bluuebunny/crossref_metadata_2025 huggingface dataset:
A simple and high-sensitivity method for analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis
Authors: Takahashi Hirotaka , Nozawa Akira , Seki Motoaki , Shinozaki Kazuo , Endo Yaeta , Sawasaki Tatsuya
Published: April 2009

Background

Ubiquitination is mediated by the sequential action of at least three enzymes: the E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme) and E3 (ubiquitin ligase) proteins. Polyubiquitination of target proteins is also implicated in several critical cellular processes. Although Arabidopsis genome research has estimated more than 1,300 proteins involved in ubiquitination, little is known about the biochemical functions of these proteins. Here we demonstrate a novel, simple and high-sensitive method for in vitro analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis and luminescent detection.

Results

Using wheat cell-free synthesis, 11 E3 proteins from Arabidopsis full-length cDNA templates were produced. These proteins were analyzed either in the translation mixture or purified recombinant protein from the translation mixture. In our luminescent method using FLAG- or His-tagged and biotinylated ubiquitins, the polyubiquitin chain on AtUBC22, UPL5 and UPL7 (HECT) and CIP8 (RING) was detected. Also, binding of ubiquitin to these proteins was detected using biotinylated ubiquitin and FLAG-tagged recombinant protein. Furthermore, screening of the RING 6 subgroup demonstrated that At1g55530 was capable of polyubiquitin chain formation like CIP8. Interestingly, these ubiquitinations were carried out without the addition of exogenous E1 and/or E2 proteins, indicating that these enzymes were endogenous to the wheat cell-free system. The amount of polyubiquitinated proteins in the crude translation reaction mixture was unaffected by treatment with MG132, suggesting that our system does not contain 26S proteasome-dependent protein degradation activity.

Conclusion

In this study, we developed a simple wheat cell-free based luminescence method that could be a powerful tool for comprehensive ubiquitination analysis.
Magnetic resonance imaging in size assessment of invasive breast carcinoma with an extensive intraductal component
Authors: Schouten van der Velden Arjan P , Boetes Carla , Bult Peter , Wobbes Theo
Published: April 2009

Background

Breast-conserving treatment of invasive breast carcinoma with an extensive intraductal component (EIC) is associated with DCIS-involved surgical margins and therefore it has an increased recurrence rate. EIC is a non-palpable lesion of which the size is frequently underestimated on mammography. This study was undertaken to evaluate the accuracy of MRI in size assessment of breast cancer with EIC.

Methods

23 patients were identified and the mammographic (n = 21) and MR (n = 23) images were re-reviewed by a senior radiologist. Size on MR images was compared with histopathological tumour extent.

Results

The correlation of radiological size with histopathological size was r = 0.20 in mammography (p = 0.39) compared to r = 0.65 in MRI (p < 0.01). Mammography underestimated histopathological tumour size in 62%. MR images over- or underestimated tumour size in 22% and 30% of the cases, respectively. In poorly differentiated EIC, MRI adequately estimated the extent more often compared to moderately differentiated EIC (60% versus 25%, respectively).

Conclusion

Size assessment of MRI imaging was more accurate compared to mammography. This was predominantly true for poorly differentiated EIC.
Plasma leptin and insulin-like growth factor I levels during acute exacerbations of chronic obstructive pulmonary disease
Authors: Kythreotis Prokopis , Kokkini Ageliki , Avgeropoulou Stavrina , Hadjioannou Argyro , Anastasakou Efgenia , Rasidakis Antonis , Bakakos Petros
Published: April 2009

Background

Recent studies have provided evidence for a link between leptin and tumor necrosis factor-alpha (TNF-α). Insulin-like growth factor I (IGF-I) mediates the metabolic effects of growth hormone (GH). The GH axis is believed to be suppressed in chronic obstructive pulmonary disease (COPD). The aim of this study is to find out whether acute exacerbations of COPD are followed by changes in plasma leptin and insulin-like growth factor I (IGF-I) levels and furthermore, whether these changes are related to systemic inflammation.

