bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations
Authors: Zare Hossein , Sangurdekar Dipen , Srivastava Poonam , Kaveh Mostafa , Khodursky Arkady
Published: June 2009

Background

Network reconstruction methods that rely on covariance of expression of transcription regulators and their targets ignore the fact that transcription of regulators and their targets can be controlled differently and/or independently. Such oversight would result in many erroneous predictions. However, accurate prediction of gene regulatory interactions can be made possible through modeling and estimation of transcriptional activity of groups of co-regulated genes.

Results

Incomplete regulatory connectivity and expression data are used here to construct a consensus network of transcriptional regulation in Escherichia coli (E. coli). The network is updated via a covariance model describing the activity of gene sets controlled by common regulators. The proposed model-selection algorithm was used to annotate the likeliest regulatory interactions in E. coli on the basis of two independent sets of expression data, each containing many microarray experiments under a variety of conditions. The key regulatory predictions have been verified by an experiment and literature survey. In addition, the estimated activity profiles of transcription factors were used to describe their responses to environmental and genetic perturbations as well as drug treatments.

Conclusion

Information about transcriptional activity of documented co-regulated genes (a core regulon) should be sufficient for discovering new target genes, whose transcriptional activities significantly co-vary with the activity of the core regulon members. Our ability to derive a highly significant consensus network by applying the regulon-based approach to two very different data sets demonstrated the efficiency of this strategy. We believe that this approach can be used to reconstruct gene regulatory networks of other organisms for which partial sets of known interactions are available.
Genomic profiling identifies common HPV-associated chromosomal alterations in squamous cell carcinomas of cervix and head and neck
Authors: Wilting Saskia M , Smeets Serge J , Snijders Peter JF , van Wieringen Wessel N , van de Wiel Mark A , Meijer Gerrit A , Ylstra Bauke , Leemans C René , Meijer Chris JLM , Brakenhoff Ruud H , Braakhuis Boudewijn JM , Steenbergen Renske DM
Published: June 2009

Background

It is well known that a persistent infection with high-risk human papillomavirus (hrHPV) is causally involved in the development of squamous cell carcinomas of the uterine cervix (CxSCCs) and a subset of SCCs of the head and neck (HNSCCs). The latter differ from hrHPV-negative HNSCCs at the clinical and molecular level.

Methods

To determine whether hrHPV-associated SCCs arising from different organs have specific chromosomal alterations in common, we compared genome-wide chromosomal profiles of 10 CxSCCs (all hrHPV-positive) with 12 hrHPV-positive HNSCCs and 30 hrHPV-negative HNSCCs. Potential organ-specific alterations and alterations shared by SCCs in general were investigated as well.

Results

Unsupervised hierarchical clustering resulted in one mainly hrHPV-positive and one mainly hrHPV-negative cluster. Interestingly, loss at 13q and gain at 20q were frequent in HPV-positive carcinomas of both origins, but uncommon in hrHPV-negative HNSCCs, indicating that these alterations are associated with hrHPV-mediated carcinogenesis. Within the group of hrHPV-positive carcinomas, HNSCCs more frequently showed gains of multiple regions at 8q whereas CxSCCs more often showed loss at 17p. Finally, gains at 3q24-29 and losses at 11q22.3-25 were frequent (>50%) in all sample groups.

Conclusion

In this study hrHPV-specific, organ-specific, and pan-SCC chromosomal alterations were identified. The existence of hrHPV-specific alterations in SCCs of different anatomical origin, suggests that these alterations are crucial for hrHPV-mediated carcinogenesis.
New clinical developments in histone deacetylase inhibitors for epigenetic therapy of cancer
Authors: Cang Shundong , Ma Yuehua , Liu Delong
Published: June 2009

DNA methylation and histone acetylation are two well known epigenetic chromatin modifications. Epigenetic agents leading to DNA hypomethylation and histone hyperacetylation have been approved for treatment of hematological disorders. The first histone deacetylase inhibitor, vorinostat, has been licensed for cutaneous T cell lymphoma treatment. More than 11 new epigenetic agents are in various stages of clinical development for therapy of multiple cancer types. In this review we summarize novel histone deacetylase inhibitors and new regimens from clinical trials for epigenetic therapy of cancer.
Impaired glucose transporter-1 degradation and increased glucose transport and oxidative stress in response to high glucose in chondrocytes from osteoarthritic versus normal human cartilage
Authors: Rosa Susana C , Gonçalves Juliana , Judas Fernando , Mobasheri Ali , Lopes Celeste , Mendes Alexandrina F
Published: June 2009

Introduction

Disorders that affect glucose metabolism, namely diabetes mellitus (DM), may favor the development and/or progression of osteoarthritis (OA). Thus far, little is known regarding the ability of chondrocytes to adjust to variations in the extracellular glucose concentration, resulting from hypoglycemia and hyperglycemia episodes, and so, to avoid deleterious effects resulting from deprivation or intracellular accumulation of glucose. The aim of this study was to compare the ability of normal and OA chondrocytes to regulate their glucose transport capacity in conditions of insufficient or excessive extracellular glucose and to identify the mechanisms involved and eventual deleterious consequences, namely the production of reactive oxygen species (ROS).

Methods

Chondrocytes, isolated from normal and OA human cartilage, were maintained in high-density monolayer cultures, in media without or with 10 or 30 mM glucose. Glucose transport was measured as the uptake of 2-deoxy-D-glucose (2-DG). Glucose transporter-1 (GLUT-1) mRNA and protein content were evaluated by real-time RT-PCR and western blot, respectively. ROS production was measured with 2',7'-dichlorodihydrofluorescein diacetate.

