view of the industries as presented to the public. Further research is needed to understand the impact this image might have on public perceptions of the future of these industries.
Reinventing Social Work Accreditation
Authors: Stoesz David , Karger Howard J.
Published: February 2008

Accreditation under the Council on Social Work Education (CSWE) has contributed to the professional decline of social work. The lack of scholarship of the Board of Directors of CSWE compromises its decision making. The quality of the professional literature suffers from the weak scholarship of editors and referees. The caliber of deans and directors of social work educational programs is low with respect to their scholarship as well. Graduate students are ill-prepared to commence studies in social work. The substitution of ideology for academic rigor makes social work education vulnerable to its critics. Proposed revisions in Accreditation Standards indicate that CSWE is unlikely to undertake the necessary steps to reform social work education; therefore, schools of social work should be free to obtain accreditation independent of CSWE.
Evaluation of an In-Service Training Program for Child Welfare Practitioners
Authors: Turcotte Daniel , Lamonde Geneviève , Beaudoin André
Published: February 2008

Objective: To test the effectiveness of an in-training program for practitioners in public child welfare organizations. Method: The sample consists of practitioners (N = 945) working in youth centers or in local community service centers. Data are collected through self-administered questionnaires prior to and after the program. Results: The data show that prior to the training program, there are few differences between workers according to their educational backgrounds. Following the training program, practitioners felt more competent, had acquired additional knowledge, and had changed some of their behaviors with families. If level of stress at work had slightly decreased, job satisfaction remained unchanged. Conclusion: Findings suggest that an in-service training program may contribute to increased knowledge and feeling of competence and to modified professional behaviors, but it is essential to develop more valid indicators of knowledge and skills necessary to perform child welfare practice.
`All you need is an idea!': the impact of values-based participation on pupils' attitudes towards social activism and enterprise
Authors: Deuchar Ross
Published: February 2008

Education for citizenship has the teaching of controversial issues, the exploration of social values and the fostering of active participation at its core. This article focuses on a case study of 11-year-old pupils in a Scottish primary school, who were exposed to a new programme underpinned by values-based participation. The pupils initiated their own research into social issues of particular concern to them and used this as the basis for promoting enterprising ideas for social change. Non-participant observation of the work of the class combined with follow-up questionnaires and discussion groups enabled the researcher to establish pupils' views about social issues in a deeper sense, as well as establishing the way in which pupils' attitudes towards `enterprise' evolved. The findings illustrate that the pupils gained some useful skills in critical reflection, became more aware of their own potential for social activism and gained a wider perspective on communitarian principles.
The implementation of education for citizenship in Scotland: recommendation of approaches for effective practice
Authors: Akhtar Shazia
Published: February 2008

This article reviews how education for citizenship could be implemented and practised in Scottish primary schools at whole school, classroom and community level within the context of the new Curriculum for Excellence. It draws upon the advice and information given in existing key literature to provide an overview of the approaches that develop effective practice in education for citizenship. It then analyses and compares the underlying theories that seem to underpin the approaches to citizenship education of the 5—14 Curriculum and the new Curriculum for Excellence. The article concludes by acknowledging that implementing the recommended approaches of education for citizenship in key literature will lead schools into following and achieving the aspirations of the new Curriculum for Excellence but that it will require a change in teachers' thinking and practice as the underlying theories between the 5—14 guidelines and the new Curriculum for Excellence seem to have shifted.
Student voice and future schools: building partnerships for student participation
Authors: Frost Ros , Holden Gary
Published: February 2008

This article describes the early stages in the formation of a partnership between the University of Cambridge Faculty of Education and a group of secondary schools to develop a variety of approaches to student participation. The article focuses primarily on research undertaken by over 100 students in 12 secondary schools in Kent, and the Highest Common Denominator Student Partnership (HCDSP), based at the University of Cambridge Faculty of Education. It describes how the initiative was taken by a group of secondary headteachers with support from the LA to inform both their vision for secondary education and their response to the government's Building Schools for the Future (BSF) initiative. This enquiry was designed to actively involve students in collecting and presenting their own data. The most significant outcome of this project is that it signals the beginning of a genuine conversation between schools and their students about learning.
Second-Trimester Findings Associated With Nonimmune Hydrops
Authors: Smith-Weaver Margaret
Published: February 2008

