bluuebunny/crossref_metadata_2025 huggingface dataset:
Feasibility and reference values of left atrial longitudinal strain imaging by two-dimensional speckle tracking
Authors: Cameli Matteo , Caputo Maria , Mondillo Sergio , Ballo Piercarlo , Palmerini Elisabetta , Lisi Matteo , Marino Enzo , Galderisi Maurizio
Published: February 2009

Background

The role of speckle tracking in the assessment of left atrial (LA) deformation dynamics is not established. We sought to determine the feasibility and reference ranges of LA longitudinal strain indices measured by speckle tracking in a population of normal subjects.

Methods

In 60 healthy individuals, peak atrial longitudinal strain (PALS) and time to peak longitudinal strain (TPLS) were measured using a 12-segment model for the left atrium. Values were obtained by averaging all segments (global PALS and TPLS) and by separately averaging segments measured in the two apical views (4- and 2-chamber average PALS and TPLS).

Results

Adequate tracking quality was achieved in 97% of segments analyzed. Inter and intra-observer variability coefficients of measurements ranged between 2.9% and 5.4%. Global PALS was 42.2 ± 6.1% (5–95° percentile range 32.2–53.2%), and global TPLS was 368 ± 30 ms (5–95° percentile range 323–430 ms). The 2-chamber average PALS was slightly higher than the 4-chamber average PALS (44.3 ± 6.0% vs 40.1 ± 7.9%, p < 0.0001), whereas no differences in TPLS were found (p = 0.93).

Conclusion

Speckle tracking is a feasible technique for the assessment of longitudinal myocardial LA deformation. Reference ranges of strain indices were reported.
Microarray study reveals that HIV-1 induces rapid type-I interferon-dependent p53 mRNA up-regulation in human primary CD4+T cells
Authors: Imbeault Michaël , Ouellet Michel , Tremblay Michel J
Published: February 2009

Background

Infection with HIV-1 has been shown to alter expression of a large array of host cell genes. However, previous studies aimed at investigating the putative HIV-1-induced modulation of host gene expression have been mostly performed in established human cell lines. To better approximate natural conditions, we monitored gene expression changes in a cell population highly enriched in human primary CD4+ T lymphocytes exposed to HIV-1 using commercial oligonucleotide microarrays from Affymetrix.

Results

We report here that HIV-1 influences expression of genes related to many important biological processes such as DNA repair, cellular cycle, RNA metabolism and apoptosis. Notably, expression of the p53 tumor suppressor and genes involved in p53 homeostasis such as GADD34 were up-regulated by HIV-1 at the mRNA level. This observation is distinct from the previously reported p53 phosphorylation and stabilization at the protein level, which precedes HIV-1-induced apoptosis. We present evidence that the HIV-1-mediated increase in p53 gene expression is associated with virus-mediated induction of type-I interferon (i.e. IFN-α and IFN-β).

Conclusion

These observations have important implications for our understanding of HIV-1 pathogenesis, particularly in respect to the virus-induced depletion of CD4+ T cells.
Expression and characterization of the UL31 protein from duck enteritis virus
Authors: Xie Wei , Cheng Anchun , Wang Mingshu , Chang Hua , Zhu Dekang , Luo Qihui , Jia Renyong , Chen Xiaoyue
Published: February 2009

Background

Previous studies indicate that the UL31 protein and its homology play similar roles in nuclear egress of all herpesviruses. However, there is no report on the UL31 gene product of DEV. In this study, we expressed and presented the basic properties of the DEV UL31 product.

Results

The entire ORF of the UL31 was cloned into pET 32a (+) prokaryotic expression vector. Escherichia coli BL21(DE3) competent cells were transformed with the construct followed by the induction of protein expression by the addition of IPTG. Band corresponding to the predicted sizes (55 kDa) was produced on the SDS-PAGE. Over expressed 6×His-UL31 fusion protein was purified by nickel affinity chromatography. The DEV UL31 gene product has been identified by using a rabbit polyclonal antiserum raised against the purified protein. A protein of approximate 35 kDa that reacted with the antiserum was detected in immunoblots of DEV-infected cellular lysates, suggesting that the 35 kDa protein was the primary translation product of the UL31 gene. RT-PCR analyses revealed that the UL31 gene was transcribed most abundantly during the late phase of replication. Subsequently, Immunofluorescence analysis revealed that the protein was widespread speckled structures in the nuclei of infected cells. Western blotting of purified virion preparations showed that UL31 was a component of intracellular virions but was absent from mature extracellular virions. Finally, an Immunofluorescence assay was established to study the distribution of the UL31 antigen in tissues of artificially DEV infected ducks. The results showed that the UL31 antigen was primarily located in the cells of digestive organs and immunological organs.

