bluuebunny/crossref_metadata_2025_split huggingface dataset:
Core indicators evaluation of effectiveness of HIV-AIDS preventive-control programmes carried out by nongovernmental organizations. A mixed method study
Authors: Berenguera Anna , Pujol-Ribera Enriqueta , Violan Concepció , Romaguera Amparo , Mansilla Rosa , Giménez Albert , Ascaso Carlos , Almeda Jesús 
Published: July 2011

Abstract

Background
The number of nongovernmental organizations working on AIDS has grown. There is great diversity in the type of activities and population groups that have been targeted. The purposes of this study are: to describe and analyze the objectives and HIV-AIDS preventive activities that are carried out by the AIDS-NGOs that work with AIDS in Catalonia and that receive subsidies from the Department of Health; and to develop a comprehensive proposal for measurable and agreed upon core quality evaluation indicators to monitor and assess those objectives and activities that can have an impact on the fight against inequalities and stigmatization, and incorporate the perspectives of the service providers and users.

Methods
A mixed method study has been carried out with professionals from the 36 NGOs that work with HIV/AIDS in Catalonia, as well as their users. This study achieved the completeness model using the following phases:
1. A systematic review of AIDS-NGOs annual reports and preparation of a catalogue of activities grouped by objectives, level of prevention and AIDS-NGOs target population; 2. A transversal study through an ad-hoc questionnaire administered to the AIDS-NGOs representatives; 3. A qualitative study with a phenomenological approach through focus groups, individual interviews and observations; 4. Consensus meetings between AIDS-NGOs professionals and the research team using Haddon matrices in order to establish a proposal of evaluation indicators.

Results
The information was classified according to level of prevention and level of intervention. A total of 248 objectives and 258 prevention activities were identified. 1564 evaluation indicators, addressed to 7 target population groups, were produced. Thirty core activities were selected. The evaluation indicators proposed for these activities were: 76 indicators for 15 primary prevention activities, 43 for 5 secondary prevention activities and 68 for 10 tertiary prevention activities.

Conclusions
The results could help to homogeneously assess the preventive-control activities carried out of AIDS-NGOs. The proposed indicators could help the professionals to improve the evaluation of the preventive-control AIDS-NGOs activities. Furthermore, the Haddon matrix enables us to identify deficiencies of activities at intervention levels and strategies to bear in mind in order to enhance the future AIDS prevention programs.
Non-cysteine linked MUC1 cytoplasmic dimers are required for Src recruitment and ICAM-1 binding induced cell invasion
Authors: Bernier Ashlyn J , Zhang Jing , Lillehoj Erik , Shaw Andrew RE , Gunasekara Nirosha , Hugh Judith C 
Published: July 2011

Abstract

Background
The mucin MUC1, a type I transmembrane glycoprotein, is overexpressed in breast cancer and has been correlated with increased metastasis. We were the first to report binding between MUC1 and Intercellular adhesion molecule-1 (ICAM-1), which is expressed on stromal and endothelial cells throughout the migratory tract of a metastasizing breast cancer cell. Subsequently, we found that MUC1/ICAM-1 binding results in pro-migratory calcium oscillations, cytoskeletal reorganization, and simulated transendothelial migration. These events were found to involve Src kinase, a non-receptor tyrosine kinase also implicated in breast cancer initiation and progression. Here, we further investigated the mechanism of MUC1/ICAM-1 signalling, focusing on the role of MUC1 dimerization in Src recruitment and pro-metastatic signalling.

Methods
To assay MUC1 dimerization, we used a chemical crosslinker which allowed for the detection of dimers on SDS-PAGE. We then generated MUC1 constructs containing an engineered domain which allowed for manipulation of dimerization status through the addition of ligands to the engineered domain. Following manipulation of dimerization, we immunoprecipitated MUC1 to investigate recruitment of Src, or assayed for our previously observed ICAM-1 binding induced events. To investigate the nature of MUC1 dimers, we used both non-reducing SDS-PAGE and generated a mutant construct lacking cysteine residues.