Nonimmune hydrops fetalis (NIHF) is a fetal condition in which an overaccumulation of fluid in the interstitial tissues of the fetus occurs. NIHF is a separate condition from fetal immune hydrops caused by Rh incompatibility. There are multiple etiologies associated with NIHF, such as genetic disorders, fetal anemia, infectious diseases, twin-to-twin transfusion syndrome, and cardiovascular abnormalities. NIHF is an uncommon, predominantly fatal finding. The obstetric patient may present large-for-gestational age but is Rh compatible. Fetal anatomy may demonstrate multiple findings, including gross skin thickening, polyhydramnios, pleural or pericardial effusions, fetal ascites, and thickened placenta.
Nitrogen diffusion and nitrogen depth profiles in expanded austenite: Experimental assessment, numerical simulation and role of stress
Authors: Christiansen T. , Dahl K. V. , Somers M. A. J.
Published: February 2008

The present paper addresses the experimental assessment of the concentration dependent nitrogen diffusion coefficient in stress free expanded austenite foils from thermogravimetry, the numerical simulation of nitrogen concentration depth profiles on growth of expanded austenite into stainless steel during gaseous nitriding, a qualitative discussion of the role of stress on local equilibrium conditions of growing expanded austenite and a discussion of the erroneous concentration dependent diffusivity of nitrogen in expanded austenite as obtained from applying the Boltzmann–Matano method to composition–depth profiles.
Effects of hot deformation and subsequent austempering on mechanical properties of high silicon and low silicon TRIP steel
Authors: Li Z. , Wu D.
Published: February 2008

In the present paper, effects of hot deformation and subsequent austempering on the mechanical properties of high silicon and low silicon transformation induced plasticity (TRIP) steel were investigated. The results have shown that polygonal ferrite, granular bainite and a large amount of stabilised retained austenite can be obtained by thermomechanical processing (TMP). Mechanical properties increase with increasing finish rolling reduction and decreasing finish rolling temperature because of the stabilisation of retained austenite. The tensile strength and the total elongation of both steels reach the maximum (791, 794 MPa and 36, 37% respectively). Isothermal holding for 20 min at 400°C after hot deformation is the optimal process. Low silicon TRIP steel shows a larger uniform elongation owing to a stable n value, and it exhibits better mechanical properties than conventional high silicon TRIP steel.
Influence of post-weld heat treatments on microstructure and mechanical properties of AISI 431 martensitic stainless steel friction welds
Authors: Rajasekhar A. , Reddy G. M. , Mohandas T. , Murti V. S. R.
Published: February 2008

The relative effects of different post-weld heat treatments (PWHTs) on microstructure and mechanical properties of friction welded martensitic stainless steel type AISI 431 were studied. The weld microstructure consists of acicular martensite in equiaxed prior austenite grains and with heat treatment, the martensitic microstructure experiences coarsening. It was observed that retained austenite content decreases with an increase in the PWHT tempering temperature. The tensile properties of welds under different PWHTs were comparable to those of parent metal in the respective treatments. Welds exhibited higher notch tensile strengths than the parent metal in the respective heat treatment condition. Double tempering (670°C + 600°C) led to maximum reduction in hardness. Welds exhibited poor impact toughness in the as welded condition. The improvement in impact toughness was found satisfactory in welds subjected to double tempering, although did not match to the level of the parent metal at respective conditions. The mechanism and reasons for the observed behaviour have been discussed, correlating the microstructure, fracture features and mechanical properties.
Integrated modelling in materials and process technology
Authors: Hattel J. H.
Published: February 2008

Integrated modelling of entire process sequences and the subsequent in-service conditions, and multiphysics modelling of the single process steps are areas that increasingly support optimisation of manufactured parts. In the present paper, three different examples of modelling manufacturing processes from the viewpoint of combined materials and process modelling are presented: solidification of thin walled ductile cast iron, integrated modelling of spray forming and multiphysics modelling of friction stir welding. The fourth example describes integrated modelling applied to a failure analysis of premature rupture of a stellite weld on a P91 valve used in a power plant. For all four examples, the focus is put on modelling results rather than describing the models in detail. Proper comparison with experimental work is given in all examples for model validation as well as relevant references to the original work.
Sol–gel derived hydroxyapatite/calcium titanate coatings on Ti6Al4V alloy
Authors: Lee B. C. , Shin E. S. , Kim T. N. , Balakrishnan A.
Published: February 2008