Conclusion

In this work, we present the basic properties of the DEV UL31 product. The results indicate that DEV UL31 shares many similarities with its HSV or PRV homolog UL31 and suggest that functional cross-complementation is possible between members of the Alpha herpesvirus subfamily. Furthermore, in vivo experiments with ducks infected with UL31-defective isolates of DEV will also be of importance in order to assess the possible role of the UL31 protein in viral pathogenesis. These properties of the UL31 protein provide a prerequisite for further functional analysis of this gene.
Associations between lamb survival and prion protein genotype: analysis of data for ten sheep breeds in Great Britain
Authors: Gubbins Simon , Cook Charlotte J , Hyder Kieran , Boulton Kay , Davis Carol , Thomas Eurion , Haresign Will , Bishop Stephen C , Villanueva Beatriz , Eglin Rachel D
Published: February 2009

Background

Selective breeding programmes, based on prion protein (PrP) genotype, have been introduced throughout the European Union to reduce the risk of sheep transmissible spongiform encephalopathies (TSEs). These programmes could have negative consequences on other important traits, such as fitness and production traits, if the PrP gene has pleiotropic effects or is in linkage disequilibrium with genes affecting these traits. This paper presents the results of an investigation into associations between lamb survival and PrP genotype in ten mainstream sheep breeds in Great Britain (GB). In addition, the reasons for lamb deaths were examined in order to identify any associations between these and PrP genotype.

Results

Survival times from birth to weaning were analysed for over 38000 lambs (2427 dead and 36096 live lambs) from 128 flocks using Cox proportional hazard models for each breed, including additive animal genetic effects. No significant associations between PrP genotype and lamb survival were identified, except in the Charollais breed for which there was a higher risk of mortality in lambs of the ARR/VRQ genotype compared with those of the ARR/ARR genotype. Significant effects of birth weight, litter size, sex, age of dam and year of birth on survival were also identified. For all breeds the reasons for death changed significantly with age; however, no significant associations between reason for death and PrP genotype were found for any of the breeds.

Conclusion

This study found no evidence to suggest that a selective breeding programme based on PrP genotype will have a detrimental effect on lamb survival. The only significant effect of PrP genotype identified was likely to be of little consequence because an increased risk of mortality was associated with a genotype that is selected against in current breeding strategies.
Enhanced relapse prevention for bipolar disorder: a qualitative investigation of value perceived for service users and care coordinators
Authors: Pontin Eleanor , Peters Sarah , Lobban Fiona , Rogers Anne , Morriss Richard K
Published: February 2009

Background

Enhanced relapse prevention (ERP) is a psychological intervention delivered by mental health professionals to help individuals with bipolar disorder (BD) recognise and manage early warning signs for mania and depression. ERP has an emerging evidence base and is recommended as good practice for mental health professionals. However, without highly perceived value to both those receiving (services users) or delivering it (health professionals), implementation will not occur. The aim of this study is to determine what values of ERP are perceived by service users (SUs) and mental health professionals (care coordinators, CCs) providing community case management.

Methods

A nested qualitative study design was employed as part of a randomised controlled trial of ERP. Semi-structured interviews were conducted with a purposive sub-sample of 21 CCs and 21 SUs, and an iterative approach used to develop a framework of conceptual categories that was applied systematically to the data.

Results

The process of implementing and receiving ERP was valued by both SUs and CCs for three similar sets of reasons: improved understanding of BD (where a knowledge deficit of BD was perceived), enhanced working relationships, and improved ways of managing the condition. There were some differences in the implications these had for both CCs and SUs who also held some reservations.

Conclusion

CCs and SUs perceive similar value in early warning signs interventions to prevent relapse, and these have particular benefits to them. If this perceived value is maintained, CCs and SUs in routine practice may use ERP long-term.
An image processing approach to computing distances between RNA secondary structures dot plots
Authors: Ivry Tor , Michal Shahar , Avihoo Assaf , Sapiro Guillermo , Barash Danny
Published: February 2009

Background

Computing the distance between two RNA secondary structures can contribute in understanding the functional relationship between them. When used repeatedly, such a procedure may lead to finding a query RNA structure of interest in a database of structures. Several methods are available for computing distances between RNAs represented as strings or graphs, but none utilize the RNA representation with dot plots. Since dot plots are essentially digital images, there is a clear motivation to devise an algorithm for computing the distance between dot plots based on image processing methods.

Results

We have developed a new metric dubbed 'DoPloCompare', which compares two RNA structures. The method is based on comparing dot plot diagrams that represent the secondary structures. When analyzing two diagrams and motivated by image processing, the distance is based on a combination of histogram correlations and a geometrical distance measure. We introduce, describe, and illustrate the procedure by two applications that utilize this metric on RNA sequences. The first application is the RNA design problem, where the goal is to find the nucleotide sequence for a given secondary structure. Examples where our proposed distance measure outperforms others are given. The second application locates peculiar point mutations that induce significant structural alternations relative to the wild type predicted secondary structure. The approach reported in the past to solve this problem was tested on several RNA sequences with known secondary structures to affirm their prediction, as well as on a data set of ribosomal pieces. These pieces were computationally cut from a ribosome for which an experimentally derived secondary structure is available, and on each piece the prediction conveys similarity to the experimental result. Our newly proposed distance measure shows benefit in this problem as well when compared to standard methods used for assessing the distance similarity between two RNA secondary structures.

Conclusion

Inspired by image processing and the dot plot representation for RNA secondary structure, we have managed to provide a conceptually new and potentially beneficial metric for comparing two RNA secondary structures. We illustrated our approach on the RNA design problem, as well as on an application that utilizes the distance measure to detect conformational rearranging point mutations in an RNA sequence.
Ascl1 is a required downstream effector of Gsx gene function in the embryonic mouse telencephalon
Authors: Wang Bei , Waclaw Ronald R , Allen Zegary J , Guillemot Francois , Campbell Kenneth
Published: February 2009

Background

The homeobox gene Gsx2 (formerly Gsh2) is known to regulate patterning in the lateral ganglionic eminence (LGE) of the embryonic telencephalon. In its absence, the closely related gene Gsx1 (previously known as Gsh1) can partially compensate in the patterning and differentiation of ventral telencephalic structures, such as the striatum. However, the cellular and molecular mechanisms underlying this compensation remain unclear.

