bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted infection of HIV-1 Env expressing cells by HIV(CD4/CXCR4) vectors reveals a potential new rationale for HIV-1 mediated down-modulation of CD4
Authors: Ye Zhiping , Harmison George G , Ragheb Jack A , Schubert Manfred 
Published: December 2005

AbstractBackgroundEfficient targeted gene transfer and cell type specific transgene expression are important for the safe and effective expression of transgenesin vivo. Enveloped viral vectors allow insertion of exogenous membrane proteins into their envelopes, which could potentially aid in the targeted transduction of specific cell types. Our goal was to specifically target cells that express the T cell tropic HIV-1 envelope protein (Env) using the highly specific interaction of Env with its cellular receptor (CD4) inserted into the envelope of an HIV-1-based viral vector.ResultsTo generate HIV-1-based vectors carrying the CD4 molecule in their envelope, the CD4 ectodomain was fused to diverse membrane anchors and inserted together with the HIV-1 coreceptor CXCR4 into the envelopes of HIV-1 vector particles. Independent of the type of CD4 anchor, all chimeric CD4 proteins inserted into HIV-1 vector envelopes and the resultant HIV(CD4/CXCR4) particles were able to selectively confer neomycin resistance to cells expressing the fusogenic T cell tropic HIV-1 Env protein. Unexpectedly, in the absence of Env on the target cells, all vector particles carrying the CD4 ectodomain anchored in their envelope adhered to various cell types without infecting these cells. This cell adhesion was very avid. It was independent of the presence of Env on the target cell, the type of CD4 anchor or the presence of CXCR4 on the particle. In mixed cell populations with defined ratios of Env+/Env-cells, the targeted transduction of Env+cells by HIV(CD4/CXCR4) particles was diminished in proportion to the number of Env-cells.ConclusionVector diversion caused by a strong, non-selective cell binding of CD4+-vector particles effectively prevents the targeted transduction of HIV-1 Env expressing cells in mixed cell populations. This Env-independent cell adhesion severely limits the effective use of targeted HIV(CD4/CXCR4) vectors designed to interfere with HIV-1 replicationin vivo. Importantly, the existence of this newly described and remarkably strong CD4-dependent cell adhesion suggests that the multiple viral efforts to reduce CD4 cell surface expression may, in part, be to prevent cell adhesion to non-target cells and thereby to increase the infectivity of viral progeny. Preventing CD4 down-modulation by HIV-1 might be an effective component of a multi-faceted antiviral strategy.
Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants
Authors: Hellens Roger P , Allan Andrew C , Friel Ellen N , Bolitho Karen , Grafton Karryn , Templeton Matthew D , Karunairetnam Sakuntala , Gleave Andrew P , Laing William A 
Published: December 2005

Abstract

Background
We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes.

Results
We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs.

Conclusion
In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation
Authors: Hackl Hubert , Burkard Thomas Rainer , Sturn Alexander , Rubio Renee , Schleiffer Alexander , Tian Sun , Quackenbush John , Eisenhaber Frank , Trajanoski Zlatko 
Published: December 2005

Abstract
Background
Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the sequences of identified gene products has not been done and global mechanisms have not been investigated. We evaluated the extent to which molecular processes can be revealed by expression profiling and functional annotation of genes that are differentially expressed during fat cell development.

Results
Mouse microarrays with more than 27,000 elements were developed, and transcriptional profiles of 3T3-L1 cells (pre-adipocyte cells) were monitored during differentiation. In total, 780 differentially expressed expressed sequence tags (ESTs) were subjected to in-depth bioinformatics analyses. The analysis of 3'-untranslated region sequences from 395 ESTs showed that 71% of the differentially expressed genes could be regulated by microRNAs. A molecular atlas of fat cell development was then constructed by de novo functional annotation on a sequence segment/domain-wise basis of 659 protein sequences, and subsequent mapping onto known pathways, possible cellular roles, and subcellular localizations. Key enzymes in 27 out of 36 investigated metabolic pathways were regulated at the transcriptional level, typically at the rate-limiting steps in these pathways. Also, coexpressed genes rarely shared consensus transcription-factor binding sites, and were typically not clustered in adjacent chromosomal regions, but were instead widely dispersed throughout the genome.