Results

Basal and IL-1β-induced 2-DG uptake, including the affinity (1.066 ± 0.284 and 1.49 ± 0.59 mM) and maximal velocity (0.27 ± 0.08 and 0.33 ± 0.08 nmol/μg protein/hour), and GLUT-1 content were identical in normal and OA chondrocytes. Glucose deprivation increased 2-DG uptake and GLUT-1 protein both in normal and OA chondrocytes. Exposure to high glucose (30 mM) for 18 or 48 hours decreased those parameters in normal but not in OA chondrocytes. GLUT-1 mRNA levels were unaffected by high glucose, either in normal or OA chondrocytes. The high glucose-induced reduction in GLUT-1 protein in normal chondrocytes was reversed by treatment with a lysosome inhibitor. High glucose induced ROS production, which lasted significantly longer in OA than in normal chondrocytes.

Conclusions

Normal human chondrocytes adjust to variations in the extracellular glucose concentration by modulating GLUT-1 synthesis and degradation which involves the lysosome pathway. Although capable of adjusting to glucose deprivation, OA chondrocytes exposed to high glucose were unable downregulate GLUT-1, accumulating more glucose and producing more ROS. Impaired GLUT-1 downregulation may constitute an important pathogenic mechanism by which conditions characterized by hyperglycemia, like DM, can promote degenerative changes in chondrocytes that can facilitate the progression of OA.
Evaluation of arthroscopy and macroscopic scoring
Authors: af Klint Erik , Catrina Anca I , Matt Peter , Neregråd Petra , Lampa Jon , Ulfgren Ann-Kristin , Klareskog Lars , Lindblad Staffan
Published: June 2009

Introduction

Arthroscopy is a minimally invasive technique for retrieving synovial biopsies in rheumatology during the past 20 years. Vital for its use is continual evaluation of its safety and efficacy. Important for sampling is the fact of intraarticular variation for synovial markers. For microscopic measurements scoring systems have been developed and validated, but for macroscopic evaluations there is a need for further comprehensive description and validation of equivalent scoring systems.

Methods

We studied the complication rate and yield of arthroscopies performed at our clinic between 1998 and 2005. We also created and evaluated a macroscopic score set of instructions for synovitis.

Results

Of 408 procedures, we had two major and one minor complication; two haemarthrosis and one wound infection, respectively. Pain was most often not a problem, but 12 procedures had to be prematurely ended due to pain. Yield of biopsies adequate for histology were 83% over all, 94% for knee joints and 34% for smaller joints. Video printer photographs of synovium taken during arthroscopy were jointly and individually reviewed by seven raters in several settings, and intra and inter rater variation was calculated. A macroscopic synovial scoring system for arthroscopy was created (Macro-score), based upon hypertrophy, vascularity and global synovitis. These written instructions were evaluated by five control-raters, and when evaluated individual parameters were without greater intra or inter rater variability, indicating that the score is reliable and easy to use.

Conclusions

In our hands rheumatologic arthroscopy is a safe method with very few complications. For knee joints it is a reliable method to retrieve representative tissue in clinical longitudinal studies. We also created an easy to use macroscopic score, that needs to be validated against other methodologies. We hope it will be of value in further developing international standards in this area.
Curvelet-based migration preconditioning and scaling
Authors: Herrmann Felix J. , Brown Cody R. , Erlangga Yogi A. , Moghaddam Peyman P.
Published: May 2009

The extremely large size of typical seismic imaging problems has been a major stumbling block for iterative techniques to attain accurate migration amplitudes. These iterative methods are important because they complement theoretical approaches hampered by difficulties controlling problems such as finite-acquisition aperture, source-receiver frequency response, and directivity. To solve these problems, we apply preconditioning, which significantly improves convergence of least-squares migration. We discuss different levels of preconditioning: corrections for the order of the migration operator, corrections for spherical spreading, and position- and reflector-dip-dependent amplitude errors. Although the first two corrections correspond to simple scalings in the Fourier and physical domain, the third correction requires phase-space (space spanned by location and dip) scaling, which we carry out with curvelets. Our combined preconditioner significantly improves the convergence of least-squares wave-equation migration on a line from the SEG/EAGE [Formula: see text] salt model.
Edge-preserving polynomial fitting method to suppress random seismic noise
Authors: Lu Yan-hong , Lu Wen-kai
Published: May 2009

This paper focuses on suppressing random seismic noise while preserving signals and edges. We propose an edge-preserving polynomial fitting (EPPF) method leading to good signal and edge preservation. The EPPF method assumes that a 1D signal can be modeled by a polynomial. A series of shifted windows are used to estimate any sample in a 1D signal. After that, the window with the minimum fitting error is selected and its output is assigned as the final estimate for this sample. For a point in 2D seismic data, several 1D signals are extracted along different directions first and then are processed by the EPPF method. After that, we select the direction with a minimum fitting error and assign its output as the final estimate for this point. Applications with synthetic and real data sets show that the EPPF method suppresses the random seismic noise effectively while preserving the signals and edges. Comparisons of results obtained by the EPPF method, the edge-preserving smoothing (EPS) method, and the polynomial fitting (PF) method show that the EPPF method outperforms EPS and PF methods in these tests.
Overall Survival and Updated Results for Sunitinib Compared With Interferon Alfa in Patients With Metastatic Renal Cell Carcinoma
Authors: Motzer Robert J. , Hutson Thomas E. , Tomczak Piotr , Michaelson M. Dror , Bukowski Ronald M. , Oudard Stéphane , Negrier Sylvie , Szczylik Cezary , Pili Roberto , Bjarnason Georg A. , Garcia-del-Muro Xavier , Sosman Jeffrey A. , Solska Ewa , Wilding George , Thompson John A. , Kim Sindy T. , Chen Isan , Huang Xin , Figlin Robert A.
Published: June 2009