Results

We show here that in the Gsx2 mutants Gsx1 is expressed in only a subset of the ventral telencephalic progenitors that normally express Gsx2. Based on the similarities in the expression of Gsx1 and Ascl1 (Mash1) within the Gsx2 mutant LGE, we examined whether Ascl1 plays an integral part in the Gsx1-based recovery. Ascl1 mutants show only modest alterations in striatal development; however, in Gsx2;Ascl1 double mutants, striatal development is severely affected, similar to that seen in the Gsx1;Gsx2 double mutants. This is despite the fact that Gsx1 is expressed, and even expands, in the Gsx2;Ascl1 mutant LGE, comparable to that seen in the Gsx2 mutant. Finally, Notch signaling has recently been suggested to be required for normal striatal development. In spite of the fact that Notch signaling is severely disrupted in Ascl1 mutants, it actually appears to be improved in the Gsx2;Ascl1 double mutants.

Conclusion

These results, therefore, reveal a non-proneural requirement of Ascl1 that together with Gsx1 compensates for the loss of Gsx2 in a subset of LGE progenitors.
Rhombomere-specific analysis reveals the repertoire of genetic cues expressed across the developing hindbrain
Authors: Chambers David , Wilson Leigh Jane , Alfonsi Fabienne , Hunter Ewan , Saxena Uma , Blanc Eric , Lumsden Andrew
Published: February 2009

Background

The Hox family of homeodomain transcription factors comprises pivotal regulators of cell specification and identity during animal development. However, despite their well-defined roles in the establishment of anteroposterior pattern and considerable research into their mechanism of action, relatively few target genes have been identified in the downstream regulatory network. We have sought to investigate this issue, focussing on the developing hindbrain and the cranial motor neurons that arise from this region. The reiterated anteroposterior compartments of the developing hindbrain (rhombomeres (r)) are normally patterned by the combinatorial action of distinct Hox genes. Alteration in the normal pattern of Hox cues in this region results in a transformation of cellular identity to match the remaining Hox profile, similar to that observed in Drosophila homeotic transformations.

Results

To define the repertoire of genes regulated in each rhombomere, we have analysed the transcriptome of each rhombomere from wild-type mouse embryos and not those where pattern is perturbed by gain or loss of Hox gene function. Using microarray and bioinformatic methodologies in conjunction with other confirmatory techniques, we report here a detailed and comprehensive set of potential Hox target genes in r2, r3, r4 and r5. We have demonstrated that the data produced are both fully reflective and predictive of rhombomere identity and, thus, may represent some the of Hox targets. These data have been interrogated to generate a list of candidate genes whose function may contribute to the generation of neuronal subtypes characteristic of each rhombomere. Interestingly, the data can also be classified into genetic motifs that are predicted by the specific combinations of Hox genes and other regulators of hindbrain anteroposterior identity. The sets of genes described in each or combinations of rhombomeres span a wide functional range and suggest that the Hox genes, as well as other regulatory inputs, exert their influence across the full spectrum of molecular machinery.

Conclusion

We have performed a systematic survey of the transcriptional status of individual segments of the developing mouse hindbrain and identified hundreds of previously undescribed genes expressed in this region. The functional range of the potential candidate effectors or upstream modulators of Hox activity suggest multiple unexplored mechanisms. In particular, we present evidence of a potential new retinoic acid signalling system in ventral r4 and propose a model for the refinement of identity in this region. Furthermore, the rhombomeres demonstrate a molecular relationship to each other that is consistent with known observations about neurogenesis in the hindbrain. These findings give the first genome-wide insight into the complexity of gene expression during patterning of the developing hindbrain.
A novel PTCH1 germline mutation distinguishes basal cell carcinoma from basaloid follicular hamartoma: a case report
Authors: Hellani Ali , Baghdadi Hiba , Dabbour Nidal , Almassri Nidal , Abu-Amero Khaled K
Published: February 2009

Introduction

Nevoid basal cell carcinoma syndrome is a rare autosomal dominant disorder characterized by numerous basal cell carcinomas, odontogenic keratocysts of the jaws and developmental defects. The disorder results from mutations in the PTCH1 gene.

Case presentation

A 15-year-old boy presented to our dental clinic with multiple jaw cysts. The patient had broad confluent eyebrows, a broad base of the nose, frontal bossing and palmoplantar pits. Examination of the jaw cysts revealed many keratinizing cysts without granular cell layers a finding that raised the suspicion of nevoid basal cell carcinoma. Radiological examinations showed calcification of the falx cerebri, spina bifida, bifid thoracic ribs and frontal bossing. Histopathological examination showed basaloid proliferation in the upper dermis with follicular differentiation surrounded by a loose mucinous stroma and retraction artifacts. These features make it difficult to differentiate between nevoid basal cell carcinoma and basaloid follicular hamartoma, especially the presence of these findings on a non-hairy area. BCL-2 staining was positive in the periphery of the basaloid proliferation, which is typical of basaloid follicular hamartoma, and not in a diffuse pattern, which is typical of nevoid basal cell carcinoma. The proband's siblings and parents were healthy with no family history of this condition in the extended family. Since histology was equivocal and palmoplantar pits are seen in both basaloid follicular hamartoma and nevoid basal cell carcinoma, molecular genetic investigation was necessary to differentiate between the two potential diagnoses. After sequencing the entire PTCH1 gene, we detected a single nucleotide deletion (c.1291delC) in codon 431 of the PTCH protein, which resulted in a premature stop translation at residue 431. This de novo mutation was not detected in both parents and in 100 normal volunteers of matching ethnicity.

