bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Analysis of Protein Structure Alignments
Authors: Mayr Gabriele , Domingues Francisco S , Lackner Peter 
Published: August 2007

Abstract

Background
Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods.

Results
We analysed and compared the structural alignments obtained by different methods using three sets of pairs of structurally related proteins. The first set corresponds to 355 pairs of remote homologous proteins according to the SCOP database (ASTRAL40 set). The second set was derived from the SISYPHUS database and includes 69 protein pairs (SISY set). The third set consists of 40 pairs that are challenging to align (RIPC set). The alignment of pairs of this set requires indels of considerable number and size and some of the proteins are related by circular permutations, show extensive conformational variability or include repetitions. Two standard methods (CE and DALI) were applied to align the proteins in the ASTRAL40 set. The extent of structural similarity identified by both methods is highly correlated and the alignments from the two methods agree on average in more than half of the aligned positions. CE, DALI, as well as four additional methods (FATCAT, MATRAS, C
α
-match and SHEBA) were then compared using the SISY and RIPC sets. The accuracy of the alignments was assessed by comparison to reference alignments. The alignments generated by the different methods on average match more than half of the reference alignments in the SISY set. The alignments obtained in the more challenging RIPC set tend to differ considerably and match reference alignments less successfully than the SISY set alignments.

Conclusion
The alignments produced by different methods tend to agree to a considerable extent, but the agreement is lower for the more challenging pairs. The results for the comparison to reference alignments are encouraging, but also indicate that there is still room for improvement.
A systematic evaluation of payback of publicly funded health and health services research in Hong Kong
Authors: Kwan Patrick , Johnston Janice , Fung Anne YK , Chong Doris SY , Collins Richard A , Lo Su V 
Published: August 2007

Abstract
Background
The Health and Health Services Research Fund (HHSRF) is dedicated to support research related to all aspects of health and health services in Hong Kong. We evaluated the fund's outcomes and explored factors associated with the translation of research findings to changes in health policy and provider behaviour.

Methods
A locally suitable questionnaire was developed based on the "payback" evaluation framework and was sent to principal investigators of the completed research projects supported by the fund since 1993. Research "payback" in six outcome areas was surveyed, namely knowledge production, use of research in the research system, use of research project findings in health system policy/decision making, application of the research findings through changed behaviour, factors influencing the utilization of research, and health/health service/economic benefits.

Results
Principal investigators of 178 of 205 (87%) completed research projects returned the questionnaire. Investigators reported research publications in 86.5% (mean = 5.4 publications per project), career advancement 34.3%, acquisition of higher qualifications 38.2%, use of results in policy making 35.4%, changed behaviour in light of findings 49.4%, evidence of health service benefit 42.1% and generated subsequent research in 44.9% of the projects. Payback outcomes were positively associated with the amount of funding awarded. Multivariate analysis found participation of investigators in policy committees and liaison with potential users were significantly associated with reported health service benefit (odds ratio [OR]participation = 2.86, 95% confidence interval [CI] 1.28–6.40; ORliaison = 2.03, 95% CI 1.05–3.91), policy and decision-making (ORparticipation = 10.53, 95% CI 4.13–26.81; ORliaison = 2.52, 95% CI 1.20–5.28), and change in behavior (ORparticipation = 3.67, 95% CI 1.53–8.81).

Conclusion
The HHSRF has produced substantial outcomes and compared favourably with similar health research funds in other developed economies. Further studies are needed to better understand the factors and pathways associated with the translation of research findings into practice.
Drug utilization and cost in a Medicaid population: A simulation study of community vs. mail order pharmacy
Authors: Valluri Satish , Seoane-Vazquez Enrique , Rodriguez-Monguio Rosa , Szeinbach Sheryl L 
Published: August 2007

Abstract

Background
Outpatient drugs are dispensed through both community and mail order pharmacies. There is no empirical evidence that substitution of community pharmacy with mail order reduces overall drug expenditures. The need for evaluating the potential effects on utilization and costs of the possible extension of mail order services in Medicaid provides the rationale for conducting this study. This study compares drug utilization and drug product cost in community vs. mail order pharmacy dispensing services in a Medicaid population.

