bluuebunny/crossref_metadata_2025_split huggingface dataset:
The monoclonal anti–VLA-4 antibody natalizumab mobilizes CD34+ hematopoietic progenitor cells in humans
Authors: Zohren Fabian , Toutzaris Diamandis , Klärner Viola , Hartung Hans-Peter , Kieseier Bernd , Haas Rainer 
Published: January 2008

Abstract
We investigated the role of adhesion molecule VLA-4 in CD34+ blood stem-cell mobilization. Therefore, we examined 20 patients with multiple sclerosis (MS) who were treated with the anti–VLA-4 antibody natalizumab. Treated patients had received a median number of 4 natalizumab infusions (range: 2-9 infusions). Blood samples were taken 4 weeks following the last infusion. With a median proportion of 7.6 CD34+ cells/μL (range: 2.2-30.4 cells/μL), these patients had a significantly higher (P = .003) amount of circulating CD34+ cells compared with 5 healthy volunteers (median: 1.4/μL; range: 0.6-2.4/μL) and 5 untreated MS patients (median: 1.0/μL; range: 0.5-1.7/μL) (P = .001). Serial measurements in 4 patients receiving their first natalizumab infusion showed a maximal significant increase in circulating CD34+ cells from 3.3/μL (range: 1.6-4.8/μL) to 10.4/μL (range: 7.5-12.04/μL) 72 hours following natalizumab infusion (P = .001), including pluripotent cells in colony-forming assays. This mobilizing ability of natalizumab might be useful for patients with poor response to granulocyte colony-stimulating factor (G-CSF)–based protocols.
Human skin keratins are the major proteins in exhaled breath condensate
Authors: Hoffmann H. J. , Tabaksblat L. M. , Enghild J. J. , Dahl R. 
Published: January 2008

Exhaled breath condensate (EBC) may be an attractive noninvasive alternative to bronchoscopy, bronchoalveolar lavage and induced sputum for diagnosis and monitoring of pulmonary disease. The aim of the present study was to identify proteins in EBC by mass spectrometry. Protein in EBC was characterised by gel electrophoresis of freeze-dried EBC samples, and individual proteins were identified by mass spectrometry.Saliva, ambient air condensate (AAC) and EBC were collected from normal human volunteers with or without a filter to remove particles from air. In some instances, EBC was condensed by breathing compressed air. Samples were freeze-dried and analysed by SDS-PAGE and peptide mass fingerprinting.Three major bands were seen in EBC and AAC, and were identified by peptide mass fingerprinting. The probability-based Mowse score was significant only for cytokeratin (CK) 1, CK2 and CK10. In the catalogue of human cytokeratins, CK1, CK2, CK9 and CK10 are described in keratinising epidermis. Saliva did not contain keratin and compressed air EBC contained markedly less keratin. Filtration of inspired air did not remove contaminating keratin.In conclusion, skin keratin in exhaled breath condensate derives from ambient air and not from the respiratory tract.
Towards an automatic classification of protein structural domains based on structural similarity
Authors: Sam Vichetra , Tai Chin-Hsien , Garnier Jean , Gibrat Jean-Francois , Lee Byungkook , Munson Peter J 
Published: January 2008

Abstract

Background
Formal classification of a large collection of protein structures aids the understanding of evolutionary relationships among them. Classifications involving manual steps, such as SCOP and CATH, face the challenge of increasing volume of available structures. Automatic methods such as FSSP or Dali Domain Dictionary, yield divergent classifications, for reasons not yet fully investigated. One possible reason is that the pairwise similarity scores used in automatic classification do not adequately reflect the judgments made in manual classification. Another possibility is the difference between manual and automatic classification procedures. We explore the degree to which these two factors might affect the final classification.

Results
We use DALI, SHEBA and VAST pairwise scores on the SCOP C class domains, to investigate a variety of hierarchical clustering procedures. The constructed dendrogram is cut in a variety of ways to produce a partition, which is compared to the SCOP fold classification.
Ward's method dendrograms led to partitions closest to the SCOP fold classification. Dendrogram- or tree-cutting strategies fell into four categories according to the similarity of resulting partitions to the SCOP fold partition. Two strategies which optimize similarity to SCOP, gave an average of 72% true positives rate (TPR), at a 1% false positive rate. Cutting the largest size cluster at each step gave an average of 61% TPR which was one of the best strategies not making use of prior knowledge of SCOP. Cutting the longest branch at each step produced one of the worst strategies.
We also developed a method to detect irreducible differences between the best possible automatic partitions and SCOP, regardless of the cutting strategy. These differences are substantial. Visual examination of hard-to-classify proteins confirms our previous finding, that global structural similarity of domains is not the only criterion used in the SCOP classification.