Conclusion

Screening the PTCH1 gene for mutations helped to differentiate between basaloid follicular hamartoma and nevoid basal cell carcinoma and confirmed the diagnosis.
Diurnal variation of the human adipose transcriptome and the link to metabolic disease
Authors: Loboda Andrey , Kraft Walter K , Fine Bernard , Joseph Jeffrey , Nebozhyn Michael , Zhang Chunsheng , He Yudong , Yang Xia , Wright Christopher , Morris Mark , Chalikonda Ira , Ferguson Mark , Emilsson Valur , Leonardson Amy , Lamb John , Dai Hongyue , Schadt Eric , Greenberg Howard E , Lum Pek Yee
Published: February 2009

Background

Circadian (diurnal) rhythm is an integral part of the physiology of the body; specifically, sleep, feeding behavior and metabolism are tightly linked to the light-dark cycle dictated by earth's rotation.

Methods

The present study examines the effect of diurnal rhythm on gene expression in the subcutaneous adipose tissue of overweight to mildly obese, healthy individuals. In this well-controlled clinical study, adipose biopsies were taken in the morning, afternoon and evening from individuals in three study arms: treatment with the weight loss drug sibutramine/fasted, placebo/fed and placebo/fasted.

Results

The results indicated that diurnal rhythm was the most significant driver of gene expression variation in the human adipose tissue, with at least 25% of the genes having had significant changes in their expression levels during the course of the day. The mRNA expression levels of core clock genes at a specific time of day were consistent across multiple subjects on different days in all three arms, indicating robust diurnal regulation irrespective of potential confounding factors. The genes essential for energy metabolism and tissue physiology were part of the diurnal signature. We hypothesize that the diurnal transition of the expression of energy metabolism genes reflects the shift in the adipose tissue from an energy-expending state in the morning to an energy-storing state in the evening. Consistent with this hypothesis, the diurnal transition was delayed by fasting and treatment with sibutramine. Finally, anin silicocomparison of the diurnal signature with data from the publicly-available Connectivity Map demonstrated a significant association with transcripts that were repressed by mTOR inhibitors, suggesting a possible link between mTOR signaling, diurnal gene expression and metabolic regulation.

Conclusion

Diurnal rhythm plays an important role in the physiology and regulation of energy metabolism in the adipose tissue and should be considered in the selection of novel targets for the treatment of obesity and other metabolic disorders.
Heavy metal exposure reverses genetic resistance to Chlamydia-induced arthritis
Authors: Inman Robert D , Chiu Basil
Published: February 2009

Introduction

We have previously observed that Brown Norway (BN) rats display a relative resistance to experimental Chlamydia-induced arthritis. In the present study, we examine an environmental toxin, mercuric chloride (HgCl2), as a modulator of this innate resistance to arthritis.

Methods

To assess the effect of the heavy metal exposure, one group of rats received two subcutaneous injections of HgCl2 (1 mg/kg) 48 hours apart. Seven days later, the animals received the intra-articular injection of synoviocyte-packaged Chlamydia.

Results

Histopathology revealed that BN rats receiving only Chlamydia had a minimal cellular infiltration in the joint, which was predominantly mononuclear in character. In contrast, mercury-exposed rats had a marked exacerbation of the histopathological severity of the arthritis, and the infiltration was predominantly neutrophilic. Mercury exposure was also associated with marked enhancement in IgE levels and an alteration in IgG2a/IgG1 ratio, reflecting a Th2 shift. The local cytokine profile in the joint was markedly altered after mercury exposure, with a suppression of tumour necrosis factor-alpha and interferon-gamma but an enhancement of vascular endothelial growth factor. This was associated with decreased host clearance capacity reflected in enhanced bacterial load in both the spleen and the joint and was accompanied by enhanced detection of microbial antigens in the synovial tissues by immunohistological staining.

Conclusions

Genetically defined cytokine production in the joint defines the severity of reactive arthritis by dictating the local clearance of the pathogen. This interplay can be altered dramatically by heavy metal exposure, which results in suppression of protective cytokines in the microenvironment of the joint.
Routine delirium monitoring in a UK critical care unit
Authors: Page Valerie J , Navarange Sachin , Gama Sibu , McAuley Danny F
Published: February 2009

Introduction

Delirium in the intensive care unit (ICU) is associated with increased morbidity and mortality. Using an assessment tool has been shown to improve the ability of clinicians in the ICU to detect delirium. The confusion assessment method for the ICU (CAM-ICU) is a validated delirium-screening tool for critically ill intubated patients. The aim of this project was to establish the feasibility of routine delirium screening using the CAM-ICU and to identify the incidence of delirium in a UK critical care unit.