A sol–gel dip coating method was used for coating hydroxyapatite (HA)/calcium titanate (CaTiO3/CTO) on a Ti6Al4V (TAV) substrate. A single CTO layer (∼500 nm thickness) was coated and heat treated at 750°C before five times of HA coating. The HA coating showed a thickness of 8–10 μm, after the heat treatment at 600°C. Phase formation, surface morphology and interfacial microstructure were investigated by X-ray diffraction and scanning electron microscopy. Scanning electron microscopy observations revealed no cracks on the HA/CTO surface. However surface cracks were observed when HA was directly coated on TAV. The bonding strength of HA/CTO increased almost three times compare to direct HA coatings. The higher bonding strength on CTO coated sample could be attributed to the formation of microcracks, the high surface roughness and high interfacial bonding between HA and CTO layer.
Thermodynamic and kinetic modelling: Creep resistant materials
Authors: Hald J. , Korcakova L. , Danielsen H. K. , Dahl K. V.
Published: February 2008

The use of thermodynamic and kinetic modelling of microstructure evolution in materials exposed to high temperatures in power plants is demonstrated with two examples. Precipitate stability in martensitic 9–12%Cr steels is modelled including equilibrium phase stability, growth of Laves phase particles and coarsening of MX, M23C6 and Laves phase particles. The modelling provided new insight into the long term stability of new steels. Modelling of the detrimental precipitation of Z phase Cr(V,Nb)N is described, which points to new approaches in alloy development for higher temperatures. Predictions of interdiffusion between a MCrAlY coating and an IN738 bulk alloy by multicomponent diffusion calculations provide a highly versatile tool for life assessment of service exposed gas turbine components as well as for the development of improved coatings.
Stress corrosion cracking behaviour of 1Cr12Ni2W1Mo1V steel after plasma hardening
Authors: Li P. L. , Zhou J. G. , Xi S. Q.
Published: February 2008

Stress corrosion cracking (SCC) behaviour of plasma hardened 1Cr12Ni2W1Mo1V steel in 22%NaCl solution and the effects of pitting corrosion cracking on fatigue properties of the steel were investigated. Experimental results show that the SCC threshold stress of the samples tempered at 250°C is 320 MPa, and the value is 240 MPa for the samples tempered at 540°C. Fatigue experiments of stress corrosion eroded samples indicate that samples tempered at 250°C have better fatigue properties. Precipitating of Cr23C6 during the process of 540°C tempering decreases Cr content near to the grain boundaries, therefore, reduces the resistance to SCC. Tempering temperatures have great effects on the corrosion resistance of 1Cr12Ni2W1Mo1 steel.
A gene pattern mining algorithm using interchangeable gene sets for prokaryotes
Authors: Hu Meng , Choi Kwangmin , Su Wei , Kim Sun , Yang Jiong
Published: February 2008

Background

Mining gene patterns that are common to multiple genomes is an important biological problem, which can lead us to novel biological insights. When family classification of genes is available, this problem is similar to the pattern mining problem in the data mining community. However, when family classification information is not available, mining gene patterns is a challenging problem. There are several well developed algorithms for predicting gene patterns in a pair of genomes, such as FISH and DAGchainer. These algorithms use the optimization problem formulation which is solved using the dynamic programming technique. Unfortunately, extending these algorithms to multiple genome cases is not trivial due to the rapid increase in time and space complexity.

Results

In this paper, we propose a novel algorithm for mining gene patterns in more than two prokaryote genomes using interchangeable sets. The basic idea is to extend the pattern mining technique from the data mining community to handle the situation where family classification information is not available using interchangeable sets. In an experiment with four newly sequenced genomes (where the gene annotation is unavailable), we show that the gene pattern can capture important biological information. To examine the effectiveness of gene patterns further, we propose an ortholog prediction method based on our gene pattern mining algorithm and compare our method to the bi-directional best hit (BBH) technique in terms of COG orthologous gene classification information. The experiment show that our algorithm achieves a 3% increase in recall compared to BBH without sacrificing the precision of ortholog detection.