Conclusions
Large-scale transcription profiling in conjunction with sophisticated bioinformatics analyses can provide not only a list of novel players in a particular setting but also a global view on biological processes and molecular networks.
Functional expression of the CD163 scavenger receptor on acute myeloid leukemia cells of monocytic lineage
Authors: Bächli Esther B , Schaer Dominik J , Walter Roland B , Fehr Jörg , Schoedon Gabriele 
Published: December 2005

Abstract
The hemoglobin–haptoglobin (Hb–Hp) scavenger receptor CD163 is a monocyte/macrophage-restricted surface antigen, whose expression is strongly up-regulated by glucocorticoids. We have previously shown that CD163 is expressed by acute myeloid leukemia (AML) cells of monocytic lineage. Herein, we expand this finding by demonstrating constitutive and glucocorticoid-enhanced CD163 expression on French-American-British M4/M5 AML cells, and leukemic blasts of other AML subtypes and normal hematopoietic progenitor cells do not express CD163. We provide evidence that the functional characteristics of CD163 are preserved on malignant cells by showing the capability of types M4/M5 blast cells to internalize Hb–Hp by a CD163-mediated mechanism. Together, our results identify CD163 as a potential target for therapeutic intervention. It is important that CD163 does not appear to be released from leukemic blasts under noninflammatory conditions, thus reducing the probability of off-target side-effects as a result of competitive binding of potential therapeutic ligands to nonmembrane-bound CD163.
Gene expression changes by amyloid β peptide-stimulated human postmortem brain microglia identify activation of multiple inflammatory processes
Authors: Walker Douglas G , Link John , Lue Lih-Fen , Dalsing-Hernandez Jessica E , Boyes Barry E 
Published: December 2005

Abstract
A central feature of the inflammatory pathology in Alzheimer’s disease is activated microglia clustered around aggregated amyloid β (Aβ) peptide-containing plaques. In vitro-cultured microglia can be activated to an inflammatory state by aggregated Aβ with the induction of a range of different neurotoxic factors and provide a model system for studying microglia Aβ interactions. Gene expression responses of human postmortem brain-derived microglia to aggregated Aβ were measured using whole genome microarrays to address the hypothesis that Aβ interactions with human microglia primarily induce proinflammatory genes and not activation of genes involved in Aβ phagocytosis and removal. The results demonstrated that Aβ activation of microglia induced a large alteration in gene transcription including activation of many proinflammatory cytokines and chemokines, most notably, interleukin (IL)-1β, IL-8, and matrix metalloproteinases (MMP), including MMP1, MMP3, MMP9, MMP10, and MMP12. All of these genes could amplify ongoing inflammation, resulting in further neuronal loss. Changes in expression of receptors associated with Aβ phagocytosis did not match the changes in proinflammatory gene expression. Time-course gene expression profiling, along with real-time polymerase chain reaction validation of expression changes, demonstrated an acute phase of gene induction for many proinflammatory genes but also chronic activation for many other potentially toxic products. These chronically activated genes included indoleamine 2,3-dioxygenase and kynureninase, which are involved in formation of the neurotoxin quinolinic acid, and S100A8, a potential proinflammatory chemokine. These studies show that activation of microglia by Aβ induces multiple genes that could be involved in inflammatory responses contributing to neurodegenerative processes.
Dendritic cells during polymicrobial sepsis rapidly mature but fail to initiate a protective Th1-type immune response
Authors: Flohé Stefanie B , Agrawal Hemant , Schmitz Daniel , Gertz Michaela , Flohé Sascha , Schade F Ulrich 
Published: December 2005