Methods

Routine CAM-ICU monitoring was implemented in a mixed critical care unit in January 2007 following a two-month educational and promotional campaign. Guidelines for the management of delirium were introduced. During a two-month prospective audit in September and October 2007, the daily CAM-ICU was recorded by the bedside nurse for consecutive level 2 and level 3 patients admitted to the mixed medical/surgical critical care ward in a district general hospital. This was repeated in January 2008. Patient outcome was recorded. The records of an additional cohort of ventilated patients were reviewed retrospectively to determine compliance with routine CAM-ICU assessments.

Results

Seventy-one patients were included in the observational cohort, with 60 patients in the retrospective cohort. In the prospective group it was not possible to assess for delirium with the CAM-ICU in nine patients due to persistent coma or inability to understand simple instructions. Excluding elective post-operative patients, the incidence of delirium was 45% in patients who could be assessed; in the 27 ventilated patients who could be assessed it was 63%. From the retrospective data compliance with the CAM-ICU assessment was 92%. The incidence of delirium in this retrospective group of ventilated patients who could be assessed was 65%.

Conclusions

We have demonstrated that delirium screening is feasible in a UK ICU population. The high incidence of delirium and the impact on outcomes in this UK cohort of patients is in line with previous reports.
Fast genomic μChIP-chip from 1,000 cells
Authors: Dahl John Arne , Reiner Andrew H , Collas Philippe
Published: February 2009

Genome-wide location analysis of histone modifications and transcription factor binding relies on chromatin immunoprecipitation (ChIP) assays. These assays are, however, time-consuming and require large numbers of cells, hindering their application to the analysis of many interesting cell types. We report here a fast microChIP (μChIP) assay for 1,000 cells in combination with microarrays to produce genome-scale surveys of histone modifications. μChIP-chip reliably reproduces data obtained by large-scale assays: H3K9ac and H3K9m3 enrichment profiles are conserved and nucleosome-free regions are revealed.
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
Authors: Bock Christoph , Halachev Konstantin , Büch Joachim , Lengauer Thomas
Published: February 2009

The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutionary conservation) for enrichment or depletion among these regions. Furthermore, EpiGRAPH learns to predictively identify similar genomic regions. This paper demonstrates EpiGRAPH's practical utility in a case study on monoallelic gene expression and describes its novel approach to reproducible bioinformatic analysis.
The role of the GPR91 ligand succinate in hematopoiesis
Authors: Hakak Yaron , Lehmann-Bruinsma Karin , Phillips Shirley , Le Thuy , Liaw Chen , Connolly Daniel T , Behan Dominic P
Published: February 2009

Regulation of cellular metabolism by the citric acid cycle occurs in the mitochondria. However, the citric acid cycle intermediate succinate was shown recently to be a ligand for the G-protein-coupled receptor GPR91. Here, we describe a role for succinate and its receptor in the stimulation of hematopoietic progenitor cell (HPC) growth. GPR91 mRNA and protein expression were detected in human bone marrow CD34+ progenitor cells, as well as in erythroid and megakaryocyte cultures and the erythroleukemic cell line TF-1. Treatment of these cell cultures with succinate resulted in increased proliferation rates. The proliferation response of TF-1 cells was pertussis toxin (PTX)-sensitive, suggesting a role for Gi signaling. Proliferation was also blocked when TF-1 cells were transfected with small interfering RNA specific for GPR91. Succinate stimulated activation of the Erk MAPK pathway and inositol phosphate accumulation in a PTX-sensitive manner. Pretreatment of TF-1 cells with the Erk1/2 kinase (MEK) inhibitor PD98059 blocked the proliferation response. Succinate treatment additionally protected TF-1 cells from cell death induced by serum deprivation. Finally, in vivo administration of succinate was found to elevate the levels of hemoglobin, platelets, and neutrophils in a mouse model of chemotherapy-induced myelosuppression. These results suggest that succinate-GPR91 signaling is capable of promoting HPC development.
Randomized Phase II Trial of Erlotinib Versus Temozolomide or Carmustine in Recurrent Glioblastoma: EORTC Brain Tumor Group Study 26034
Authors: van den Bent Martin J. , Brandes Alba A. , Rampling Roy , Kouwenhoven Mathilde C.M. , Kros Johan M. , Carpentier Antoine F. , Clement Paul M. , Frenay Marc , Campone Mario , Baurain Jean-Francois , Armand Jean-Paul , Taphoorn Martin J.B. , Tosoni Alicia , Kletzl Heidemarie , Klughammer Barbara , Lacombe Denis , Gorlia Thierry
Published: February 2009

Purpose

Approximately 50% of glioblastomas (GBMs) are characterized by overexpression of the epidermal growth factor receptor (EGFR) and EGFR gene amplification. In approximately 25% of instances, constitutively activated EGFR mutants are present. These observations make EGFR-inhibiting drugs a logical approach for trials in recurrent GBM.

Patients and Methods

In a randomized, controlled, phase II trial, 110 patients with progressive GBM after prior radiotherapy were randomly assigned to either erlotinib or a control arm that received treatment with either temozolomide or carmustine (BCNU). The primary end point was 6-month progression-free survival (PFS). Tumor specimens obtained at first surgery were investigated for EGFR expression; EGFRvIII mutants; EGFR amplification; EGFR mutations in exons 18, 19, and 21; and pAkt. These results were correlated with outcome. Pharmacokinetic analysis was part of the study.