Conclusion
Different clustering procedures give rise to different levels of agreement between automatic and manual protein classifications. None of the tested procedures completely eliminates the divergence between automatic and manual protein classifications. Achieving full agreement between these two approaches would apparently require additional information.
A novel method to quantify local CpG methylation density by regional methylation elongation assay on microarray
Authors: Zhang Dingdong , Wang Yan , Bai Yunfei , Ge Qinyu , Qiao Yingjuan , Luo Junfeng , Jia Chao , Lu Zuhong 
Published: January 2008

Abstract

Background
DNA methylation based techniques are important tools in both clinical diagnostics and therapeutics. But most of these methods only analyze a few CpG sites in a target region. Indeed, difference of site-specific methylation may also lead to a change of methylation density in many cases, and it has been found that the density of methylation is more important than methylation of single CpG site for gene silencing.

Results
We have developed a novel approach for quantitative analysis of CpG methylation density on the basis of microarray-based hybridization and incorporation of Cy5-dCTP into the Cy3 labeled target DNA by using Taq DNA Polymerase on microarray. The quantification is achieved by measuring Cy5/Cy3 signal ratio which is proportional to methylation density. This methylation-sensitive technique, termed RMEAM (regional methylation elongation assay on microarray), provides several advantages over existing methods used for methylation analysis. It can determine an exact methylation density of the given region, and has potential of high throughput. We demonstrate a use of this method in determining the methylation density of the promoter region of the tumor-related gene MLH1, TERT and MGMT in colorectal carcinoma patients.

Conclusion
This technique allows for quantitative analysis of regional methylation density, which is the representative of all allelic methylation patterns in the sample. The results show that this technique has the characteristics of simplicity, rapidness, specificity and high-throughput.
Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants
Authors: Gorman Paul M , Kim Sanguk , Guo Meng , Melnyk Roman A , McLaurin Joanne , Fraser Paul E , Bowie James U , Chakrabartty Avijit 
Published: January 2008

Abstract

Background
Amyloid precursor protein (APP) is enzymatically cleaved by γ-secretase to form two peptide products, either Aβ40 or the more neurotoxic Aβ42. The Aβ42/40 ratio is increased in many cases of familial Alzheimer's disease (FAD). The transmembrane domain (TM) of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains.

Results
Using synthetic peptides derived from the APP-TM domain, we show that this segment is capable of forming stable transmembrane dimers. A model of a dimeric APP-TM domain reveals a putative dimerization interface, and interestingly, majority of FAD mutations in APP are localized to this interface region. We find that FAD-APP mutations destabilize the APP-TM dimer and increase the population of APP peptide monomers.

Conclusion
The dissociation constants are correlated to both the Aβ42/Aβ40 ratio and the mean age of disease onset in AD patients. We also show that these TM-peptides reduce Aβ production and Aβ42/Aβ40 ratios when added to HEK293 cells overexpressing the Swedish FAD mutation and γ-secretase components, potentially revealing a new class of γ-secretase inhibitors.
COX-2 and PPARγ expression are potential markers of recurrence risk in mammary duct carcinoma in-situ
Authors: Kulkarni Swati , Patil Deepa B , Diaz Leslie K , Wiley Elizabeth L , Morrow Monica , Khan Seema A 
Published: January 2008

Abstract

Background
In women with duct carcinoma in-situ (DCIS) receiving breast conservation therapy (BCT), in-breast recurrences are seen in approximately 10%, but cannot be accurately predicted using clinical and histological criteria. We performed a case-control study to identify protein markers of local recurrence risk in DCIS.

Methods
Women treated for DCIS with BCT, who later developed in-breast recurrence (cases) were matched by age and year of treatment to women who remained free of recurrence (controls).

Results
A total of 69 women were included in the study, 31 cases and 38 controls. Immunohistochemical evaluation of DCIS tissue arrays was performed for estrogen receptor, progesterone receptor, HER-2/neu, cyclin D1, p53, p21, cycloxygenase-2 (COX-2) and peroxisome proliferator activated receptor γ (PPARγ). Two markers were significantly different between cases and controls on univariate analysis: strong COX-2 expression was associated with increased risk of recurrence, with 67% vs. 24% positivity in cases and controls p = 0.006; and nuclear expression of PPARγ was associated with protection from recurrence with 4% vs. 27% positivity in cases and controls, p = 0.024. In a multivariate model which included size, grade, COX-2 and PPARγ positivity, we found COX-2 positivity to be a strong independent risk factor for recurrence (OR 7.90, 95% CI 1.72–36.23)., whereas size and grade were of borderline significance. PPARγ expression continued to demonstrate a protective trend, (OR 0.14, 95% CI 0.06–1.84).