Methods
This study is a retrospective cohort study comparing utilization and cost patterns in community vs. mail order pharmacy. A simulation model was employed to assess drug utilization and cost in mail order pharmacy using community pharmacy claim data. The model assumed that courses of drug therapy (CDT) in mail order pharmacy would have utilization patterns similar to those found in community pharmacy. A 95% confidence interval surrounding changes in average utilization and average cost were estimated using bootstrap analysis. A sensitivity analysis was performed by varying drug selection criteria and supply, fill point, and medication possession ratio (MPR). Sub-analyses were performed to address differences between mail order and community pharmacy related to therapeutic class and dual-eligible patients.
Data for the study derived from pharmacy claims database of Ohio Medicaid State program for the period January 2000-September 2004. Drug claims were aggregated to obtain a set of CDTs representing unique patient IDs and unique drug products. Drug product cost estimates excluded dispensing fees and were used to estimate the cost reduction required in mail order to become cost neutral in comparison with community pharmacy.

Results
The baseline model revealed that the use of mail order vs. community pharmacy would result in a 5.5% increase in drug utilization and a 5.4% cost reduction required in mail order to become cost neutral. Results from Ohio Medicaid drugs for chronic use revealed a 5.1% increase in utilization and a 4.9% cost reduction required to become cost neutral in comparison with community pharmacy.

Conclusion
The results of the simulation model indicate that mail order pharmacy increases drug utilization and can also increase drug product cost if the cost per unit is not reduced accordingly. Prior consideration should be given to the patient population, day-supply, disease, therapy, and insurance characteristics to ensure the appropriate use of mail order pharmacy services.
A low-cost repellent for malaria vectors in the Americas: results of two field trials in Guatemala and Peru
Authors: Moore Sarah J , Darling Samuel T , Sihuincha Moisés , Padilla Norma , Devine Gregor J 
Published: August 2007

Abstract

Background
The cost of mosquito repellents in Latin America has discouraged their wider use among the poor. To address this problem, a low-cost repellent was developed that reduces the level of expensive repellent actives by combining them with inexpensive fixatives that appear to slow repellent evaporation. The chosen actives were a mixture of para-menthane-diol (PMD) and lemongrass oil (LG).

Methods
To test the efficacy of the repellent, field trials were staged in Guatemala and Peru. Repellent efficacy was determined by human-landing catches on volunteers who wore the experimental repellents, control, or 15% DEET. The studies were conducted using a balanced Latin Square design with volunteers, treatments, and locations rotated each night.

Results
In Guatemala, collections were performed for two hours, commencing three hours after repellent application. The repellent provided >98% protection for five hours after application, with a biting pressure of >100 landings per person/hour. The 15% DEET control provided lower protection at 92% (p < 0.0001). In Peru, collections were performed for four hours, commencing two hours after repellent application. The PMD/LG repellent provided 95% protection for six hours after application with a biting pressure of >46 landings per person/hour. The 20% DEET control provided significantly lower protection at 64% (p < 0.0001).

Conclusion
In both locations, the PMD/LG repellent provided excellent protection up to six hours after application against a wide range of disease vectors including Anopheles darlingi. The addition of fixatives to the repellent extended its longevity while enhancing efficacy and significantly reducing its cost to malaria-endemic communities.
Self assembly of amphiphilic C60 fullerene derivatives into nanoscale supramolecular structures
Authors: Partha Ranga , Lackey Melinda , Hirsch Andreas , Casscells S Ward , Conyers Jodie L 
Published: August 2007

Abstract

Background
The amphiphilic fullerene monomer (AF-1) consists of a "buckyball" cage to which a Newkome-like dendrimer unit and five lipophilic C12 chains positioned octahedrally to the dendrimer unit are attached. In this study, we report a novel fullerene-based liposome termed 'buckysome' that is water soluble and forms stable spherical nanometer sized vesicles. Cryogenic electron microscopy (Cryo-EM), transmission electron microscopy (TEM), and dynamic light scattering (DLS) studies were used to characterize the different supra-molecular structures readily formed from the fullerene monomers under varying pH, aqueous solvents, and preparative conditions.