Conclusion

The discovered gene patterns can be used for the detecting of ortholog and genes that collaborate for a common biological function.
DOVIS: an implementation for high-throughput virtual screening using AutoDock
Authors: Zhang Shuxing , Kumar Kamal , Jiang Xiaohui , Wallqvist Anders , Reifman Jaques
Published: February 2008

Background

Molecular-docking-based virtual screening is an important tool in drug discovery that is used to significantly reduce the number of possible chemical compounds to be investigated. In addition to the selection of a sound docking strategy with appropriate scoring functions, another technical challenge is to in silico screen millions of compounds in a reasonable time. To meet this challenge, it is necessary to use high performance computing (HPC) platforms and techniques. However, the development of an integrated HPC system that makes efficient use of its elements is not trivial.

Results

We have developed an application termed DOVIS that uses AutoDock (version 3) as the docking engine and runs in parallel on a Linux cluster. DOVIS can efficiently dock large numbers (millions) of small molecules (ligands) to a receptor, screening 500 to 1,000 compounds per processor per day. Furthermore, in DOVIS, the docking session is fully integrated and automated in that the inputs are specified via a graphical user interface, the calculations are fully integrated with a Linux cluster queuing system for parallel processing, and the results can be visualized and queried.

Conclusion

DOVIS removes most of the complexities and organizational problems associated with large-scale high-throughput virtual screening, and provides a convenient and efficient solution for AutoDock users to use this software in a Linux cluster platform.
Molecular evolution of rDNA in early diverging Metazoa: First comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera
Authors: Voigt Oliver , Erpenbeck Dirk , Wörheide Gert
Published: February 2008

Background

The cytoplasmic ribosomal small subunit (SSU, 18S) ribosomal RNA (rRNA) is the most frequently-used gene for molecular phylogenetic studies. However, information regarding its secondary structure is neglected in most phylogenetic analyses. Incorporation of this information is essential in order to apply specific rRNA evolutionary models to overcome the problem of co-evolution of paired sites, which violates the basic assumption of the independent evolution of sites made by most phylogenetic methods. Information about secondary structure also supports the process of aligning rRNA sequences across taxa. Both aspects have been shown to increase the accuracy of phylogenetic reconstructions within various taxa.

Here, we explore SSU rRNA secondary structures from the three extant classes of Phylum Porifera (Grant, 1836), a pivotal, but largely unresolved taxon of early branching Metazoa. This is the first phylogenetic study of poriferan SSU rRNA data to date that includes detailed comparative secondary structure information for all three sponge classes.

Results

We found base compositional and structural differences in SSU rRNA among Demospongiae, Hexactinellida (glass sponges) and Calcarea (calcareous sponges). We showed that analyses of primary rRNA sequences, including secondary structure-specific evolutionary models, in combination with reconstruction of the evolution of unusual structural features, reveal a substantial amount of additional information. Of special note was the finding that the gene tree topologies of marine haplosclerid demosponges, which are inconsistent with the current morphology-based classification, are supported by our reconstructed evolution of secondary structure features. Therefore, these features can provide alternative support for sequence-based topologies and give insights into the evolution of the molecule itself. To encourage and facilitate the application of rRNA models in phylogenetics of early metazoans, we present 52 SSU rRNA secondary structures over the taxonomic range of Porifera in a database, along with some basic tools for relevant format-conversion.

Conclusion

We demonstrated that sophisticated secondary structure analyses can increase the potential phylogenetic information of already available rDNA sequences currently accessible in databases and conclude that the importance of SSU rRNA secondary structure information for phylogenetic reconstruction is still generally underestimated, at least among certain early branching metazoans.
Vesicle-independent extracellular release of a proinflammatory outer membrane lipoprotein in free-soluble form
Authors: Karched Maribasappa , Ihalin Riikka , Eneslätt Kjell , Zhong Deyu , Oscarsson Jan , Wai Sun N , Chen Casey , Asikainen Sirkka E
Published: February 2008

Background

Aggregatibacter actinomycetemcomitansis an oral bacterium associated with aggressively progressing periodontitis. Extracellular release of bacterial outer membrane proteins has been suggested to mainly occur via outer membrane vesicles. This study investigated the presence and conservation of peptidoglycan-associated lipoprotein (AaPAL) amongA. actinomycetemcomitansstrains, the immunostimulatory effect of AaPAL, and whether live cells release this structural outer membrane lipoprotein in free-soluble form independent of vesicles.