Purpose

A randomized, phase III trial demonstrated superiority of sunitinib over interferon alfa (IFN-α) in progression-free survival (primary end point) as first-line treatment for metastatic renal cell carcinoma (RCC). Final survival analyses and updated results are reported.

Patients and Methods

Seven hundred fifty treatment-naïve patients with metastatic clear cell RCC were randomly assigned to sunitinib 50 mg orally once daily on a 4 weeks on, 2 weeks off dosing schedule or to IFN-α 9 MU subcutaneously thrice weekly. Overall survival was compared by two-sided log-rank and Wilcoxon tests. Progression-free survival, response, and safety end points were assessed with updated follow-up.

Results

Median overall survival was greater in the sunitinib group than in the IFN-α group (26.4 v 21.8 months, respectively; hazard ratio [HR] = 0.821; 95% CI, 0.673 to 1.001; P = .051) per the primary analysis of unstratified log-rank test (P = .013 per unstratified Wilcoxon test). By stratified log-rank test, the HR was 0.818 (95% CI, 0.669 to 0.999; P = .049). Within the IFN-α group, 33% of patients received sunitinib, and 32% received other vascular endothelial growth factor–signaling inhibitors after discontinuation from the trial. Median progression-free survival was 11 months for sunitinib compared with 5 months for IFN-α (P < .001). Objective response rate was 47% for sunitinib compared with 12% for IFN-α (P < .001). The most commonly reported sunitinib-related grade 3 adverse events included hypertension (12%), fatigue (11%), diarrhea (9%), and hand-foot syndrome (9%).

Conclusion

Sunitinib demonstrates longer overall survival compared with IFN-α plus improvement in response and progression-free survival in the first-line treatment of patients with metastatic RCC. The overall survival highlights an improved prognosis in patients with RCC in the era of targeted therapy.
Ischaemia-modified albumin elevation after percutaneous coronary intervention reflects albumin concentration rather than ischaemia
Authors: Demir H , Topkaya B Ç , Erbay A R , Doğan M , Yücel D
Published: June 2009

Background

Percutaneous coronary intervention (PCI) is accepted as a model of myocardial ischaemia in studies of ischaemia markers, especially of ischaemia-modified albumin (IMA). However, there is concern that IMA levels may reflect changes in albumin concentrations rather than myocardial ischaemia also during PCI.

Methods

Twenty-one consecutive patients (17 men and 4 women) undergoing single-vessel percutaneous coronary angioplasty were enrolled in the study. IMA and albumin levels were measured together with myoglobin, creatine kinase 2 and cardiac troponin I, before (Group 1), immediately after (Group 2) and 6 h after (Group 3) the procedure of PCI.

Results

The IMA levels of Group 2 were significantly higher than those of Group 1 and Group 3 ( P < 0.05 for both). However, correction of IMA by multiplying with the (individual albumin concentration of the patient/median albumin concentration of Group 1) ratio gave no statistical differences between the groups ( P > 0.05). There were strong negative correlations between IMA levels and albumin concentrations within individual groups ( r = −0.757, P < 0.001; r = −0.712, P < 0.001; and r = −0.705, P < 0.001 for Group 1, Group 2 and Group 3, respectively).

Conclusion

The results confirm the close dependency of IMA results on albumin concentrations. Therefore, IMA results reflect albumin concentrations rather than myocardial ischaemia also in PCI. This situation and lack of standard reference materials for the albumin cobalt binding assay can lessen the diagnostic performance of IMA.
Relative Performance Compensation, Contests, and Dynamic Incentives
Authors: Casas-Arce Pablo , Martínez-Jerez F. Asís
Published: June 2009

Contests (or tournaments) are pervasive in organizations. They help performance evaluation by eliminating common shocks affecting agents' performance. However, tournaments are less effective when participants have heterogeneous ability because participants may conclude that the ability gap is too large to be overcome by their effort. Our theoretical analysis shows that a similar loss of motivation arises when tournaments take place over multiple periods because interim performance acts in a way that is similar to heterogeneous ability. Analyzing the sales contests organized by a commodities company, we document that winning participants decrease their effort as their lead extends, whereas the effort of trailing participants fades only when the gap to a winning position is very large. We also show that, on average, when contests are introduced they induce a higher level of effort among participants, although the incentives weaken as the number of participants increases. Finally, we demonstrate that although retailers respond to the multiple performance dimensions of the incentive program in part by shifting effort toward sales of more expensive products, they channel most of the increased effort toward reaching more customers.
The Exeter Universal cemented femoral component at 15 to 17 years
Authors: Carrington N. C. , Sierra R. J. , Gie G. A. , Hubble M. J. W. , Timperley A. J. , Howell J. R.
Published: May 2009