Results
Electron microscopy results indicate the formation of bilayer membranes with a width of ~6.5 nm, consistent with previously reported molecular dynamics simulations. Cryo-EM indicates the formation of large (400 nm diameter) multilamellar, liposome-like vesicles and unilamellar vesicles in the size range of 50–150 nm diameter. In addition, complex networks of cylindrical, tube-like aggregates with varying lengths and packing densities were observed. Under controlled experimental conditions, high concentrations of spherical vesicles could be formed. In vitro results suggest that these supra-molecular structures impose little to no toxicity. Cytotoxicity of 10–200 μM buckysomes were assessed in various cell lines. Ongoing studies are aimed at understanding cellular internalization of these nanoparticle aggregates.

Conclusion
In this current study, we have designed a core platform based on a novel amphiphilic fullerene nanostructure, which readily assembles into supra-molecular structures. This delivery vector might provide promising features such as ease of preparation, long-term stability and controlled release.
A cross-sectional look at patient concerns in the first six weeks following primary total knee arthroplasty
Authors: Rastogi Ravi , Davis Aileen M , Chesworth Bert M 
Published: August 2007

Abstract

Background
To date, no researchers have investigated patient concerns in the first six weeks following primary total knee arthroplasty (TKA). An understanding of patient concerns at a time when physical therapists are involved in the treatment of these patients will aid clinicians in providing patient-centered care. Linking of items to the International Classification of Functioning, Disability and Health (ICF) allows for comparison and sharing of data amongst researchers, as the ICF is the accepted framework for evaluating disability in rehabilitation. The objective of this study was to identify patient concerns in the first six weeks following primary TKA and link these concerns to components of the ICF and map them to commonly used outcome measures.

Methods
Individual interviews were conducted to identify patient concerns during their recovery following primary TKA. Concerns identified by patients were analysed for content and linked to the components of the ICF using the operational definitions of the ICF components. These concerns were mapped to the WOMAC, KOOS and Oxford Knee Scale.

Results
Thirty patients (18 female) with an average age (SD) of 68.4 (11.1) years completed the study. Patients identified 32 concerns. Twenty-two percent (n = 7) of the concerns linked to Body Function and Structure, 47% (n = 15) to Activity, 13% (n = 4) to Participation, and 13% (n = 4) to the Environmental Factors component of the ICF. Six percent (n = 2) of the concerns did not link to the ICF. Of the 32 concerns identified by patients 14 mapped to the KOOS, 11 to the WOMAC and 4 to the Oxford Knee Scale.

Conclusion
Patient concerns linked to four different components of the ICF indicating that patients are involved in or are thinking of multiple aspects of life even in this early phase of recovery. The KOOS was found to be the most appropriate for use based on the patients' perspective. However, less than half of the concerns identified by patients were covered by the KOOS, WOMAC or Oxford Knee Scale indicating that other existing measures that evaluate the concepts identified as important to patients should be considered when evaluating outcomes during this acute phase of recovery following primary TKA.
The effect of versican G3 domain on local breast cancer invasiveness and bony metastasis
Authors: Yee Albert JM , Akens Margarete , Yang Bing L , Finkelstein Joel , Zheng Peng-Sheng , Deng Zhaoqiong , Yang Burton 
Published: August 2007

Abstract
Introduction
Increased versican expression has been associated with local breast cancer invasiveness and a more aggressive tumor phenotype. The cellular mechanisms are not fully understood and this study evaluated versican G3 domain with its EGF-like motifs in influencing tumor invasion and metastasis.