Results

Thepallocus and its gene product were confirmed in clinicalA. actinomycetemcomitansstrains by PCR-restriction fragment length polymorphism and immunoblotting. Culturing under different growth conditions revealed no apparent requirement for the AaPAL expression. Inactivation ofpalin a wild-type strain (D7S) and in its spontaneous laboratory variant (D7SS) resulted in pleiotropic cellular effects. In a cell culture insert model (filter pore size 0.02 μm), AaPAL was detected from filtrates when strains D7S and D7SS were incubated in serum or broth in the inserts. Electron microscopy showed thatA. actinomycetemcomitansvesicles (0.05–0.2 μm) were larger than the filter pores and that there were no vesicles in the filtrates. The filtrates were immunoblot negative for a cytoplasmic marker, cyclic AMP (cAMP) receptor protein. An ex vivo model indicated cytokine production from human whole blood stimulated by AaPAL.

Conclusion

Free-soluble AaPAL can be extracellularly released in a process independent of vesicles.
Gastrointestinal symptoms and motility disorders in patients with systemic scleroderma
Authors: Di Ciaula Agostino , Covelli Michele , Berardino Massimo , Wang David QH , Lapadula Giovanni , Palasciano Giuseppe , Portincasa Piero
Published: February 2008

Background

Studies on gastrointestinal symptoms, dysfunctions, and neurological disorders in systemic scleroderma are lacking so far.

Methods

Thirty-eight scleroderma patients (34 limited, 4 diffuse), 60 healthy controls and 68 dyspeptic controls were scored for upper and lower gastrointestinal symptoms (dyspepsia, bowel habits), gastric and gallbladder emptying to liquid meal (functional ultrasonography) and small bowel transit (H2-breath test). Autonomic nerve function was assessed by cardiovascular tests.

Results

The score for dyspepsia (mainly gastric fullness) was greater in scleroderma patients than healthy controls, but lower than dyspeptic controls who had multiple symptoms, instead. Scleroderma patients with dyspepsia had a longer disease duration. Fasting antral area and postprandial antral dilatation were smaller in scleroderma patients than dyspeptic and healthy controls. Gastric emptying was delayed in both scleroderma patients (particularly in those with abnormal dyspeptic score) and dyspeptic controls, who also showed a larger residual area. Despite gallbladder fasting and postprandial volumes were comparable across the three groups, gallbladder refilling appeared delayed in dyspeptic controls and mainly dependent on delayed gastric emptying in scleroderma. Small intestinal transit was also delayed in 74% of scleroderma and 66% of dyspeptic controls. Bowel habits were similar among the three groups. Autonomic neuropathy was not associated with dyspepsia, gastric and gallbladder motility and small intestinal transit.

Conclusion

In scleroderma patients dyspepsia (mainly gastric fullness), restricted distension of the gastric antrum and diffuse gastrointestinal dysmotility are frequent features. These defects are independent from the occurrence of autonomic neuropathy.
Individual nutrition therapy and exercise regime: A controlled trial of injured, vulnerable elderly (INTERACTIVE trial)
Authors: Thomas Susie K , Humphreys Karen J , Miller Michelle D , Cameron Ian D , Whitehead Craig , Kurrle Susan , Mackintosh Shylie , Crotty Maria
Published: February 2008

Background

Proximal femoral fractures are amongst the most devastating consequences of osteoporosis and injurious accidental falls with 25–35% of patients dying in the first year post-fracture. Effective rehabilitation strategies are evolving however, despite established associations between nutrition, mobility, strength and strength-related functional outcomes; there has been only one small study with older adults immediately following fragility fracture where a combination of both exercise and nutrition have been provided. The aim of the INTERACTIVE trial is to establish whether a six month, individualised exercise and nutrition program commencing within fourteen days of surgery for proximal femur fracture, results in clinically and statistically significant improvements in physical function, body composition and quality of life at an acceptable level of cost and resource use and without increasing the burden of caregivers.