Results

Treatment was well tolerated in general; skin toxicity was the most frequent adverse effect of erlotinib. The 6-month PFS rate in the erlotinib arm was 11.4% (95% CI, 4.6% to 21.5%), and it was 24% in the control arm. Of all explored biomarkers, only low pAkt expression appeared to be of borderline significance to an improved outcome. None of the eight patients who had tumors with EGFRvIII mutant presence and PTEN expression had 6-month PFS. The use of enzyme-inducing anticonvulsants significantly increased erlotinib clearance, but pharmacokinetic findings were not related to outcome.

Conclusion

Erlotinib has insufficient single-agent activity in unselected GBM. No clear biomarker associated with improved outcome to erlotinib was identified.
Breast Cancer Subtypes and Response to Docetaxel in Node-Positive Breast Cancer: Use of an Immunohistochemical Definition in the BCIRG 001 Trial
Authors: Hugh Judith , Hanson John , Cheang Maggie Chon U. , Nielsen Torsten O. , Perou Charles M. , Dumontet Charles , Reed John , Krajewska Maryla , Treilleux Isabelle , Rupin Matthieu , Magherini Emmanuelle , Mackey John , Martin Miguel , Vogel Charles
Published: February 2009

Purpose

To investigate the prognostic and predictive significance of subtyping node-positive early breast cancer by immunohistochemistry in a clinical trial of a docetaxel-containing regimen.

Methods

Pathologic data from a central laboratory were available for 1,350 patients (91%) from the BCIRG 001 trial of docetaxel, doxorubicin, and cyclophosphamide (TAC) versus fluorouracil, doxorubicin, and cyclophosphamide (FAC) for operable node-positive breast cancer. Patients were classified by tumor characteristics as (1) triple negative (estrogen receptor [ER]–negative, progesterone receptor [PR]–negative, HER2/neu [HER2]–negative), (2) HER2 (HER2-positive, ER-negative, PR-negative), (3) luminal B (ER-positive and/or PR-positive and either HER2-positive and/or Ki67high), and (4) luminal A (ER-positive and/or PR-positive and not HER2-positive or Ki67high), and assessed for prognostic significance and response to adjuvant chemotherapy.

Results

Patients were subdivided into triple negative (14.5%), HER2 (8.5%), luminal B (61.1%), and luminal A (15.9%). Three-year disease-free survival (DFS) rates (P values with luminal B as referent) were 67% (P < .0001), 68% (P = .0008), 82% (referent luminal B), and 91% (P = .0027), respectively, with hazard ratios of 2.22, 2.12, and 0.46. Improved 3-year DFS with TAC was found in the luminal B group (P = .025) and a combined ER-positive/HER2-negative group treated with tamoxifen (P = .041), with a marginal trend in the triple negatives (P = .051) and HER2 (P = .068) subtypes. No DFS advantage was seen in the luminal A population.

Conclusion

A simple immunopanel can divide breast cancers into biologic subtypes with strong prognostic effects. TAC significantly complements endocrine therapy in patients with luminal B subtype and, in the absence of targeted therapy, is effective in the triple-negative population.
Follicular Lymphoma in the United States: First Report of the National LymphoCare Study
Authors: Friedberg Jonathan W. , Taylor Michael D. , Cerhan James R. , Flowers Christopher R. , Dillon Hildy , Farber Charles M. , Rogers Eric S. , Hainsworth John D. , Wong Elaine K. , Vose Julie M. , Zelenetz Andrew D. , Link Brian K.
Published: February 2009

Purpose

Optimal therapy of follicular lymphoma (FL) is not defined. We analyzed a large prospective cohort study to identify current demographics and patterns of care of FL in the United States.

Patients and Methods

The National LymphoCare Study is a multicenter, longitudinal, observational study designed to collect information on treatment regimens and outcomes for patients with newly diagnosed FL in the United States. Patients were enrolled between 2004 and 2007. There is no study-specific prescribed treatment regimen or intervention.

Results

Two thousand seven hundred twenty-eight subjects were enrolled at 265 sites, including the 80% of patients enrolled from nonacademic sites. Using the Follicular Lymphoma International Prognostic Index (FLIPI), three distinct groups independent of histologic grade could be defined. Initial therapeutic strategy was: observation, 17.7%; rituximab monotherapy, 13.9%; clinical trial 6.1%; radiation therapy, 5.6%; chemotherapy only, 3.2%; chemotherapy plus rituximab, 51.9%. Chemotherapy plus rituximab regimens were: rituximab plus cyclophosphamide, doxorubicin, vincristine, prednisone, 55.0%; rituximab plus cyclophosphamide, vincristine, and prednisone, 23.1%; rituximab plus fludarabine based, 15.5%; other, 6.4%. The choice to initiate therapy rather than observe was associated with age, FLIPI, stage, and grade (P < .01). Significant differences in treatment (P < .01) across regions of the United States were noted. Contrary to practice guidelines, treatment of stage I FL frequently omits radiation therapy.