Conclusion
Our findings suggest that COX-2 and PPARγ should be investigated further as biologic markers to predict DCIS recurrence, particularly since they are also potential therapeutic targets.
Development of fragment-specific osteopontin antibodies and ELISA for quantification in human metastatic breast cancer
Authors: Plumer Alicia , Duan Hongyi , Subramaniam Sripriya , Lucas F Lee , Miesfeldt Susan , Ng Ah-Kau , Liaw Lucy 
Published: January 2008

Abstract

Background
Osteopontin (OPN) is associated with human cancers, and circulating blood OPN may have diagnostic or prognostic value in clinical oncology.

Methods
To evaluate OPN as a cancer biomarker, we generated and characterized five novel mouse monoclonal antibodies against the human full-length OPN (fl-OPN). Epitopes recognized by four antibodies (2C5, 2F10, 2H9, and 2E11) map to N-terminal OPN (aa1-166); one (1F11) maps to C-terminal OPN (aa167-314). These antibodies recognize recombinant and native OPN by ELISA and immunoblot, cross reacting with human and mouse OPN. Two of these novel antibodies (2F10 and 1F11) were used to develop a quantitative enzyme linked immunosorbent assay (ELISA) for fl-OPN.

Results
In comparison with commercially available ELISAs, our assay had high accuracy in measuring fl-OPN standards, and high sensitivity. Specifically, our ELISA has a linear dose response between 0.078 ng/ml-10 ng/ml, with a sensitivity of 13.9 pg/ml. We utilized this assay to quantify fl-OPN in the plasma of healthy volunteers in comparison with patients with metastatic breast cancer. The average circulating plasma fl-OPN in healthy volunteers was 1.2 ng/ml, compared to 4.76 ng/ml in patients with metastatic breast cancer (p = 0.0042). Although the increase in fl-OPN in cancer patients is consistent with previous studies, the measured quantity varied greatly between all existing fl-OPN ELISAs.

Conclusion
Because OPN is a complex molecule with diversity from alternative splicing, post-translational modification, extracellular proteolytic modification, and participation in protein complexes, we suggest that further understanding of specific isoform recognition of multiple OPN species is essential for future studies of OPN biomarker utility.
Intracellular gold nanoparticles enhance non-invasive radiofrequency thermal destruction of human gastrointestinal cancer cells
Authors: Gannon Christopher J , Patra Chitta Ranjan , Bhattacharya Resham , Mukherjee Priyabrata , Curley Steven A 
Published: January 2008

Abstract

Background
Novel approaches to treat human cancer that are effective with minimal toxicity profiles are needed. We evaluated gold nanoparticles (GNPs) in human hepatocellular and pancreatic cancer cells to determine: 1) absence of intrinsic cytotoxicity of the GNPs and 2) external radiofrequency (RF) field-induced heating of intracellular GNPs to produce thermal destruction of malignant cells. GNPs (5 nm diameter) were added to 2 human cancer cell lines (Panc-1, Hep3B). 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and propidium iodide-fluorescence associated cell sorting (PI-FACS) assessed cell proliferation and GNP-related cytotoxicity. Other GNP-treated cells were exposed to a 13.56 MHz RF field for 1, 2, or 5 minutes, and then incubated for 24 hours. PI-FACS measured RF-induced cytotoxicity.

Results
GNPs had no impact on cellular proliferation by MTT assay. PI-FACS confirmed that GNPs alone produced no cytotoxicity. A GNP dose-dependent RF-induced cytotoxicity was observed. For Hep3B cells treated with a 67 μM/L dose of GNPs, cytotoxicity at 1, 2 and 5 minutes of RF was 99.0%, 98.5%, and 99.8%. For Panc-1 cells treated at the 67 μM/L dose, cytotoxicity at 1, 2, and 5 minutes of RF was 98.5%, 98.7%, and 96.5%. Lower doses of GNPs were associated with significantly lower rates of RF-induced thermal cytotoxicity for each cell line (P < 0.01). Cells not treated with GNPs but treated with RF for identical time-points had less cytotoxicity (Hep3B: 17.6%, 21%, and 75%; Panc-1: 15.3%, 26.4%, and 39.8%, all P < 0.01).

