bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Pre-S Protein-Containing Hepatitis B Virus Surface Antigens and a Powerful Adjuvant To Develop an Immune Therapy for Chronic Hepatitis B Virus Infection
Authors: Yum Jung Sun , Ahn Byung Cheol , Jo Hyun Jin , Kim Dong Yeon , Kim Ki Hyun , Kim Hyo Sun , Sung Young Chul , Yoon Jaeseung , Morrey John , Moon Hong Mo 
Published: December 2011

ABSTRACT
A hepatitis B virus (HBV) vaccine has been developed using a new adjuvant and HBV surface antigens produced from a CHO cell line. The purified HBV surface antigens are composed of L protein, M protein, and S protein in a mixture of 20- and 40-nm-diameter particles and filamentous forms. This HBV surface antigen, formulated with L-pampo, a proprietary adjuvant, induced 10 times more antibody than the same antigen with alum and was capable of inducing strong immune responses in three different HBV transgenic mice. In spite of the presence of a large amount of HBV antigen in the blood, no antibody against HBV surface antigen was normally detected in these transgenic mice. After immunization, the HBV antigen was also cleared from the blood.
Clostridium difficile Carriage in Elderly Subjects and Associated Changes in the Intestinal Microbiota
Authors: Rea Mary C. , O'Sullivan Orla , Shanahan Fergus , O'Toole Paul W. , Stanton Catherine , Ross R. Paul , Hill Colin 
Published: December 2011

ABSTRACT

Clostridium difficile
is an important nosocomial pathogen associated particularly with diarrheal disease in elderly individuals in hospitals and long-term care facilities. We examined the carriage rate of
Clostridium difficile
by culture as a function of fecal microbiota composition in elderly subjects recruited from the community, including outpatient, short-term respite, and long-term hospital stay subjects. The carriage rate ranged from 1.6% (
n
= 123) for subjects in the community, to 9.5% (
n
= 43) in outpatient settings, and increasing to 21% (
n
= 151) for patients in short- or long-term care in hospital. The dominant 072 ribotype was carried by 43% (12/28) of subjects, while the hypervirulent strain R027 (B1/NAP1/027) was isolated from 3 subjects (11%), 2 of whom displayed
C. difficile
associated diarrhea (CDAD) symptoms at the time of sampling. Emerging ribotypes with enhanced virulence (078 and 018) were also isolated from two asymptomatic subjects. Pyrosequencing of rRNA gene amplicons was used to determine the composition of the fecal microbiota as a surrogate for the microbial population structure of the distal intestine. Asymptomatic subjects (
n
= 20) from whom
C. difficile
was isolated showed no dramatic difference at the phylum or family taxonomic level compared to those that were culture negative (
n
= 252). However, in contrast, a marked reduction in microbial diversity at genus level was observed in patients who had been diagnosed with CDAD at the time of sampling and from whom
C. difficile
R027 was isolated.
Use of Quantitative HIV RNA Detection for Early Diagnosis of HIV Infection in Infants and Acute HIV Infections in Alberta, Canada
Authors: Lee Bonita E. , Plitt Sabrina S. , Jayaraman Gayatri C. , Chui Linda , Singh Ameeta E. , Preiksaitis Jutta K. 
Published: December 2011

ABSTRACT
Quantitative HIV RNA viral load (QVL) assays (Roche Diagnostics) were sensitive and specific when used to diagnose HIV infection in (i) HIV-exposed infants (sensitivity of 100% [63.1 to 100%] and specificity of 100% [97.9 to 100%]) and (ii) suspected acute HIV infection patients with a negative/indeterminate Western blot (sensitivity of 97.6% [91.6 to 99.7%] and specificity of 100% [96.1 to 100%]). No false-positive QVL results were identified.
Most HIV Type 1 Non-B Infections in the Spanish Cohort of Antiretroviral Treatment-Naïve HIV-Infected Patients (CoRIS) Are Due to Recombinant Viruses
Authors: Yebra Gonzalo , de Mulder Miguel , Martín Leticia , Rodríguez Carmen , Labarga Pablo , Viciana Isabel , Berenguer Juan , Alemán María Remedios , Pineda Juan Antonio , García Federico , Holguín África ,   Cohort of the Spanish AIDS Research Network (CoRIS)
Published: December 2011