Results
We first demonstrate that the previously observed MUC1/ICAM-1signalling events are dependent on the activity of Src kinase. We then report that MUC1 forms constitutive cytoplasmic domain dimers which are necessary for Src recruitment, ICAM-1 induced calcium oscillations and simulated transendothelial migration. The dimers are not covalently linked constitutively or following ICAM-1 binding. In contrast to previously published reports, we found that membrane proximal cysteine residues were not involved in dimerization or ICAM-1 induced signalling.

Conclusions
Our data implicates non-cysteine linked MUC1 dimerization in cell signalling pathways required for cancer cell migration.
The relationship between self-reported substance use and psychiatric symptoms in low-threshold methadone maintenance treatment clients
Authors: Fulton Heather G , Barrett Sean P , MacIsaac Cindy , Stewart Sherry H 
Published: July 2011

Abstract

Background
Ongoing psychiatric symptoms and substance use are common difficulties experienced by clients enrolled in methadone maintenance treatment (MMT). However, little research to date has evaluated if specific types of current substance use are related to specific types of current psychiatric symptoms. The present study investigated these relationships with a sample of clients enrolled in a low-threshold MMT program (i.e., clients are not expelled if they continue to use substances). Some clients enrolled in low-threshold programs may never achieve complete abstinence from all substances. Thus, understanding the possibly perpetuating relationships between concurrent substance use and psychiatric symptoms is important. Understanding such relationships may aid in developing possible target areas of treatment to reduce substance use and/or related harms in this population.

Methods
Seventy-seven individuals were interviewed regarding methadone usage and current and past substance use. Current psychiatric symptoms were assessed using a modified version of the Psychiatric Diagnostic Screening Questionnaire (PDSQ). Relationships between types of substances used in the past 30 days and the types and number of psychiatric symptoms experienced in the same timeframe were examined.

Results
The majority of participants (87.0%) reported using alcohol, illicit substances, non-prescribed prescription opioids, or non-prescribed benzodiazepines in the past 30 days and 77.9% of participants reported currently experiencing psychiatric symptoms at levels that would likely warrant diagnosis. Current non-prescribed benzodiazepine use was a predictor for increased severity (i.e., symptom count) of almost all anxiety and mood disorders assessed. Conversely, number and presence of generalized anxiety symptoms and presence of social phobia symptoms predicted current non-prescribed benzodiazepine and alcohol use, respectively.

Conclusions
Individuals enrolled in the present low-threshold MMT program experience a wide variety of psychiatric symptoms and continue to use a variety of substances, including opioids. There was a particularly consistent pattern of associations between non-prescribed benzodiazepine use and a variety of psychiatric symptoms (particularly anxiety) suggesting that addressing concurrent illicit benzodiazepine use and anxiety symptoms in MMT clients warrants further clinical attention and research.
Molecular evolution of Azagny virus, a newfound hantavirus harbored by the West African pygmy shrew (Crocidura obscurior) in Côte d'Ivoire
Authors: Kang Hae Ji , Kadjo Blaise , Dubey Sylvain , Jacquet François , Yanagihara Richard 
Published: July 2011

Abstract

Background
Tanganya virus (TGNV), the only shrew-associated hantavirus reported to date from sub-Saharan Africa, is harbored by the Therese's shrew (Crocidura theresae), and is phylogenetically distinct from Thottapalayam virus (TPMV) in the Asian house shrew (Suncus murinus) and Imjin virus (MJNV) in the Ussuri white-toothed shrew (Crocidura lasiura). The existence of myriad soricid-borne hantaviruses in Eurasia and North America would predict the presence of additional hantaviruses in sub-Saharan Africa, where multiple shrew lineages have evolved and diversified.