The first 325 Exeter Universal stems (309 patients) implanted at the originating centre were inserted between March 1988 and February 1990 by a group of surgeons with differing experience. In this report we describe the clinical and radiological results at a mean of 15.7 years (14.7 to 17.3) after operation with no loss to follow-up. There were 97 patients (108 hips) with replacements still in situ and 31 (31 hips) who had undergone a further procedure. With an endpoint of revision for aseptic loosening, the survivorship at 17 years was 100% and 90.4% for the femoral and acetabular component, respectively. The mean Merle D’Aubigné and Postel scores at review were 5.4 (sd 0.97) for pain and 4.5 (sd 1.72) for function. The mean Oxford score was 38.4 (sd 9.8) (0 to 48 worst-to-best scale) and the mean combined Harris pain and function score was 73.2 (sd 16.9). Radiological review showed excellent preservation of bone stock in the proximal femur and no failures of the femoral component.
Circulating levels of cobalt and chromium from metal-on-metal hip replacement are associated with CD8+ T-cell lymphopenia
Authors: Hart A. J. , Skinner J. A. , Winship P. , Faria N. , Kulinskaya E. , Webster D. , Muirhead-Allwood S. , Aldam C. H. , Anwar H. , Powell J. J.
Published: May 2009

We carried out a cross-sectional study with analysis of the demographic, clinical and laboratory characteristics of patients with metal-on-metal hip resurfacing, ceramic-on-ceramic and metal-on-polyethylene hip replacements. Our aim was to evaluate the relationship between metal-on-metal replacements, the levels of cobalt and chromium ions in whole blood and the absolute numbers of circulating lymphocytes. We recruited 164 patients (101 men and 63 women) with hip replacements, 106 with metal-on-metal hips and 58 with non-metal-on-metal hips, aged < 65 years, with a pre-operative diagnosis of osteoarthritis and no pre-existing immunological disorders.

Laboratory-defined T-cell lymphopenia was present in13 patients (15%) (CD8+ lymphopenia) and 11 patients (13%) (CD3+ lymphopenia) with unilateral metal-on-metal hips. There were significant differences in the absolute CD8+ lymphocyte subset counts for the metal-on-metal groups compared with each control group (p-values ranging between 0.024 and 0.046). Statistical modelling with analysis of covariance using age, gender, type of hip replacement, smoking and circulating metal ion levels, showed that circulating levels of metal ions, especially cobalt, explained the variation in absolute lymphocyte counts for almost all lymphocyte subsets.
The Anatomical Graduated Component total knee replacement
Authors: Ritter M. A.
Published: May 2009

The long-term success of total knee replacement is multifactorial, including factors relating to the patient, the operation and the implant. The purpose of this study was to examine the 20-year survival of the cemented Anatomical Graduated Component (AGC) total knee replacement. Between 1983 and 2004, 7760 of these were carried out at our institution. Of these, 6726 knees which received the non-modular metal-backed tibial component with compression-moulded polyethylene and had a minimum two-year follow-up were available for study. In all, 36 knees were followed over 20 years with a survival of the tibial and femoral components together of 97.8% (95% confidence interval (CI) 0.9851 to 0.9677), with no implants being revised for polyethylene wear or osteolysis. Age > 70 was associated with increased survival (99.6%, 95% CI 99.0 to 99.8) (p < 0.0001) but pre-operative valgus alignment reduced survival (95.1%, 95% CI 90.0 to 97.6) (p = 0.0056). Age < 55 (p = 0.129), pre-operative varus alignment (p = 0.707), osteonecrosis (p = 0.06), rheumatoid arthritis (p = 0.247), and gender (p = 0.666) were not statistically associated with failure.

We attribute the success of the AGC implant to its relatively unconstrained articular geometry and the durability of a non-modular metal-backed tibial component with compression moulded polyethylene.
A comparative study of two methods of surgical treatment for painful neuroma
Authors: Balcin H. , Erba P. , Wettstein R. , Schaefer D. J. , Pierer G. , Kalbermatten D. F.
Published: May 2009

Painful neuromas may follow traumatic nerve injury. We carried out a double-blind controlled trial in which patients with a painful neuroma of the lower limb (n = 20) were randomly assigned to treatment by resection of the neuroma and translocation of the proximal nerve stump into either muscle tissue or an adjacent subcutaneous vein. Translocation into a vein led to reduced intensity of pain as assessed by visual analogue scale (5.8 (sd 2.7) vs 3.8 (sd 2.4); p < 0.01), and improved sensory, affective and evaluative dimensions of pain as assessed by the McGill pain score (33 (sd 18) vs 14 (sd 12); p < 0.01). This was associated with an increased level of activity (p < 0.01) and improved function (p < 0.01).

Transposition of the nerve stump into an adjacent vein should be preferred to relocation into muscle.
Saying Hullo Again: Remembering Michael White
Authors: Epston David
Published: May 2009

This contribution was a speech that David Epston delivered at ‘Remembering Michael’ at The Family Therapy Centre in Auckland, New Zealand on May 23, 2008; it was also read aloud by Suzanne Pregerson/Rick Maisel in a ‘Remembering Michael White’ ceremony in San Rafael, California.
Zur Sozialarchäologie der befestigten Siedlung von Monkodonja (Istrien) und ihrer Gräber am Tor
Authors: Hänsel Bernhard , Matošević Damir , Mihovilić Kristina , Teržan Biba
Published: June 2009