Abstract
Polymicrobial sepsis is associated with immunosuppression caused by the predominance of anti-inflammatory mediators and profound loss of lymphocytes through apoptosis. Dendritic cells (DC) are potent antigen-presenting cells and play a key role in T cell activation. We tested the hypothesis that DC are involved in sepsis-mediated immunosuppression in a mouse cecal ligation and puncture (CLP) model, which resembles human polymicrobial sepsis. At different time-points after CLP, DC from the spleen and peripheral lymph nodes were characterized in terms of expression of costimulatory molecules, cytokine synthesis, and subset composition. Splenic DC strongly up-regulated CD86 and CD40 but not CD80 as soon as 8 h after CLP. In contrast, lymph node DC equally increased the expression of CD86, CD40, and CD80. However, this process of maturation occurred later in the lymph nodes than in the spleen. Splenic DC from septic mice were unable to secrete interleukin (IL)-12, even upon stimulation with CpG or lipopolysaccharide + CD40 ligand, but released high levels of IL-10 in comparison to DC from control mice. Neutralization of endogenous IL-10 could not restore IL-12 secretion by DC of septic mice. In addition, the splenic CD4+CD8– and CD4–CD8+ subpopulations were lost during sepsis, and the remaining DC showed a reduced capacity for allogeneic T cell activation associated with decreased IL-2 synthesis. Thus, during sepsis, splenic DC acquire a state of aberrant responsiveness to bacterial stimuli, and two DC subtypes are selectively lost. These changes in DC behavior might contribute to impaired host response against bacteria during sepsis.
Validation of Probabilistic Linkage to Match De‐identified Ambulance Records to a State Trauma Registry
Authors: Newgard Craig D. 
Published: December 2005

Abstract
Objectives:
To validate the accuracy of using probabilistic linkage for matching de‐identified ambulance records to a state trauma registry.
Methods:
This was a retrospective cohort analysis. Three thousand nine hundred nineteen true matches between ambulance and state trauma registry data from 1998 to 2003 were identified by deterministic matching on trauma identification number and verified by human review. Two thousand thirty‐eight ambulance records from trauma patients not meeting criteria for a true match, and an identical number of trauma registry records randomly selected from the one local county served by a different EMS provider, were included as nonmatches. There were 17 variables considered for linkage, which included the following: age, gender, race, county, hospital, date, rural setting, call and arrival times, mechanism, penetrating injury, vital signs, intubation, and intoxication. Probabilistic linkage was used to link the two data sets, using seven different combinations of common variables (maximum, 17; minimum, 4). The sensitivity and specificity of identifying true matches and nonmatches (95% confidence intervals [95% CI]) were calculated for each combination of variables.
Results:
Using all 17 available variables, 3,766 of 3,919 true matches were appropriately linked (sensitivity, 96.1%; 95% CI = 95.4% to 96.7%), with eight mismatches (specificity, 99.6%; 95% CI = 99.2% to 99.8%). Sensitivity fell below 95% with < 15 variables; however, sensitivity was very dependent on the inclusion of variables with high discriminatory power. Specificity remained >98% regardless of the number of variables included.
Conclusions:
Probabilistic linkage is a valid method for matching ambulance records to a trauma registry without the use of patient identifiers; however, the sensitivity of identifying true matches is critically dependent on the number and type of common variables included in the analysis.
Synthesis of Degradable Polymer Exhibiting LCST-type Phase Separation by Radical Copolymerization of Sorbic Esters and Molecular Oxygen
Authors: Taketani Shuji , Matsumoto Akikazu 
Published: December 2005

Abstract
We synthesized water-soluble polyperoxides (PP) by radical copolymerization of hydrophilic sorbic esters with oxygen. A phase separation with a lower critical solution temperature (LCST) was observed under the onset temperature of thermal degradation for the aqueous solutions of PP containing a tetra(ethylene oxide) unit in the side chain. A critical temperature for the LCST-type phase separation depended on the composition of the hydrophilic and hydrophobic esters of PP.
Photophysicochemical Properties of Chlorophyll-a Adsorbed on Mg-containing Mesoporous Silica
Authors: Nakamura Takahiko , Takeuchi Masato , Yamashita Hiromi , Anpo Masakazu 
Published: December 2005