Conclusion

Widely disparate therapeutic approaches are utilized for FL. Initial therapy is deferred in a small subset of patients. There is no single standard of care for the treatment of de novo FL, although antibody use is ubiquitous when therapy is initiated. These disparate approaches to the initial care of patients with FL render a heterogeneous group of patients at relapse.
Docetaxel With Cyclophosphamide Is Associated With an Overall Survival Benefit Compared With Doxorubicin and Cyclophosphamide: 7-Year Follow-Up of US Oncology Research Trial 9735
Authors: Jones Stephen , Holmes Frankie Ann , O'Shaughnessy Joyce , Blum Joanne L. , Vukelja Svetislava J. , McIntyre Kristi J. , Pippen John E. , Bordelon James H. , Kirby Robert L. , Sandbach John , Hyman William J. , Richards Donald A. , Mennel Robert G. , Boehm Kristi A. , Meyer Wally G. , Asmar Lina , Mackey Daniel , Riedel Stefan , Muss Hyman , Savin Michael A.
Published: February 2009

Purpose

We previously reported that four cycles of docetaxel/cyclophosphamide (TC) produced superior disease-free survival (DFS) compared with four cycles of doxorubicin/cyclophosphamide (AC) in early breast cancer. Older women are under-represented in adjuvant chemotherapy trials. In our trial 16% of patients were ≥ 65 years. We now report 7-year results for DFS and overall survival (OS) as well as the impact of age, hormone receptor status, and HER2 status on outcome and toxicity.

Patients and Methods

Patients were randomly assigned to receive either four cycles of standard-dose AC (60/600 mg/m2; n = 510), or TC (75/600 mg/m2; n = 506), administered by intravenous infusion every 3 weeks.

Results

The median age in women younger than 65, was 50 years (range, 27 to 64) and for women ≥ 65 was 69 years (range, 65 to 77). Baseline characteristics in the two age subgroups were generally well matched, except that older women tended to have more lymph node involvement. At a median of 7 years follow-up, the difference in DFS between TC and AC was significant (81% TC v 75% AC; P = .033; hazard ratio [HR], 0.74; 95% CI 0.56 to 0.98) as was OS (87% TC v 82% AC; P = .032; HR, 0.69; 95% CI, 0.50 to 0.97). TC was superior in older patients as well as younger patients. There was no interaction of hormone-receptor status or HER-2 status and treatment. Older women experienced more febrile neutropenia with TC and more anemia with AC.

Conclusion

With longer follow-up, four cycles of TC was superior to standard AC (DFS and OS) and was a tolerable regimen in both older and younger patients.
Heterogeneity and Power in Clinical Biomarker Studies
Authors: Pintilie Melania , Iakovlev Vladimir , Fyles Anthony , Hedley David , Milosevic Michael , Hill Richard P.
Published: February 2009

Purpose

Many recent studies have suggested the possibility that a variety of different biomarkers may be associated with treatment outcome. However, it is also apparent that some of these biomarkers are heterogeneously distributed within a tumor. Due to this heterogeneous distribution of the biomarker, the association sought may appear weak or nonexistent. Thus, there is a wide range of conclusions in the literature on the association between a biomarker and an outcome.

Results

This article presents how to quantify the heterogeneity and how it influences the observed effect size and the ability to detect it (power of the study). It can be shown that the estimated effect size and the power of the study are diminished when the biomarker is measured with error. The estimated effect of the association with outcome of the average of several replicates per patient is closer to the true effect size when the number of replicates increases.

Conclusion

The first step in designing a study of association between a biomarker and outcome is to conduct a pilot study in which several measurements per patient are taken. Based on these data, the heterogeneity of the marker within and between individuals can be estimated and used in the process of designing an appropriate study of the association between the biomarker and outcome.
Phase II Trial of Temozolomide Plus O6-Benzylguanine in Adults With Recurrent, Temozolomide-Resistant Malignant Glioma
Authors: Quinn Jennifer A. , Jiang Sara Xiaoyin , Reardon David A. , Desjardins Annick , Vredenburgh James J. , Rich Jeremy N. , Gururangan Sridharan , Friedman Allan H. , Bigner Darell D. , Sampson John H. , McLendon Roger E. , Herndon James E. , Walker Amy , Friedman Henry S.
Published: February 2009

Purpose

This phase II trial was designed to define the role of O6-benzylguanine (O6-BG) in restoring temozolomide sensitivity in patients with recurrent or progressive, temozolomide-resistant malignant glioma and to evaluate the safety of administering O6-BG in combination with temozolomide.

Patients and Methods

Patients were accrued into two independent strata on the basis of histology: glioblastoma multiforme (GBM) and anaplastic glioma. Both temozolomide and O6-BG were administered on day 1 of a 28-day treatment cycle. Patients were administered a 1-hour O6-BG infusion at a dose of 120 mg/m2 followed immediately by a 48-hour infusion at a dose of 30 mg/m2/d. Temozolomide was administered orally within 60 minutes of the end of the 1-hour O6-BG infusion at a dose of 472 mg/m2. The primary end point was objective response rate. Secondary end points included progression-free survival, overall survival, and safety.

Results

Sixty-six of 67 patients who enrolled were treated with temozolomide and O6-BG. One of 34 patients (3%) with GBM (95% CI, 0.1% to 15%) and five of 32 assessable patients (16%) with anaplastic glioma (95% CI, 5% to 33%) were responders. The most commonly reported adverse events were grade 4 hematologic events experienced in 48% of the patients.