Thema des Beitrags ist die soziale Differenzierung im früh- bis mittelbronzezeitlichen Istrien. Drei für die Fragestellung relevante Bereiche aus den Forschungen in der befestigten Siedlung von Monkodonja werden angesprochen. Erstens geht es um die Unterschiede innerhalb der Siedlung in Struktur und Architektur. Zum Zweiten wird versucht, für den weiteren Raum von Rovinj Herrschaftsbezirke als ein System von in Istrien ebenbürtigen Zentralsiedlungen mit zugehörigen Neben- und Satellitenplätzen herauszuarbeiten. Die kleinen, kaum mehr als 10 km großen Einheiten sind durch unbesiedelte, wahrscheinlich jedoch wirtschaftlich genutzte Freiräume voneinander getrennt. Drittens werden die wenigen Elitegräber, die sich als solche weniger durch Beigaben als vielmehr durch ihre herausgehobene Position im Haupttor der Siedlung auszeichnen, besprochen. Der komplizierte, mehrphasige Bestattungsritus wird beschrieben und die in den Baukörper eingebundenen Steinkistengräber in Zusammenhang zu einer Ahnenverehrung gebracht.
The Ccr4-Pop2-NOT mRNA Deadenylase Contributes to Septin Organization in Saccharomyces cerevisiae
Authors: Traven Ana , Beilharz Traude H , Lo Tricia L , Lueder Franziska , Preiss Thomas , Heierhorst Jörg
Published: June 2009

In yeast, assembly of the septins at the cell cortex is required for a series of key cell cycle events: bud-site selection, the morphogenesis and mitotic exit checkpoints, and cytokinesis. Here we establish that the Ccr4-Pop2-NOT mRNA deadenylase contributes to septin organization. mRNAs encoding regulators of septin assembly (Ccd42, Cdc24, Rga1, Rga2, Bem3, Gin4, Cla4, and Elm1) presented with short poly(A) tails at steady state in wild-type (wt) cells, suggesting their translation could be restricted by deadenylation. Deadenylation of septin regulators was dependent on the major cellular mRNA deadenylase Ccr4-Pop2-NOT, whereas the alternative deadenylase Pan2 played a minor role. Consistent with deadenylation of septin regulators being important for function, deletion of deadenylase subunits CCR4 or POP2, but not PAN2, resulted in septin morphology defects (e.g., ectopic bud-localized septin rings), particularly upon activation of the Cdc28-inhibitory kinase Swe1. Aberrant septin staining was also observed in the deadenylase-dead ccr4-1 mutant, demonstrating the deadenylase activity of Ccr4-Pop2 is required. Moreover, ccr4Δ, pop2Δ, and ccr4-1 mutants showed aberrant cell morphology previously observed in septin assembly mutants and exhibited genetic interactions with mutations that compromise septin assembly (shs1Δ, cla4Δ, elm1Δ, and gin4Δ). Mutations in the Not subunits of Ccr4-Pop2-NOT, which are thought to predominantly function in transcriptional control, also resulted in septin organization defects. Therefore, both mRNA deadenylase and transcriptional functions of Ccr4-Pop2-NOT contribute to septin organization in yeast.
Functional and biological properties of the nuclear receptor coregulator PELP1/MNAR
Authors: Vadlamudi Ratna K. , Kumar Rakesh
Published: June 2009

Proline-, glutamic acid-, and leucine-rich protein (PELP)1, also known as modulator of nongenomic actions of the estrogen receptor (MNAR), is a novel nuclear receptor coregulator with a multitude of functions. PELP1/MNAR serves as a scaffolding protein that couples various signaling complexes with nuclear receptors and participates in genomic and nongenomic functions. Recent data suggest that PELP1/MNAR expression is deregulated in several cancers, including breast, endometrial, prostate, and ovarian cancer, and that PELP1/MNAR interacts with several oncogenes. In this review, we summarize the emerging biological properties and functions of PELP1/MNAR.
Evaluation of steroid hormone receptor protein expression in intact cells using flow cytometry
Authors: Butts Cherie L. , Shukair Shetha A. , Duncan Kristina M. , Harris Christopher W. , Belyavskaya Elena , Sternberg Esther M.
Published: June 2009

Several methods are currently employed to evaluate expression of steroid hormone receptors in tissues and cells, including real-time reverse-transcriptase polymerase chain reaction (real-time RT-PCR) and western blot assays. These methods require homogenization of cells, thereby preventing evaluation of individual cells or specific cell types in a given tissue sample. In addition, methods such as real-time RT-PCR assess mRNA levels, which may be subject to posttranslational modifications that prevent subsequent production of functional proteins. Flow cytometry is a fluorescence-based technique commonly used to evaluate expression of cell surface and intracellular proteins. This method is especially useful as it allows for single-cell analysis and can be utilized to determine the amount of receptor expressed by individual cells. Flow cytometry is commonly used to analyze immune cell activity and determine functionality based on changes in expression of cell surface molecules, as well as intracellular proteins (such as cytokines). Here, we describe a method to identify protein expression of steroid hormone receptors by rat leukocytes from different organs (spleen, liver and thymus) using flow cytometry. We examined expression of glucocorticoid receptor (GR), androgen receptor (AR) and progesterone receptor (PR) by cells at these sites and were able to demonstrate expression of receptors, as well as the intensity of expression of each receptor. This method is useful for rapid, high throughput measurement of steroid hormone receptors at the protein level in single, intact cells and would be valuable to determine which cells are more likely to respond to steroid hormone treatment.
The NR3B Subgroup: An Overrview
Authors: Tremblay Annie M. , Giguère Vincent
Published: June 2009