ABSTRACTHIV-1 group M is classified into 9 subtypes, as well as recombinants favored by coinfection and superinfection events with different variants. Although HIV-1 subtype B is predominant in Europe, intersubtype recombinants are increasing in prevalence and complexity. In this study, phylogenetic analyses ofpolsequences were performed to detect the HIV-1 circulating and unique recombinant forms (CRFs and URFs, respectively) in a Spanish cohort of antiretroviral treatment-naïve HIV-infected patients included in the Research Network on HIV/AIDS (CoRIS). Bootscanning and other methods were used to define complex recombinants not assigned to any subtype or CRF. A total of 670 available HIV-1polsequences from different patients were collected, of which 588 (87.8%) were assigned to HIV-1 subtype B and 82 (12.2%) to HIV-1 non-B variants. Recombinants caused the majority (71.9%) of HIV-1 non-B infections and were found in 8.8% of CoRIS patients. Eleven URFs (accounting for 13.4% of HIV-1 non-B infections), presenting complex mosaic patterns, were detected. Among them, 10 harbored subtype B fragments. Four of the 11 URFs were found in Spanish natives. A cluster of three B/CRF02_AG recombinants was detected. We conclude that complex variants, including unique recombinant forms, are being introduced into Spain through both immigrants and natives. An increase in the frequency of mosaic viruses, reflecting the increasing heterogeneity of the HIV epidemic in our country, is expected.
Clinical Significance of Quantifying Pneumocystis jirovecii DNA by Using Real-Time PCR in Bronchoalveolar Lavage Fluid from Immunocompromised Patients
Authors: Botterel Françoise , Cabaret Odile , Foulet Françoise , Cordonnier Catherine , Costa Jean-Marc , Bretagne Stéphane 
Published: December 2011

ABSTRACT

Quantitative PCR (qPCR) is more sensitive than microscopy for detecting
Pneumocystis jirovecii
in bronchoalveolar lavage (BAL) fluid. We therefore developed a qPCR assay and compared the results with those of a routine immunofluorescence assay (IFA) and clinical data. The assay included automated DNA extraction, amplification of the mitochondrial large-subunit rRNA gene and an internal control, and quantification of copy numbers with the help of a plasmid clone. We studied 353 consecutive BAL fluids obtained for investigation of unexplained fever and/or pneumonia in 287 immunocompromised patients. No qPCR inhibition was observed. Seventeen (5%) samples were both IFA and qPCR positive, 63 (18%) were IFA negative and qPCR positive, and 273 (77%) were both IFA and qPCR negative. The copy number was significantly higher for IFA-positive/qPCR-positive samples than for IFA-negative/qPCR-positive samples (4.2 ± 1.2 versus 1.1 ± 1.1 log
10
copies/μl;
P
< 10
−4
). With IFA as the standard, the qPCR assay sensitivity was 100% for ≥2.6 log
10
copies/μl and the specificity was 100% for ≥4 log
10
copies/μl. Since qPCR results were not available at the time of decision-making, these findings did not trigger cotrimoxazole therapy. Patients with systemic inflammatory diseases and IFA-negative/qPCR-positive BAL fluid had a worse 1-year survival rate than those with IFA-negative/qPCR-negative results (
P
< 10
−3
), in contrast with solid-organ transplant recipients (
P
= 0.88) and patients with hematological malignancy (
P
= 0.26). Quantifying
P. jirovecii
DNA in BAL fluids independently of IFA positivity should be incorporated into the investigation of pneumonia in immunocompromised patients. The relevant threshold remains to be determined and may vary according to the underlying disease.
Human Cytomegalovirus UL44 Concentrates at the Periphery of Replication Compartments, the Site of Viral DNA Synthesis
Authors: Strang Blair L. , Boulant Steeve , Chang Lynne , Knipe David M. , Kirchhausen Tomas , Coen Donald M. 
Published: December 2011

ABSTRACT
The formation of replication compartments, the subnuclear structures in which the viral DNA genome is replicated, is a hallmark of herpesvirus infections. The localization of proteins and viral DNA within human cytomegalovirus replication compartments is not well characterized. Immunofluorescence analysis demonstrated the accumulation of the viral DNA polymerase subunit UL44 at the periphery of replication compartments and the presence of different populations of UL44 in infected cells. In contrast, the viral single-stranded-DNA binding protein UL57 was distributed throughout replication compartments. Using “click chemistry” to detect 5-ethynyl-2′-deoxyuridine (EdU) incorporation into replicating viral DNA and pulse-chase protocols, we found that viral DNA synthesis occurs at the periphery of replication compartments and that replicated viral DNA subsequently localizes to the interior of replication compartments. The interiors of replication compartments also contain regions in which UL44 and EdU-labeled DNA are absent. The treatment of cells with a viral DNA polymerase inhibitor reversibly caused the dispersal of both UL44 and EdU-labeled viral DNA from replication compartments, indicating that ongoing viral DNA synthesis is necessary to maintain the organization of replication compartments. Our results reveal a previously unappreciated complexity of the organization of human cytomegalovirus replication compartments.
Laser-induced optical nonlinearities in Orange G dye: polyacrylamide gel
Authors: Badran Hussain A. , Hassan Qusay M. Ali , Al-Ahmad Alaa Y. , Emshary Chassib A. 
Published: December 2011