Conclusion

O6-BG when added to a 1-day dosing regimen of temozolomide was able to restore temozolomide sensitivity in patients with temozolomide-resistant anaplastic glioma, but there seemed to be no significant restoration of temozolomide sensitivity in patients with temozolomide-resistant GBM.
Breast Cancer With Synchronous Metastases: Survival Impact of Exclusive Locoregional Radiotherapy
Authors: Le Scodan Romuald , Stevens Denise , Brain Etienne , Floiras Jean Louis , Cohen-Solal Christine , De La Lande Brigitte , Tubiana-Hulin Michelle , Yacoub Sameh , Gutierrez Maya , Ali David , Gardner Miriam , Moisson Patricia , Villette Sylviane , Lerebours Florence , Munck Jean Nicolas , Labib Alain
Published: February 2009

Purpose

Several studies suggest that surgical excision of the primary tumor improves survival among patients with stage IV breast cancer at diagnosis. Exclusive locoregional radiotherapy (LRR) is an alternative form of locoregional treatment (LRT) in this setting. We retrospectively studied the impact of LRT on the survival of breast cancer patients with synchronous metastases.

Patients and Methods

Among 18,753 breast cancer patients treated in our institution between 1980 and 2004, 598 patients (3.2%) had synchronous metastasis at diagnosis. Demographic data, tumor characteristics, metastatic sites, and treatments were prospectively recorded. The impact of LRT on overall survival (OS) was evaluated by multivariate analysis including known prognostic factors.

Results

Among 581 eligible patients, 320 received LRT (group A), and 261 received no LRT (group B). LRT consisted of exclusive LRR in 249 patients (78%), surgery of the primary tumor with adjuvant LRR in 41 patients (13%), and surgery alone in 30 patients (9%). With a median follow-up time of 39 months, the 3-year OS rates were 43.4% and 26.7% in group A and group B (P =.00002), respectively. The association between LRT and improved survival was particularly marked in women with visceral metastases. LRT was an independent prognostic factor in multivariate analysis (hazard ratio [HR] = 0.70; 95% CI, 0.58 to 0.85; P = .0002). The adjusted HR for late death (≥ 1 year) was 0.76 (95% CI, 0.61 to 0.96; P = .02).

Conclusion

In our experience, LRT, consisting mainly of exclusive LRR, was associated with improved survival in breast cancer patients with synchronous metastases. Exclusive LRR may thus represent an active alternative to surgery.
Treatment of Nonmetastatic Cranial Parameningeal Rhabdomyosarcoma in Children Younger Than 3 Years Old: Results From International Society of Pediatric Oncology Studies MMT 89 and 95
Authors: Defachelles Anne-Sophie , Rey Annie , Oberlin Odile , Spooner David , Stevens Michael C.G.
Published: February 2009

Purpose

To explore a strategy by which radiotherapy (RT) could be avoided in the treatment of young children with parameningeal rhabdomyosarcoma (PM RMS).

Patients and Methods

Fifty-nine children (median age, 2 years 3 months) with nonmetastatic cranial PM RMS were treated in the International Society of Pediatric Oncology MMT 89 and 95 trials between 1989 and 2003.

Results

Five-year EFS and OS rates were 46% and 54%, respectively, for the whole group. No standard clinical or pathologic variables had prognostic impact. Fifty (85%) of 59 patients achieved complete local control either with (n = 28) or without (n = 22) RT administered as part of their primary treatment. Nine patients (15%) did not achieve local control (four of whom had had RT), and all died. Patients who received RT had a significantly superior 5-year EFS rate compared with patients who did not receive RT (59% v 28%, respectively). Twenty-three patients (48%) experienced relapse at a median interval of 15 months. Ultimately, only seven patients (12%) were cured without RT, although this represented 32% of those who achieved local control with initial chemotherapy.

Conclusion

Despite concerns about the late effects of its use in young children, cure of PM RMS remains unlikely without systematic use of RT. The accurate prediction of the small subset of patients who achieve local control without RT and who do not experience relapse would provide an opportunity for a minority of patients to avoid RT.
Operation sequencing optimization for five-axis prismatic parts using a particle swarm optimization approach
Authors: Guo Y W , Mileham A R , Owen G W , Maropoulos P G , Li W D
Published: February 2009

Operation sequencing is one of the crucial tasks in process planning. However, it is an intractable process to identify an optimized operation sequence with minimal machining cost in a vast search space constrained by manufacturing conditions. Also, the information represented by current process plan models for three-axis machining is not sufficient for five-axis machining owing to the two extra degrees of freedom and the difficulty of set-up planning. In this paper, a representation of process plans for five-axis machining is proposed, and the complicated operation sequencing process is modelled as a combinatorial optimization problem. A modern evolutionary algorithm, i.e. the particle swarm optimization (PSO) algorithm, has been employed and modified to solve it effectively. Initial process plan solutions are formed and encoded into particles of the PSO algorithm. The particles ‘fly’ intelligently in the search space to achieve the best sequence according to the optimization strategies of the PSO algorithm. Meanwhile, to explore the search space comprehensively and to avoid being trapped into local optima, several new operators have been developed to improve the particle movements to form a modified PSO algorithm. A case study used to verify the performance of the modified PSO algorithm shows that the developed PSO can generate satisfactory results in optimizing the process planning problem.