Members of the NR3B group of the nuclear receptor superfamily, known as the estrogen-related receptors (ERRs), were the first orphan receptors to be identified two decades ago. Despite the fact that a natural ligand has yet to be associated with the ERRs, considerable knowledge about their mode of action and biological functions has emerged through extensive biochemical, genetic and functional genomics studies. This review describes our current understanding of how the ERRs work as transcription factors and as such, how they control diverse developmental and physiological programs.
The Mineralocorticoid Receptor: Insights into its Molecular and (Patho)Physiological Biology
Authors: Viengchareun Say , Le Menuet Damien , Martinerie Laetitia , Munier Mathilde , Tallec Laurent Pascual-Le , Lombès Marc
Published: June 2009

The last decade has witnessed tremendous progress in the understanding of the mineralocorticoid receptor (MR), its molecular mechanism of action, and its implications for physiology and pathophysiology. After the initial cloning of MR, and identification of its gene structure and promoters, it now appears as a major actor in protein-protein interaction networks. The role of transcriptional coregulators and the determinants of mineralocorticoid selectivity have been elucidated. Targeted oncogenesis and transgenic mouse models have identified unexpected sites of MR expression and novel roles for MR in non-epithelial tissues. These experimental approaches have contributed to the generation of new cell lines for the characterization of aldosterone signaling pathways, and have also facilitated a better understanding of MR physiology in the heart, vasculature, brain and adipose tissues. This review describes the structure, molecular mechanism of action and transcriptional regulation mediated by MR, emphasizing the most recent developments at the cellular and molecular level. Finally, through insights obtained from mouse models and human disease, its role in physiology and pathophysiology will be reviewed. Future investigations of MR biology should lead to new therapeutic strategies, modulating cell-specific actions in the management of cardiovascular disease, neuroprotection, mineralocorticoid resistance, and metabolic disorders.
The steroid and xenobiotic receptor (SXR), beyond xenobiotic metabolism
Authors: Zhou Changcheng , Verma Suman , Blumberg Bruce
Published: June 2009

The steroid and xenobiotic receptor (SXR) (also known as pregnane X receptor or PXR) is a nuclear hormone receptor activated by a diverse array of endogenous hormones, dietary steroids, pharmaceutical agents, and xenobiotic compounds. SXR has an enlarged, flexible, hydrophobic ligand binding domain (LBD) which is remarkably divergent across mammalian species and SXR exhibits considerable differences in its pharmacology among mammals. The broad response profile of SXR has led to the development of “the steroid and xenobiotic sensor hypothesis”. SXR has been established as a xenobiotic sensor that coordinately regulates xenobiotic clearance in the liver and intestine via induction of genes involved in drug and xenobiotic metabolism. In the past few years, research has revealed new and mostly unsuspected roles for SXR in modulating inflammation, bone homeostasis, vitamin D metabolism, lipid homeostasis, energy homeostasis and cancer. The identification of SXR as a xenobiotic sensor has provided an important tool for studying new mechanisms through which diet, chemical exposure, and environment ultimately impact health and disease. The discovery and pharmacological development of new PXR modulators might represent an interesting and innovative therapeutic approach to combat various diseases.
A novel approach to investigate the subcellular distribution of nuclear receptors in vivo
Authors: Matic Marko , Nakhel Sarah , Lehnert Anne M. , Polly Patsie , Clarke Stephen J. , Robertson Graham R.
Published: June 2009

Subcellular compartmentalisation and the intracellular movement of nuclear receptors are major regulatory steps in executing their transcriptional function. Though significant progress has been made in understanding these regulatory processes in cultured mammalian cells, such results have rarely been confirmed within cells of a living mammal. This article describes a simple, time-efficient approach to study the nuclear versus cytoplasmic accumulation of nuclear receptors and the regions of nuclear receptor proteins that govern subcellular trafficking within hepatocytes of live mice. Pregnane X receptor, a xenobiotic-activated member of the nuclear receptor family, was used to exemplify the approach. Using dual-labeled wild-type and mutant PXR expression constructs, we outline their in vivo delivery, simultaneous cellular expression, visualization and categorical classification within hepatocytes of live mice. Using this approach, we identified three mutants that had an altered subcellular distribution in the presence and absence of a PXR ligand. This novel in vivo method complements the current cell culture-based experimental systems in protein subcellular localisation studies.
Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs)
Authors: Rochette-Egly Cécile , Germain Pierre
Published: June 2009

Nuclear retinoic acid receptors (RARs) are transcriptional regulators controlling the expression of specific subsets of genes in a ligand-dependent manner. The basic mechanism for switching on transcription of cognate target genes involves RAR binding at specific response elements and a network of interactions with coregulatory protein complexes, the assembly of which is directed by the C-terminal ligand-binding domain of RARs. In addition to this scenario, new roles for the N-terminal domain and the ubiquitin-proteasome system recently emerged. Moreover, the functions of RARs are not limited to the regulation of cognate target genes, as they can transrepress other gene pathways. Finally, RARs are also involved in nongenomic biological activities such as the activation of translation and of kinase cascades. Here we will review these mechanisms, focusing on how kinase signaling and the proteasome pathway cooperate to influence the dynamics of RAR transcriptional activity.
The Effect of Doxycycline Hyclate, Chlorhexidine Gluconate, and Minocycline Hydrochloride on Osteoblastic Proliferation and Differentiation In Vitro
Authors: Almazin Salah M. , Dziak Rosemary , Andreana Sebastiano , Ciancio Sebastian G.
Published: June 2009

Background: The purpose of this study was to determine the effect of the active substance of three types of local delivery systems, doxycycline hyclate 10% (DOXY), chlorhexidine gluconate, 2.5 mg (CHX), and minocycline hydrochloride, 1 mg (MINO), on osteoblastic cell proliferation and differentiation.