We observed multiple diffraction rings of a continuous-wave solid-state laser beam from an Orange G dye doped polyacrylamide gel. The number of rings increases almost exponentially with increasing input power and the concentration of the samples. The refractive index change, Δn, and effective nonlinear refractive index, n2, were determined from the number of observed rings. We obtained good values of Δn ∼ 0.004 788 and n2 = 10−5 cm2/W. Variation of refractive index with temperature (dn/dT) and figure of merit (H) are found to be 1.01 × 10−4 1/°C and 0.45 × 10−4, respectively. This large nonlinearity is attributed to a thermal effect resulting from linear absorption.
Effect of WO3 on structural and optical properties of PbO-B2O3 glasses
Authors: Singh G. Pal , Singh D.P. 
Published: December 2011

Glass samples of compositions xWO3-(30-x) PbO-70B2O3 with x varying from 0 to 10 mol percent are prepared using the melt–quench technique. The structural and optical analysis of glasses is carried out by using X-ray diffraction, Fourier transform infrared (FTIR), density, and ultraviolet-visible spectroscopic measurement techniques. FTIR analysis indicates the transformation of structural units of BO3 into BO4 and formation of WO4 units with W–O–W vibration are observed with WO3 doping. Decrease of band gap from 2.89 to 2.22 eV has been observed and discussed. This decrease in band gap causes an approach to semiconducting behavior with WO3 doping. It shows that WO3 causes more compaction of the borate network by breaking the bonds between trigonal elements, which results in the decrease of optical band gap energy and increase of density.
FREE DETERMINISTIC EQUIVALENTS, RECTANGULAR RANDOM MATRIX MODELS, AND OPERATOR-VALUED FREE PROBABILITY THEORY
Authors: SPEICHER ROLAND , VARGAS CARLOS 
Published: December 2011

Motivated by the asymptotic collective behavior of random and deterministic matrices, we propose an approximation (called "free deterministic equivalent") to quite general random matrix models, by replacing the matrices with operators satisfying certain freeness relations. We comment on the relation between our free deterministic equivalent and deterministic equivalents considered in the engineering literature. We do not only consider the case of square matrices, but also show how rectangular matrices can be treated. Furthermore, we emphasize how operator-valued free probability techniques can be used to solve our free deterministic equivalents. As an illustration of our methods we show how the free deterministic equivalent of a random matrix model from [6] can be treated and we thus recover in a conceptual way the results from [6]. On a technical level, we generalize a result from scalar-valued free probability, by showing that randomly rotated deterministic matrices of different sizes are asymptotically free from deterministic rectangular matrices, with amalgamation over a certain algebra of projections. In Appendix A, we show how estimates for differences between Cauchy transforms can be extended from a neighborhood of infinity to a region close to the real axis. This is of some relevance if one wants to compare the original random matrix problem with its free deterministic equivalent.
Measuring Patterns in Team Interaction Sequences Using a Discrete Recurrence Approach
Authors: Gorman Jamie C. , Cooke Nancy J. , Amazeen Polemnia G. , Fouse Shannon 
Published: December 2011

Objective: Recurrence-based measures of communication determinism and pattern information are described and validated using previously collected team interaction data. Background: Team coordination dynamics has revealed that “mixing” team membership can lead to flexible interaction processes, but keeping a team “intact” can lead to rigid interaction processes. We hypothesized that communication of intact teams would have greater determinism and higher pattern information compared to that of mixed teams. Method: Determinism and pattern information were measured from three-person Uninhabited Air Vehicle team communication sequences over a series of 40-minute missions. Because team members communicated using push-to-talk buttons, communication sequences were automatically generated during each mission. Results: The Composition × Mission determinism effect was significant. Intact teams’ determinism increased over missions, whereas mixed teams’ determinism did not change. Intact teams had significantly higher maximum pattern information than mixed teams. Conclusion: Results from these new communication analysis methods converge with content-based methods and support our hypotheses. Application: Because they are not content based, and because they are automatic and fast, these new methods may be amenable to real-time communication pattern analysis.
Effect of thermal conductive fillers on the properties of polypropylene composites
Authors: Nurul MS , Mariatti M 
Published: December 2011