Abstract
Chlorophyll-a (chl-a) was found to easily change to pheophytin-a during its adsorption on hexagonal mesoporous silica (HMS) since the centered Mg ions of chl-a easily react with silanol groups as Brønsted acid sites (pheophytinization). This pheophytinization process could be suppressed by adding small amounts of Mg species into the frameworks of HMS. The highly dispersed Mg species work as adsorption sites for chl-a and/or the porphyrin ring of pheophytin-a, resulting in the formation of an original chl-a like complex species.
Dynamic Axial Chirality Control of a Carboxybiphenol through Acid–Base Interaction
Authors: Morioka Kohei , Tamagawa Norio , Maeda Katsuhiro , Yashima Eiji 
Published: December 2005

Abstract
A novel, fluorescent 2,2′-biphenol bearing two carboxyl and two ethynyl groups was found to be sensitive to the chirality of the chiral diamines, thus showing an induced circular dichroism due to an excess single-handed, axially twisted conformation.
Formation of Micrometer-sized Supramolecular Assemblies with Unique Morphologies from Triple-chain Lipids with Two Sugar Head Groups
Authors: Kida Toshiyuki , Tanaka Toshiki , Nakatsuji Yohji , Akashi Mitsuru 
Published: December 2005

Abstract
Triple-chain lipids with two sugar head groups spontaneously formed the giant vesicles in aqueous media, and their morphologies were remarkably affected by the structure of the sugar head group as well as the incubation temperature.
General Microwave-assisted Protocols for the Expedient Synthesis of Furo[3,2-c]chromen-4-ones
Authors: Wu Jie 
Published: December 2005

Abstract
Functionalized furo[3,2-c]chromen-4-ones are expediently prepared in excellent yields (92–99%) from common 4-hydroxycoumarins, isocyanides, and aldehydes under microwave irradiation.
Microwave-polyol Process for Functionalizing Carbon Nanotubes with SnO2 and CeO2 Coating
Authors: Bai Jingyi , Xu Zhude , Zheng Yifan 
Published: December 2005

Abstract
Multiwalled carbon nanotubes (MWNTs) coated with CeO2 and SnO2 nanoparticles were successfully prepared by microwave-polyol process. The samples are characterized by XRD, TEM, HRTEM, and UV–vis analysis. SnO2 and CeO2 nanoparticles are homogeneously distributed on the wall of the MWNTs.
Current assays overestimate 25-hydroxyvitamin D3 and underestimate 25-hydroxyvitamin D2 compared with HPLC: need for assay-specific decision limits and metabolite-specific assays
Authors: Glendenning P , Taranto M , Noble JM , Musk AA , Hammond C , Goldswain PR , Fraser WD , Vasikaran SD 
Published: December 2005

Background: Clinical demand for quick, cheap, precise and accurate 25-hydroxyvitamin D (25(OH)D) results has led to the development of a variety of assay methods. Lack of standardization of these methods has resulted in intermethod disagreement and challenged whether current assays recognize 25(OH)D2 and 25(OH)D3 equally. Methods: We studied 172 patient samples from hip fracture cases using DiaSorin (DS) and IDS radioimmunoassays and the Nichols Advantage-automated protein binding assay (NA-CLPBA) in comparison to high-performance liquid chromatography (HPLC). 52 patient samples were analysed before and after three months treatment with 1000 IU of daily ergocalciferol (vitamin D2). Results: Linear regression analysis in pre-treatment samples demonstrated a positive Y-intercept for each immunoassay compared with HPLC, and a slope that varied from 0.64 (IDS) to 0.97 (DS, NA-CLPBA). Bland Altman analysis demonstrated that all the three assays had a proportional positive bias relative to HPLC at values from 20 to 50 nmol/L. Regression analysis of post-treatment samples demonstrated a slope that was not significantly different from zero for the IDS and NA-CLPBA and 0.2 for the DS method, with a positive intercept for all assays of between 8 and 22, indicating less than 50% of 25(OH)D2 measured by HPLC was detected. Conclusions: These results demonstrate the need for assay-specific decision limits for 25(OH)D3 in order to define appropriate thresholds for treatment institution. Treatment with vitamin D2 may not be accurately monitored with any of the three commercial assays studied. Clinicians and biochemists who continue to use 25(OH)D assays need to be urgently informed of these issues.
Mechanism of interference by haemolysis in the cardiac troponin T immunoassay
Authors: Sodi Ravinder , Darn Simon M , Davison Andrew S , Stott Anthony , Shenkin Alan 
Published: December 2005