Methods
One recombinant construct was synthesized (a signal peptide for product secretion and the versican G3 domain). The construct was stably transfected into human breast carcinoma MT-1 cells. Cell viability in vitro was evaluated in low serum and serum starvation conditions. In vivo study of tumor growth was evaluated in a nude mouse model. G3 effects on rodent vascular endothelial cells were evaluated in vitro on cell survival, apoptosis, migration, and vascular formation. The effects of VEGF, fibronectin, and G3 on vascular formation were examined. An intracardiac injection model of metastatic human breast carcinoma tested the effect of G3 on distant bony and soft tissue metastasis. Analysis of metastatic burden included histology, radiographs, and micro-CT quantification of osteolysis.

Results
A greater viability of cancer cells was observed in low serum and serum-free conditions in the presence of versican G3. Larger subcutaneous tumors were obtained in the G3 group following tumor cell injection into CD1 mice. G3 induced a greater degree of rodent vascular endothelial cell proliferation and migration in vitro. Simultaneous presence of fibronectin, VEGF, and G3 promoted endothelial cell migration in wound-healing assays as compared to the treatments containing none, one or two of these molecules. Systemic tumor burden to distant bony and soft tissue metastatic sites was greater in the G3 group using the intracardiac injection metastatic model

Conclusion
Versican G3 domain appears to be important in local and systemic tumor invasiveness of human breast cancer. Effects include enhancing cell viability, proliferation, migration and enhancing local tumor growth. Potential effects on angiogenesis include enhancing vascular endothelial proliferation, migration, and vessel formation. The interactions between tumor cells, surrounding stromal components and neo-vascularization in breast cancer may include interactions with VEGF and fibronectin. The propensity of versican G3 to influence tumor invasion to bone and the mechanisms of G3 mediated osteolysis warrants ongoing studies.
The effect of different volumes and temperatures of saline on the bladder pressure measurement in critically ill patients
Authors: Chiumello Davide , Tallarini Federica , Chierichetti Monica , Polli Federico , Li Bassi Gianluigi , Motta Giuliana , Azzari Serena , Carsenzola Cristian , Gattinoni Luciano 
Published: August 2007

Abstract
Introduction
Intra-abdominal hypertension is common in critically ill patients and is associated with increased severity of organ failure and mortality. The techniques most commonly used to estimate intra-abdominal pressure are measurements of bladder and gastric pressures. The bladder technique requires that the bladder be infused with a certain amount of saline, to ensure that there is a conductive fluid column between the bladder and the transducer. The aim of this study was to evaluate the effect of different volumes and temperatures of infused saline on bladder pressure measurements in comparison with gastric pressure.

Methods
Thirteen mechanically ventilated critically ill patients (11 male; body mass index 25.5 ± 4.6 kg/m2; arterial oxygen tension/fractional inspired oxygen ratio 225 ± 48 mmHg) were enrolled. Bladder pressure was measured using volumes of saline from 50 to 200 ml at body temperature (35 to 37°C) and room temperature (18 to 20°C).

Results
Bladder pressure was no different between 50 ml and 100 ml saline (9.5 ± 3.7 mmHg and 13.7 ± 5.6 mmHg), but it significantly increased with 150 and 200 ml (21.1 ± 10.4 mmHg and 27.1 ± 15.5 mmHg). Infusion of saline at room temperature caused a significantly greater bladder pressure compared with saline at body temperature. The lowest difference between bladder and gastric pressure was obtained with a volume of 50 ml.

Conclusion
The bladder acts as a passive structure, transmitting intra-abdominal pressure only with saline volumes between 50 ml and 100 ml. Infusion of a saline at room temperature caused a higher bladder pressure, probably because of contraction of the detrusor bladder muscle.
PHIDIAS: a pathogen-host interaction data integration and analysis system
Authors: Xiang Zuoshuang , Tian Yuying , He Yongqun 
Published: August 2007

AbstractThe Pathogen-Host Interaction Data Integration and Analysis System (PHIDIAS) is a web-based database system that serves as a centralized source to search, compare, and analyze integrated genome sequences, conserved domains, and gene expression data related to pathogen-host interactions (PHIs) for pathogen species designated as high priority agents for public health and biological security. In addition, PHIDIAS allows submission, search and analysis of PHI genes and molecular networks curated from peer-reviewed literature. PHIDIAS is publicly available at http://www.phidias.us.
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
Authors: Zheng Bin , Lu Xinghua 
Published: August 2007