Methods: There were four groups: control osteoblastic cells (OB) alone, OB + DOXY, OB + CHX, and OB + MINO. Trypan blue and MTT [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide] assays were used to test osteoblastic cell viability. Cell differentiation was tested by measuring alkaline phosphatase levels. Osteoblast morphology was investigated by light and scanning electron microscopy.

Results: At a concentration of 0.5 mg/ml, the Trypan blue test showed that DOXY, MINO, and CHX had significant toxicity effects on osteoblast cells compared to the control group, with a mean cell viability of 84%, 74%, and 51%, respectively (P <0.05). The MTT test showed that the control and DOXY groups were statistically significantly different (P <0.05) compared to CHX and MINO groups. The DOXY group showed a significantly higher alkaline phosphatase activity (∼56%) than the control and MINO groups, and it was nearly 178% higher than the CHX group (P <0.05). The morphology of the osteoblasts seemed to be slightly altered when they were incubated with DOXY; however, with MINO, they appeared rounded with minimal attachment. In the CHX group, the osteoblasts assumed a shape of a very thin filopodia with a volcano‐like nucleus.

Conclusions: At a concentration of 0.5 mg/ml, CHX and, to a lesser extent, MINO had a cytotoxic effect on osteoblast proliferation in vitro. However, DOXY seemed to enhance maturation and differentiation rather than proliferation. In addition to DOXY's beneficial effect as an adjunctive therapy to mechanical debridement in the treatment of periodontal disease, it may have an effect on periodontal regeneration.
Uptake of Metronidazole by Human Gingival Fibroblasts
Authors: Yu Liqiang , Liu Hongchen , E Lingling , Wu Xia , Wang Dongsheng
Published: June 2009

Background: Metronidazole is an important antimicrobial agent for the therapeutic management of periodontal diseases and dentoalveolar infections. As in other tissues, the metronidazole concentration in gingival crevicular fluid is about equal to the plasma level. Thus, we hypothesized that metronidazole is not actively transported into human gingival fibroblasts.

Methods: Using high performance liquid chromatography, the influences of extracellular metronidazole concentrations, temperature, pH, and inhibitors of transporters on the uptake of metronidazole by cultured human gingival fibroblasts were tested.

Results: Metronidazole was taken up rapidly by fibroblasts; the intracellular metronidazole concentration reached the extracellular level in 3 minutes at 37°C and in 2 minutes at 4°C. The uptake of metronidazole by human gingival fibroblasts was not saturable, and the intracellular metronidazole concentrations increased linearly with the extracellular level. Temperature and pH had no significant influence on the uptake of metronidazole by fibroblasts. Probenecid and adenine had no influence on the uptake of metronidazole by fibroblasts. These findings indicate that metronidazole uptake does not involve a transporter. Metronidazole bound rapidly to human gingival fibroblasts, but the cell‐associated drug declined progressively until it reached a stable plateau in 15 minutes.

Conclusions: Metronidazole rapidly entered human gingival fibroblasts via simple diffusion. Metronidazole easily reached the minimal inhibitory concentration in fibroblasts and gingiva. Given the fact that intracellular concentrations of metronidazole in other tissues and cells are also close to the plasma level, we speculate that metronidazole enters other tissues and cells via simple diffusion.
Periodontal Wound Healing With and Without Platelet‐Rich Plasma: Histologic Observations and Assessment of Flap Tensile Strength
Authors: Powell Charles A. , Bannister Sharon R. , Mackey Scott A. , Maller Steven C. , McDonnell Howard T. , Deas David E.
Published: June 2009

Background: Platelet‐rich plasma (PRP) has been promoted as a surgical adjunct to enhance hard and soft tissue wound healing. Although anecdotally reported to be of value, the results of controlled studies examining the added effects of PRP on surgical procedures have been mixed. The purpose of this study was to test the effect of PRP on flap strength at various post‐surgical time points in a minipig animal model.

Methods: Twelve Yucatan minipigs provided four sites per animal. PRP was prepared from each animal at the time of surgery. Following reflection of a mucoperiosteal flap in each quadrant, subgingival plaque and calculus were removed. Each surgical site was irrigated with sterile saline; prior to suturing, one randomly selected test quadrant in each arch was treated with PRP. Four animals were euthanized at day 14, and two animals were euthanized at 2, 7, 10, and 28 days. The flap strength in each quadrant was tested by attaching to a loop of 3‐0 silk suture through the tissue; the force required to separate the flap from the tooth/bone interface was recorded for each site. A separate portion of each flap site was prepared for descriptive histologic examination, including inflammation, hemorrhage, and new bone growth.

Results: Flap strength was significantly less on day 2 compared to later time points, and there were no significant differences between the test and control groups. No histologic differences in healing between test and control sites were seen at any time point.