We investigated the effects of various fillers such as carbon nanotube (CNT), synthetic diamond (SND), boron nitride (BN), and copper (Cu) on the properties of polypropylene (PP) composites. The thermal conductivity and stability of PP were enhanced upon the addition of thermally conductive fillers. Young’s modulus increased with filler loading, while tensile strength increased at up to 2 vol.% then decreased with elongation in all filler types. The morphology of the composite samples showed agglomeration and void content in PP/Cu composites, leading to the deterioration of thermal and mechanical properties at high-volume loading. Findings indicate that PP/CNT has better thermal and mechanical properties compared with the other types of fillers.
Effects of surveillance failure on airborne-based continuous descent approach
Authors: Itoh E , Everdij M , Bakker G J (B) , Blom H 
Published: December 2011

For higher density operation in terminal manoeuvring area, Airborne Surveillance Application System (ASAS) is seen as a promising option in the future air traffic management (ATM). One idea of recent interest in ASAS application is Interval Management (IM), which is expected to support energy-saving arrivals, commonly referred as Continuous Descent Approach (CDA). The questions are how the IM application achieves safety and capacity in the CDA environment, and how to identify any potential emergent behaviour that should be taken into account in the operation design. The motivation for this study is the need to properly understand the nominal and non-nominal behaviour of many aircraft when the ASAS application is applied to the CDA environment. For this purpose, this study has conducted a preliminary safety assessment of the ASAS speed control for multiple trailing aircraft in CDA operation. This article focuses on ASAS surveillance failure as one of the critical events during flight. Using Stochastically and Dynamically Coloured Petri Net (SDCPN), ASAS core components and their interactions are modelled. Through Monte Carlo simulation via the SDCPN models, the impact of the ASAS surveillance failure on the airborne-based CDA operation is assessed.
Developing Women Leaders on Campus
Authors: Bonebright Denise A. , Cottledge Anitra D. , Lonnquist Peg 
Published: December 2011

The Problem. Despite significant gains in the number of women leaders in higher education, there are still challenges for developing women leaders in higher education. The Solution. Effective collaboration between women’s centers and other campus organizations that support women’s leadership can provide opportunities to overcome these barriers. This article presents leadership development programs offered by the Women’s Center at the University of Minnesota, focusing on those facilitated in partnership with the university’s Office of Human Resources. Several lessons emerged from the review: the value of collaborative relationships, the importance of emphasis on individual and system-level leadership, and the need for ongoing assessment and evaluation of the climate for women leaders within postsecondary institutions. The Stakeholders. These lessons, and the principles used in implementing them, reveal practices that may be useful for other Women’s Centers, HR departments, and internal and external entities who seek to develop more women leaders in higher education.
Generation of subject-specific, dynamic, multisegment ankle and foot models to improve orthotic design: a feasibility study
Authors: Oosterwaal Michiel , Telfer Scott , Tørholm Søren , Carbes Sylvain , van Rhijn Lodewijk W , Macduff Ross , Meijer Kenneth , Woodburn Jim 
Published: December 2011

Abstract

Background
Currently, custom foot and ankle orthosis prescription and design tend to be based on traditional techniques, which can result in devices which vary greatly between clinicians and repeat prescription. The use of computational models of the foot may give further insight in the biomechanical effects of these devices and allow a more standardised approach to be taken to their design, however due to the complexity of the foot the models must be highly detailed and dynamic.

Methods/Design
Functional and anatomical datasets will be collected in a multicentre study from 10 healthy participants and 15 patients requiring orthotic devices. The patient group will include individuals with metarsalgia, flexible flat foot and drop foot.
Each participant will undergo a clinical foot function assessment, 3D surface scans of the foot under different loading conditions, and detailed gait analysis including kinematic, kinetic, muscle activity and plantar pressure measurements in both barefoot and shod conditions. Following this each participant will undergo computed tomography (CT) imaging of their foot and ankle under a range of loads and positions while plantar pressures are recorded. A further subgroup of participants will undergo magnetic resonance imaging (MRI) of the foot and ankle.
Imaging data will be segmented to derive the geometry of the bones and the orientation of the joint axes. Insertion points of muscles and ligaments will be determined from the MRI and CT-scans and soft tissue material properties computed from the loaded CT data in combination with the plantar pressure measurements. Gait analysis data will be used to drive the models and in combination with the 3D surface scans for scaling purposes. Predicted plantar pressures and muscle activation patterns predicted from the models will be compared to determine the validity of the models.

Discussion
This protocol will lead to the generation of unique datasets which will be used to develop linked inverse dynamic and forward dynamic biomechanical foot models. These models may be beneficial in predicting the effect of and thus improving the efficacy of orthotic devices for the foot and ankle.
High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes
Authors: Lochlainn Seosamh Ó , Amoah Stephen , Graham Neil S , Alamer Khalid , Rios Juan J , Kurup Smita , Stoute Andrew , Hammond John P , Østergaard Lars , King Graham J , White Phillip J , Broadley Martin R 
Published: December 2011

Abstract

Background
Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes.

Results
We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes.

Conclusions
Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.