Methods
Lung tissues, collected in RNAlater®, from 39 Buettikofer's shrews (Crocidura buettikoferi), 5 Jouvenet's shrews (Crocidura jouvenetae), 9 West African pygmy shrews (Crocidura obscurior) and 21 African giant shrews (Crocidura olivieri) captured in Côte d'Ivoire during 2009, were systematically examined for hantavirus RNA by RT-PCR.

Results
A genetically distinct hantavirus, designated Azagny virus (AZGV), was detected in the West African pygmy shrew. Phylogenetic analysis of the S, M and L segments, using maximum-likelihood and Bayesian methods, under the GTR+I+Γ model of evolution, showed that AZGV shared a common ancestry with TGNV and was more closely related to hantaviruses harbored by soricine shrews than to TPMV and MJNV. That is, AZGV in the West African pygmy shrew, like TGNV in the Therese's shrew, did not form a monophyletic group with TPMV and MJNV, which were deeply divergent and basal to other rodent- and soricomorph-borne hantaviruses. Ancestral distributions of each hantavirus lineage, reconstructed using Mesquite 2.74, suggested that the common ancestor of all hantaviruses was most likely of Eurasian, not African, origin.

Conclusions
Genome-wide analysis of many more hantaviruses from sub-Saharan Africa are required to better understand how the biogeographic origin and radiation of African shrews might have contributed to, or have resulted from, the evolution of hantaviruses.
Classification and treatment of proximal humerus fractures: inter-observer reliability and agreement across imaging modalities and experience
Authors: Foroohar Abtin , Tosti Rick , Richmond John M , Gaughan John P , Ilyas Asif M 
Published: July 2011

Abstract

Summary
Proximal humerus fractures (PHF) are common injuries, but previous studies have documented poor inter-observer reliability in fracture classification. This disparity has been attributed to multiple variables including poor imaging studies and inadequate surgeon experience. The purpose of this study is to evaluate whether inter-observer agreement can be improved with the application of multiple imaging modalities including X-ray, CT, and 3D CT reconstructions, stratified by physician experience, for both classification and treatment of PHFs.

Methods
Inter-observer agreement was measured for classification and treatment of PHFs. A total of sixteen fractures were imaged by plain X-ray (scapular AP and lateral), CT scan, and 3D CT reconstruction, yielding 48 randomized image sets. The observers consisted of 16 orthopaedic surgeons (4 upper extremity specialists, 4 general orthopedists, 4 senior residents, 4 junior residents), who were asked to classify each image set using the Neer system, and recommend treatment from four pre-selected choices. The results were evaluated by kappa reliability coefficients for inter-observer agreement between all imaging modalities and sub-divided by: fracture type and observer experience.

Results
All kappa values ranged from "slight" to "moderate" (k = .03 to .57) agreement. For overall classification and treatment, no advanced imaging modality had significantly higher scores than X-ray. However, when sub-divided by experience, 3D reconstruction and CT scan both had significantly higher agreement on classification than X-ray, among upper extremity specialists. Agreement on treatment among upper extremity specialists was best with CT scan. No other experience sub-division had significantly different kappa scores. When sub-divided by fracture type, CT scan and 3D reconstruction had higher scores than X-ray for classification only in 4-part fractures. Agreement on treatment of 4 part fractures was best with CT scan. No other fracture type sub-division had significantly different kappa scores.

Conclusions
Although 3D reconstruction showed a slight improvement in the inter-observer agreement for fracture classification among specialized upper extremity surgeons compared to all imaging modalities, fracture types, and surgeon experience; overall all imaging modalities continue to yield low inter-observer agreement for both classification and treatment regardless of physician experience.
DNA vaccines delivered by human papillomavirus pseudovirions as a promising approach for generating antigen-specific CD8+ T cell immunity
Authors: Peng Shiwen , Ma Barbara , Chen Shu-Hsia , Hung Chien-Fu , Wu TC 
Published: July 2011

Abstract

Background
Human papillomavirus (HPV) pseudovirions have recently been shown to deliver DNA efficiently in vivo, resulting in the priming of antigen-specific CD8+ T cells in vaccinated mice. In the current study, we compare the different preparation methods for the generation of HPV pseudovirions for their ability to efficiently infect cells. We also compare the antigen-specific CD8+ T cell immune responses generated by different DNA delivery methods and several commonly used forms of vaccination with that of HPV pseudovirions.