Conclusions: PRP did not seem to contribute to greater flap strength at any post‐surgical time point, nor was it associated with any histologic differences in wound healing in this Yucatan minipig model. The time points chosen for observation post‐surgery, as well as the variability in the PRP platelet count, may have contributed to the lack of positive findings in this study.
Automatic Continuity of Group Homomorphisms
Authors: Rosendal Christian
Published: June 2009

We survey various aspects of the problem of automatic continuity of homomorphisms between Polish groups.
Fractional Newtonian mechanics
Authors: Baleanu Dumitru , Golmankhaneh Alireza , Nigmatullin Raoul , Golmankhaneh Ali
Published: May 2009

In the present paper, we have introduced the generalized Newtonian law and fractional Langevin equation. We have derived potentials corresponding to different kinds of forces involving both the right and the left fractional derivatives. Illustrative examples have worked out to explain the formalism.
Towards a Theory of Good History Through Gaming
Authors: Kee Kevin , Graham Shawn , Dunae Pat , Lutz John , Large Andrew , Blondeau Michel , Clare Mike
Published: May 2009

History computer games have become an economic and cultural phenomenon, and historians should seize the opportunity to participate in their development. Players of history games are interested in the past and in the big questions that drive historical scholarship. In this way, games have the potential to draw players into the discipline if we can discover the best way to express history though simulation. But what research do we draw on as we study how to accomplish this transformation? This essay is the product of a meeting of historians, educators, and gamers who joined previously separate lines of inquiry to identify literature and models that we believe form the foundation for developing a theory of good history through gaming.
Aggressive meningeal tumors: review of a series
Authors: Younis George A. , Sawaya Raymond , DeMonte Franco , Hess Kenneth R. , Albrecht Steffen , Bruner Janet M.
Published: June 2009

✓ A series of 25 patients with aggressive meningeal tumors was studied to determine the efficacy of various management options. The median age of the patients was 52 years, with a range of 13 to 73 years. A marked male preponderance (64%) was noted. Twenty of 25 patients experienced recurrence during a median follow-up time of 47 months. Survival and freedom from recurrence varied with histological diagnosis. Recurrence was noted sooner in patients who had received partial resections on first presentation of tumor than in those who had received total resections at first presentation. Survival time was also shorter for patients who underwent partial resections at first presentation than for patients who underwent total resections.

Patients' prognoses did not improve as a result of either chemotherapy or radiotherapy. Of six patients with extracranial metastases, the median time to metastasis was 102 months, with a 5-year metastasis-free rate of 85%. The most common sites of metastasis in these six patients were lung and bone. In each tumor type, histological features used in diagnosis and radiological features studied from computerized tomography and magnetic resonance imaging were evaluated, compared, and discussed. Of eight patients studied with an in vivo bromodeoxyuridine (BUdR) labeling index (LI), seven showed an LI of 1% or more. The authors support the incorporation of the BUdR LI into the diagnostic process to provide a better estimate of the potential for tumor recurrence.
Dorsal root entry zone lesions for intractable pain after trauma to the conus medullaris and cauda equina
Authors: Sampson John H. , Cashman Robert E. , Nashold Blaine S. , Friedman Allan H.
Published: June 2009

✓ This review was undertaken to determine the efficacy of using dorsal root entry zone (DREZ) lesions to treat intractable pain caused by trauma to the conus medullaris and cauda equina. Traumatic lesions of this area are unique in that both the spinal cord and the peripheral nerve roots are injured. Although DREZ lesions have been shown to relieve pain of spinal cord origin in many patients, they have been shown not to relieve pain of peripheral nerve origin. Therefore, 39 patients with trauma to the conus medullaris and cauda equina who underwent DREZ lesioning for intractable pain were reviewed retrospectively.

The results of this review demonstrate the efficacy of DREZ lesions in these patients. At a mean follow-up period of 3.0 years, 54% of patients were pain-free without medications, and 20% required only nonnarcotic analgesic drugs for pain that no longer interfered with their daily activities. Better outcomes were noted in patients with an incomplete neurological deficit, with pain having an “electrical” character, and with injuries due to blunt trauma. Operative complications included weakness (four patients), bladder or sexual dysfunction (three), cerebrospinal fluid leak (two), and wound infection (two), but overall, 79.5% of patients (31 of 39) were without serious complications. Complications were limited to patients with prior tissue damage at the surgical exploration site and were most prevalent in patients who underwent bilateral DREZ lesions.

In conclusion, this preliminary report suggests that DREZ lesions may be useful in combating intractable pain from traumatic injuries to the conus medullaris and cauda equina, with some risk to neurological function that may be acceptable in this group of patients.
Hemihypoglossal—facial nerve anastomosis in treating unilateral facial palsy after acoustic neurinoma resection
Authors: Arai Hajime , Sato Kiyoshi , Yanai Akira
Published: June 2009

✓ Eight patients underwent hemihypoglossal—facial nerve anastomosis (anastomosis of a split hypoglossal nerve to the facial nerve) for treatment of unilateral facial palsy. All patients previously had undergone resection of a large acoustic neurinoma and the facial nerve had been resected at that time. The interval between tumor resection and hemihypoglossal—facial nerve anastomosis ranged from 1 to 6 months, with an average of 2.1 months. Postoperative recovery of facial movement was good in all cases during an average follow-up period of 4.2 years. In all eight patients, the degree of hypoglossal nerve atrophy on the operated side was graded mild or moderate, but not severe. It was concluded that hemihypoglossal—facial nerve anastomosis results in good facial reanimation as long as the procedure is performed early after the onset of facial palsy and that this procedure may reduce the degree of hemiglossal atrophy in comparison with classic hypoglossal—facial nerve anastomosis.