Methods and Design

This randomised controlled trial will be performed across two sites, a 500 bed acute hospital in Adelaide, South Australia and a 250 bed acute hospital in Sydney, New South Wales. Four hundred and sixty community-dwelling older adults aged > 70 will be recruited after suffering a proximal femoral fracture and followed into the community over a 12-month period. Participants allocated to the intervention group will receive a six month individualised care plan combining resistance training and nutrition therapy commencing within 14 days post-surgery. Outcomes will be assessed by an individual masked to treatment allocation at six and 12 months. To determine differences between the groups at the primary end-point (six months), ANCOVA or logistic regression will be used with models adjusted according to potential confounders.

Discussion

The INTERACTIVE trial is among the first to combine nutrition and exercise therapy as an early intervention to address the serious consequence of rapid deconditioning and weight loss and subsequent ability to regain pre-morbid function in older patients post proximal femoral fracture. The results of this trial will guide the development of more effective rehabilitation programs, which may ultimately lead to reduced health care costs, and improvements in mobility, independence and quality of life for proximal femoral fracture sufferers.

Trial registration

Australian Clinical Trials Registry: ACTRN12607000017426.
Effect of ionic strength and presence of serum on lipoplexes structure monitorized by FRET
Authors: Madeira Catarina , Loura Luís MS , Prieto Manuel , Fedorov Aleksander , Aires-Barros M Raquel
Published: February 2008

Background

Serum and high ionic strength solutions constitute important barriers to cationic lipid-mediated intravenous gene transfer. Preparation or incubation of lipoplexes in these media results in alteration of their biophysical properties, generally leading to a decrease in transfection efficiency. Accurate quantification of these changes is of paramount importance for the success of lipoplex-mediated gene transfer in vivo.

Results

In this work, a novel time-resolved fluorescence resonance energy transfer (FRET) methodology was used to monitor lipoplex structural changes in the presence of phosphate-buffered saline solution (PBS) and fetal bovine serum. 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP)/pDNA lipoplexes, prepared in high and low ionic strength solutions, are compared in terms of complexation efficiency. Lipoplexes prepared in PBS show lower complexation efficiencies when compared to lipoplexes prepared in low ionic strength buffer followed by addition of PBS. Moreover, when serum is added to the referred formulation no significant effect on the complexation efficiency was observed. In physiological saline solutions and serum, a multilamellar arrangement of the lipoplexes is maintained, with reduced spacing distances between the FRET probes, relative to those in low ionic strength medium.

Conclusion

The time-resolved FRET methodology described in this work allowed us to monitor stability and characterize quantitatively the structural changes (variations in interchromophore spacing distances and complexation efficiencies) undergone by DOTAP/DNA complexes in high ionic strength solutions and in presence of serum, as well as to determine the minimum amount of potentially cytotoxic cationic lipid necessary for complete coverage of DNA. This constitutes essential information regarding thoughtful design of future in vivo applications.
Switching the mode of sucrose utilization by Saccharomyces cerevisiae
Authors: Badotti Fernanda , Dário Marcelo G , Alves Sergio L , Cordioli Maria Luiza A , Miletti Luiz C , de Araujo Pedro S , Stambuk Boris U
Published: February 2008

Background

Overflow metabolism is an undesirable characteristic of aerobic cultures of Saccharomyces cerevisiae during biomass-directed processes. It results from elevated sugar consumption rates that cause a high substrate conversion to ethanol and other bi-products, severely affecting cell physiology, bioprocess performance, and biomass yields. Fed-batch culture, where sucrose consumption rates are controlled by the external addition of sugar aiming at its low concentrations in the fermentor, is the classical bioprocessing alternative to prevent sugar fermentation by yeasts. However, fed-batch fermentations present drawbacks that could be overcome by simpler batch cultures at relatively high (e.g. 20 g/L) initial sugar concentrations. In this study, a S. cerevisiae strain lacking invertase activity was engineered to transport sucrose into the cells through a low-affinity and low-capacity sucrose-H+ symport activity, and the growth kinetics and biomass yields on sucrose analyzed using simple batch cultures.