Results
We found that the preparation method of pseudovirions is important for the efficient delivery of encapsidated DNA. We have shown that vaccination with DNA encoding model antigen ovalbumin (OVA) delivered by HPV-16 pseudovirions was capable of generating therapeutic antitumor effects against OVA-expressing tumor. In addition, vaccination with DNA encoding OVA delivered by HPV-16 pseudovirions generated the highest number of OVA-specific CD8+ T cells in mice in our system compared to DNA delivered by other delivery methods. We also found that vaccination with OVA DNA delivered by HPV-16 pseudovirions generated the highest number of OVA-specific CD8+ T cells in mice compared to other forms of antigen-specific vaccines. Furthermore, HPV-16 pseudovirions were capable of carrying DNA vaccine encoding clinically relevant antigen, telomerase reverse transcriptase, to generate antigen-specific CD8+ T cell immune responses.

Conclusions
Our data suggest that DNA vaccines delivered by HPV-16 pseudovirions may be advantageous compared to other delivery methods and other forms of antigen-specific vaccines for application to antigen-specific immunotherapy.
Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits
Authors: Wong Daniel , Teixeira Ana , Oikonomopoulos Spyros , Humburg Peter , Lone Imtiaz Nisar , Saliba David , Siggers Trevor , Bulyk Martha , Angelov Dimitar , Dimitrov Stefan , Udalova Irina A , Ragoussis Jiannis 
Published: July 2011

Abstract
Background
Genetic studies have provided ample evidence of the influence of non-coding DNA polymorphisms on trait variance, particularly those occurring within transcription factor binding sites. Protein binding microarrays and other platforms that can map these sites with great precision have enhanced our understanding of how a single nucleotide polymorphism can alter binding potential within an in vitro setting, allowing for greater predictive capability of its effect on a transcription factor binding site.

Results
We have used protein binding microarrays and electrophoretic mobility shift assay-sequencing (EMSA-Seq), a deep sequencing based method we developed to analyze nine distinct human NF-κB dimers. This family of transcription factors is one of the most extensively studied, but our understanding of its DNA binding preferences has been limited to the originally described consensus motif, GGRRNNYYCC. We highlight differences between NF-κB family members and also put under the spotlight non-canonical motifs that have so far received little attention. We utilize our data to interpret the binding of transcription factors between individuals across 1,405 genomic regions laden with single nucleotide polymorphisms. We also associated binding correlations made using our data with risk alleles of disease and demonstrate its utility as a tool for functional studies of single nucleotide polymorphisms in regulatory regions.

Conclusions
NF-κB dimers bind specifically to non-canonical motifs and these can be found within genomic regions in which a canonical motif is not evident. Binding affinity data generated with these different motifs can be used in conjunction with data from chromatin immunoprecipitation-sequencing (ChIP-Seq) to enable allele-specific analyses of expression and transcription factor-DNA interactions on a genome-wide scale.
Predictive genetic testing for the identification of high-risk groups: a simulation study on the impact of predictive ability
Authors: Mihaescu Raluca , Moonesinghe Ramal , Khoury Muin J , Janssens A Cecile JW 
Published: July 2011

Abstract
Background
Genetic risk models could potentially be useful in identifying high-risk groups for the prevention of complex diseases. We investigated the performance of this risk stratification strategy by examining epidemiological parameters that impact the predictive ability of risk models.

Methods
We assessed sensitivity, specificity, and positive and negative predictive value for all possible risk thresholds that can define high-risk groups and investigated how these measures depend on the frequency of disease in the population, the frequency of the high-risk group, and the discriminative accuracy of the risk model, as assessed by the area under the receiver-operating characteristic curve (AUC). In a simulation study, we modeled genetic risk scores of 50 genes with equal odds ratios and genotype frequencies, and varied the odds ratios and the disease frequency across scenarios. We also performed a simulation of age-related macular degeneration risk prediction based on published odds ratios and frequencies for six genetic risk variants.