Conclusion
We demonstrate that GNPs 1) have no intrinsic cytotoxicity or anti-proliferative effects in two human cancer cell lines in vitro and 2) GNPs release heat in a focused external RF field. This RF-induced heat release is lethal to cancer cells bearing intracellular GNPs in vitro.
Data mining of plasma peptide chromatograms for biomarkers of air contaminant exposures
Authors: Karthikeyan Subramanian , Kumarathasan Premkumari , Vincent Renaud 
Published: January 2008

Abstract

Background
Interrogation of chromatographic data for biomarker discovery becomes a tedious task due to stochastic variability in retention times arising from solvent and column performance. The difficulty is further compounded when the effects of exposure (e.g. to environmental contaminants) and biological variability result in varying numbers and intensities of peaks among chromatograms.

Results
We developed a software tool to correct the stochastic time shifts in chromatographic data through iterative selection of landmark peaks and isometric interpolation to improve alignment of all chromatographic peaks. To illustrate application of the tool, plasma peptides from Fischer rats exposed for 4 h to clean air or Ottawa urban particles (EHC-93) were separated by HPLC with autofluorescence detection, and the retention time shifts between chromatograms were corrected (dewarped). Both dewarped and non-dewarped datasets were then mined for models containing peptide peaks that best discriminate among the treatment groups using ClinproTools™. In general, models generated by dewarped datasets were able to better classify test sample chromatograms into either clean air or EHC-93 exposure groups, and 0 or 24 h post-recovery time groups. Peak areas of peptides in a model that produced the best discrimination of treatment groups were analyzed by two-way ANOVA with exposure (clean air, EHC-93) and recovery time (0 h, 24 h) as factors. Statistically significant (p < 0.05) time-dependent and exposure-dependent increases and decreases were noted establishing these as biomarker candidates for further validation.

Conclusion
Our software tool provides a simple and portable approach for alignment of chromatograms with complex, bi-directional retention time shifts prior to data mining. Reliable biomarker discovery can be achieved through chromatographic dewarping using our software followed by pattern recognition by commercial data mining applications.
Akt inhibitors as an HIV-1 infected macrophage-specific anti-viral therapy
Authors: Chugh Pauline , Bradel-Tretheway Birgit , Monteiro-Filho Carlos MR , Planelles Vicente , Maggirwar Sanjay B , Dewhurst Stephen , Kim Baek 
Published: January 2008

Abstract

Background
Unlike CD4+ T cells, HIV-1 infected macrophages exhibit extended life span even upon stress, consistent with their in vivo role as long-lived HIV-1 reservoirs.

Results
Here, we demonstrate that PI3K/Akt inhibitors, including clinically available Miltefosine, dramatically reduced HIV-1 production from long-living virus-infected macrophages. These PI3K/Akt inhibitors hyper-sensitize infected macrophages to extracellular stresses that they are normally exposed to, and eventually lead to cell death of infected macrophages without harming uninfected cells. Based on the data from these Akt inhibitors, we were able to further investigate how HIV-1 infection utilizes the PI3K/Akt pathway to establish the cytoprotective effect of HIV-1 infection, which extends the lifespan of infected macrophages, a key viral reservoir. First, we found that HIV-1 infection activates the well characterized pro-survival PI3K/Akt pathway in primary human macrophages, as reflected by decreased PTEN protein expression and increased Akt kinase activity. Interestingly, the expression of HIV-1 or SIV Tat is sufficient to mediate this cytoprotective effect, which is dependent on the basic domain of Tat – a region that has previously been shown to bind p53. Next, we observed that this interaction appears to contribute to the downregulation of PTEN expression, since HIV-1 Tat was found to compete with PTEN for p53 binding; this is known to result in p53 destabilization, with a consequent reduction in PTEN protein production.

Conclusion
Since HIV-1 infected macrophages display highly elevated Akt activity, our results collectively show that PI3K/Akt inhibitors may be a novel therapy for interfering with the establishment of long-living HIV-1 infected reservoirs.
Does "ichthyosis uteri" have malignant potential? : A case report of squamous cell carcinoma of endometrium associated with extensive ichthyosis uteri
Authors: Murhekar Kanchan , Majhi Urmila , Sridevi V , Rajkumar T 
Published: January 2008

Abstract
Ichthyosis uteri is a rare condition in which the entire surface of the endometrium is replaced by stratified squamous epithelium. Though the condition often is considered as benign, anaplastic and dysplastic changes have been reported. We describe herein a rare case of low-grade squamous cell carcinoma of endometrium associated with extensive ichthyosis uteri with dysplasia. The cervix showed moderate to severe dysplastic changes while the right fallopian tube showed extensive squamous metaplasia with dysplastic changes. We conclude that squamous cell carcinoma could develop into pre-existing ichthyosis uteri.
Evidence of probabilistic behaviour in protein interaction networks
Authors: Ivanic Joseph , Wallqvist Anders , Reifman Jaques 
Published: January 2008

Abstract

Background
Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour.

Results
We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links.

Conclusion
The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.