Results

We have deleted from the genome of a S. cerevisiae strain lacking invertase the high-affinity sucrose-H+ symporter encoded by the AGT1 gene. This strain could still grow efficiently on sucrose due to a low-affinity and low-capacity sucrose-H+ symport activity mediated by the MALx1 maltose permeases, and its further intracellular hydrolysis by cytoplasmic maltases. Although sucrose consumption by this engineered yeast strain was slower than with the parental yeast strain, the cells grew efficiently on sucrose due to an increased respiration of the carbon source. Consequently, this engineered yeast strain produced less ethanol and 1.5 to 2 times more biomass when cultivated in simple batch mode using 20 g/L sucrose as the carbon source.

Conclusion

Higher cell densities during batch cultures on 20 g/L sucrose were achieved by using a S. cerevisiae strain engineered in the sucrose uptake system. Such result was accomplished by effectively reducing sucrose uptake by the yeast cells, avoiding overflow metabolism, with the concomitant reduction in ethanol production. The use of this modified yeast strain in simpler batch culture mode can be a viable option to more complicated traditional sucrose-limited fed-batch cultures for biomass-directed processes of S. cerevisiae.
Mapping of immunogenic and protein-interacting regions at the surface of the seven-bladed β-propeller domain of the HIV-1 cellular interactor EED
Authors: Rakotobe Dina , Violot Sébastien , Hong Saw See , Gouet Patrice , Boulanger Pierre
Published: February 2008

Background

The human EED protein, a member of the superfamily of Polycomb group proteins, is involved in multiple cellular protein complexes. Its C-terminal domain, which is common to the four EED isoforms, contains seven repeats of a canonical WD-40 motif. EED is an interactor of three HIV-1 proteins, matrix (MA), integrase (IN) and Nef. An antiviral activity has been found to be associated with isoforms EED3 and EED4 at the late stage of HIV-1 replication, due to a negative effect on virus assembly and genomic RNA packaging. The aim of the present study was to determine the regions of the EED C-terminal core domain which were accessible and available to protein interactions, using three-dimensional (3D) protein homology modelling with a WD-40 protein of known structure, and epitope mapping of anti-EED antibodies.

Results

Our data suggested that the C-terminal domain of EED was folded as a seven-bladed β-propeller protein. During the completion of our work, crystallographic data of EED became available from co-crystals of the EED C-terminal core with the N-terminal domain of its cellular partner EZH2. Our 3D-model was in good congruence with the refined structural model determined from crystallographic data, except for a unique α-helix in the fourth β-blade. More importantly, the position of flexible loops and accessible β-strands on the β-propeller was consistent with our mapping of immunogenic epitopes and sites of interaction with HIV-1 MA and IN. Certain immunoreactive regions were found to overlap with the EZH2, MA and IN binding sites, confirming their accessibility and reactivity at the surface of EED. Crystal structure of EED showed that the two discrete regions of interaction with MA and IN did not overlap with each other, nor with the EZH2 binding pocket, but were contiguous, and formed a continuous binding groove running along the lateral face of the β-propeller.

Conclusion

Identification of antibody-, MA-, IN- and EZH2-binding sites at the surface of the EED isoform 3 provided a global picture of the immunogenic and protein-protein interacting regions in the EED C-terminal domain, organized as a seven-bladed β-propeller protein. Mapping of the HIV-1 MA and IN binding sites on the 3D-model of EED core predicted that EED-bound MA and IN ligands would be in close vicinity at the surface of the β-propeller, and that the occurrence of a ternary complex MA-EED-IN would be possible.
Perforated diverticulitis presenting as necrotising fasciitis of the leg
Authors: Underwood Timothy J , Southgate Jeremy , Talbot Robert , Nash Guy F
Published: February 2008

Diverticulosis of the colon is a common condition of increasing age. Complications of diverticulitis including stricture, perforation and fistula formation often require surgery. Perforated diverticulitis may rarely present with spreading superficial sepsis. We describe for the first time, to our knowledge, a case of retroperitoneal diverticula perforation presenting as necrotising fasciitis of the leg necessitating hind-quarter amputation.