Results
We show that when the frequency of the high-risk group was lower than the disease frequency, positive predictive value increased with the AUC but sensitivity remained low. When the frequency of the high-risk group was higher than the disease frequency, sensitivity was high but positive predictive value remained low. When both frequencies were equal, both positive predictive value and sensitivity increased with increasing AUC, but higher AUC was needed to maximize both measures.

Conclusions
The performance of risk stratification is strongly determined by the frequency of the high-risk group relative to the frequency of disease in the population. The identification of high-risk groups with appreciable combinations of sensitivity and positive predictive value requires higher AUC.
Characterization of Transparent Soil for Unsaturated Applications
Authors: Peters S. B. , Siemens G. , Take W. A. 
Published: July 2011

AbstractExperimental characterization of unsaturated soils is of primary importance to further understanding of fundamental behavior, as well as allow for accurate modeling and predictions, of constitutive and field behavior. In the laboratory, the most common research methodology used to investigate the hydraulic behavior of unsaturated soils involves placing the unsaturated soil in a column apparatus with measurements of pore pressure and moisture content being made at discrete locations distributed along the elevation of column. These types of tests have provided many valuable insights into unsaturated flow phenomena; however, there are some limitations with this methodology including the discrete nature of the measurement points. In this paper, an alternative method is proposed which aims to combine the use of digital image analysis with a transparent soil to avoid the ambiguity of traditional boundary image measurements of moisture content in column experiments. At 100% saturation, the transparent soil particles appear invisible and allows for the ability to see through the soil mass. Any air bubbles will be visible within the soil voids and as a result, at varying degrees of saturation less than 100%, the soil will become progressively non-transparent. The relationship between pixel intensity of the unsaturated soil and degree of saturation is defined and validated. This relationship allows definition of the degree of saturation throughout the column profile thus giving the opportunity to verify and further develop constitutive models for unsaturated hydraulic behavior.
Strength and Small-Strain Stiffness Characteristics of Unsaturated Sand
Authors: Nyunt T. T. , Leong E. C. , Rahardjo H. 
Published: July 2011

AbstractExperiments were performed to investigate the effects of initial matric suction and net confining pressure on the small-strain stiffness and shear strength of reconstituted unsaturated sand. A series of constant water content tests was carried out using a modified triaxial apparatus equipped with local displacement transducers and bender elements. Reconstituted sand specimens were allowed to equalize at the required matric suction under net confining pressure using the axis- translation technique before shearing. After reaching matric suction equilibrium, shear wave velocities were measured prior to shearing. Multi-stage shearing tests were performed in order to investigate the effect of initial matric suction using the same specimen. The experimental results showed that at each net confining pressure, small-strain stiffness and peak shear strength showed a nonlinear relationship with matric suction with the change point near the air-entry value of the soil-water characteristic curve. Relationship between small-strain stiffness and net confining pressure was observed to be similar for saturated and unsaturated sands.
A Flexible Wall Permeameter for the Determination of the Water Permeability Function in Unsaturated Soils
Authors: Moncada M. P. H. , de Campos T. M. P. , Steger G. 
Published: July 2011

Abstract
This paper describes the development of a suction controlled flexible wall permeameter for the direct determination of the water permeability function in unsaturated soils. The new permeameter works with applied constant head or constant rate of flow, i.e., the common steady-state techniques. Total volume change of soil specimens during the test are monitored using a high resolution electronic scale. Numerical simulations were performed to evaluate the influence of factors such as flow velocity and matric suction distribution within the specimen and effects of sample height on such factors. Analyses of tests conducted on two tropical soil samples are used to evaluate conventional proposals for the determination of the water permeability function. It is shown that such proposals do not apply in the case of the materials tested and solutions to that are put forwards.