AbstractWe present the metrics for assessing overall functional coherence of a group of proteins based on associated biomedical literature. A probabilistic topic model is applied to extract biologic concepts from a corpus of protein-related biomedical literature. Bipartite protein semantic networks are constructed, so that the functional coherence of a protein group can be evaluated with metrics that measure the closeness and strength of connectivity of the proteins in the network.
Sexual health services for South Asians in London, UK: a case–control study
Authors: Tariq S , Edwards S G , Nalabanda A , Ward H , Allen E , Fenton K , Mercey D , Sethi G 
Published: August 2007

National guidance on sexual health in England recommends service development to meet the specific needs of ethnic minority populations. Our aim was to evaluate mode of referral, number of sexually transmitted infections (STIs) diagnosed, and the offering and uptake of HIV testing in patients of South Asian ethnicity. A retrospective case–control study was undertaken in two London genito-urinary (GU) medicine clinics. There were 250 case–control pairs with approximately equal numbers of men and women. South Asians were less likely to have an STI (Odds ratio [OR] 0.66, 95% confidence interval [CI] 0.45, 0.97) or to report risk factors for HIV (OR 0.45, 95% CI 0.28, 0.71). Offering and uptake of HIV antibody testing were high in both South Asian and non-South Asian groups (OR 0.62, 95% CI 0.27, 1.51). South Asians were significantly more likely than controls to have been referred by other medical services rather than self-referred (OR 2.00, 95% CI 1.32, 3.01), which is in keeping with poorer access to GU medicine services in London.
The use of graduated compression stockings in association with fondaparinux in surgery of the hip
Authors: Cohen A. T. , Skinner J. A. , Warwick D. , Brenkel I. 
Published: August 2007

Little is known about the efficacy of graduated compression stockings in preventing venous thromboembolism after hip surgery. We conducted a prospective, randomised single-blind study to determine whether the addition of compression stockings to fondaparinux conferred any additional benefit. The study included 874 patients, of whom 795 could be evaluated (400 in the fondaparinux group and 395 in the fondaparinux plus compression stocking group). Fondaparinux was given post-operatively for five to nine days, either alone or combined with wearing stockings, which were worn for a mean 42 days (35 to 49). The study outcomes were venous thromboembolism, or sudden death before day 42. Duplex ultrasonography was scheduled within a week of day 42. Safety outcomes were bleeding and death from venous thromboembolism. The prevalence of deep-vein thrombosis was similar in the two groups 5.5% (22 of 400) in the fondaparinux group and 4.8 (19 of 395) in the fondaparinux plus stocking group (odds ratio 0.88, 95% confidence interval 0.46 to 1.65, p = 0.69). Major bleeding occurred in only one patient. The addition of graduated compression stockings to fondaparinux appears to offer no additional benefit over the use of fondaparinux alone.
The value of MRI undertaken immediately after reduction of the hip as a predictor of long-term acetabular dysplasia
Authors: Mitchell P. D. , Chew N. S. , Goutos I. , Healy J. C. , Lee J. C. , Evans S. , Hulme A. 
Published: August 2007

Our aim was to determine whether abnormalities noted on MRI immediately after reduction for developmental dysplasia of the hip could predict the persistance of dysplasia and aid surgical planning. Scans of 13 hips in which acetabular dysplasia had resolved by the age of four years were compared with those of five which had required pelvic osteotomy for persisting dysplasia. The scans were analysed by two consultant musculoskeletal radiologists who were blinded to the outcome in each child. The postreduction scans highlighted a number of anatomical abnormalities secondary to developmental dysplasia of the hip, but statistical analysis showed that none were predictive of persisting acetabular dysplasia in the older child, suggesting that the factors which determine the long-term outcome were not visible on these images.