Background: The cardiac troponins have been shown to be sensitive and specific biochemical markers of myocardial infarction and highly prognostic for future adverse events in patients with acute coronary syndromes. There have been reports suggesting that haemolysis causes a negative interference in the cardiac troponin T (cTnT) assay but the mechanism(s) involved remain unknown. Here we show the effects of haemolysis and haemoglobin per se on the cTnT assay. Methods: The effect of haemolysis was studied by the addition of prepared haemolysate to serum samples with known and clinically relevant cTnT levels. The effect of haemoglobin was studied by the addition of haemoglobin of increasing concentrations and noting its effect on the level of cTnT measured. The effect of putative proteases was determined indirectly by incubating samples with spiked cTnT with various protease inhibitors and observing the changes in the measured cTnT levels. Results: The results show that both haemolysis, which is the release of haemoglobin and corpuscular contents, and haemoglobin itself negatively interfere in the cTnT assay in a concentration-dependent manner, although the former had a greater magnitude of effect. On haemolysis, indirect evidence suggests that proteases are released which degrade the cTnT in serum, thus causing the decreased levels detected. Pepstatin A, a reversible inhibitor of aspartic proteinases, effectively inhibited the loss of cTnT in serum at 37°C and pH 7.4 over a 48-h period. We found that at a haemoglobin level of 0.75 g/L, cTnT declined by more than 10% of the initial concentration, suggesting that falsely decreased levels due to haemolysis may significantly affect the clinical utility of the assay. Conclusions: Haemolysis, haemoglobin per se and possibly proteolysis play a role in the negative interference in cTnT assays. Measures to reduce this interference must be implemented.
Prostate-specific antigen: bias and molarity of commercial assays for PSA in use in England
Authors: Roddam Andrew W , Rimmer Janet , Nickerson Claire , Ward Anthony Milford ,   The NHS Prostate Cancer Risk Management Programme
Published: December 2005

Background: The UK Prostate Cancer Risk Management Programme has recommended that all assays for prostate-specific antigen (PSA) should be both equimolar in their response to free and complexed PSA and calibrated to the World Health Organization (WHO) First International Standard for PSA (90:10). To determine which assays currently being used by diagnostic laboratories in England fulfil these criteria, a PSA recovery experiment was performed. Methods: In all, 15 samples containing varying mixtures and concentrations of the WHO International Standards for PSA and free PSA were sent to 223 laboratories in England who participate in the UK National External Quality Assessment Service (UK NEQAS) scheme for analysis. Analytical platforms were assigned to one of 11 methods, and the results were converted into recovery percentages and analysed by means of a linear random intercept model. Results: No method was both unbiased and equimolar; estimates of bias ranged from -5% to 22% and estimates of non-equimolarity (change in bias per percent increase in free PSA) ranged from -0.18% to 0.28%. Conclusions: Analytical methods currently in use for PSA in England have inter-method differences; some methods have estimated biases over 10% which can result in unacceptable clinical performance characteristics. Methods for PSA should be equimolar and calibrated to the international standard to minimize the likelihood of clinical errors.