Methods

We measured serum leptin, IGF-I, TNF-α, interleukin 1β (IL-1β), interleukin 6 (IL-6) and interleukin 8 (IL-8) levels in 52 COPD patients with acute exacerbation on admission to hospital (Day 1) and two weeks later (Day 15). 25 healthy age-matched subjects served as controls. COPD patients were also divided into two subgroups (29 with chronic bronchitis and 23 with emphysema). Serum leptin and IGF-I were measured by radioimmunoassay and TNF-α, IL-1β, IL-6 and IL-8 were measured by ELISA.

Results

Serum leptin levels were significantly higher and serum IGF-I levels significantly lower in COPD patients on Day 1 than in healthy controls (p < 0.001). A positive correlation was observed between leptin and TNF-α on Day 1 (r = 0.620, p < 0.001). Emphysematous patients had significantly lower IGF-I levels compared to those with chronic bronchitis both on Day 1 and Day 15 (p = 0.003 and p < 0.001 respectively).

Conclusion

Inappropriately increased circulating leptin levels along with decreased IGF-I levels occured during acute exacerbations of COPD. Compared to chronic bronchitis, patients with emphysema had lower circulating IGF-I levels both at the onset of the exacerbation and two weeks later.
Classification of gluteal muscle contracture in children and outcome of different treatments
Authors: Zhao Chen-Guang , He Xi-Jing , Lu Bin , Li Hao-Peng , Wang Dong , Zhu Zhen-Zhong
Published: April 2009

Background

Gluteal muscle contracture (GMC) is a clinical syndrome due to multiple etiologies in which hip movements may be severely limited. The aim of this study was to propose a detailed classification of GMC and evaluate the statistical association between outcomes of different management and patient conditions.

Methods

One hundred fifty-eight patients, who were treated between January 1995 and December 2004, were reviewed at a mean duration of follow-up of 4.8 years. Statistical analyses were performed using X2 and Fisher's exact tests.

Results

Non-operative management (NOM), as a primary treatment, was effective in 19 of 49 patients (38.8%), while operative management was effective in all 129 patients, with an excellence rating of 83.7% (108/129). The outcome of NOM in level I patients was significantly higher than in level II and III patients (P < 0.05). The results of NOM and operative management in the child group were better than the adolescent group (P < 0.05). Complications in level III were more than in level II.

Conclusion

NOM was more effective in level I patients than in level II and III patients. Operative management was effective in patients at all levels, with no statistical differences between levels or types. We recommend NOM as primary treatment for level I patients and operative management for level II and III patients. Either NOM or operative management should be carried out as early as possible.
Development of estimates of dietary nitrates, nitrites, and nitrosamines for use with the short willet food frequency questionnaire
Authors: Griesenbeck John S , Steck Michelle D , Huber John C , Sharkey Joseph R , Rene Antonio A , Brender Jean D
Published: April 2009

Background

Studies have suggested that nitrates, nitrites, and nitrosamines have an etiologic role in adverse pregnancy outcomes and chronic diseases such as cancer. Although an extensive body of literature exists on estimates of these compounds in foods, the extant data varies in quality, quantified estimates, and relevance.

Methods

We developed estimates of nitrates, nitrites, and nitrosamines for food items listed in the Short Willet Food Frequency Questionnaire (WFFQ) as adapted for use in the National Birth Defects Prevention Study. Multiple reference databases were searched for published literature reflecting nitrate, nitrite, and nitrosamine values in foods. Relevant published literature was reviewed; only publications reporting results for items listed on the WFFQ were selected for inclusion. The references selected were prioritized according to relevance to the U.S. population.

Results

Based on our estimates, vegetable products contain the highest levels of nitrate, contributing as much as 189 mg/serving. Meat and bean products contain the highest levels of nitrites with values up to 1.84 mg/serving. Alcohol, meat and dairy products contain the highest values of nitrosamines with a maximum value of 0.531 μg/serving. The estimates of dietary nitrates, nitrites, and nitrosamines generated in this study are based on the published values currently available.

Conclusion

To our knowledge, these are the only estimates specifically designed for use with the adapted WFFQ and generated to represent food items available to the U.S. population. The estimates provided may be useful in other research studies, specifically in those exploring the relation between exposure to these compounds in foods and adverse health outcomes.
Formulation of polylactide-co-glycolic acid nanospheres for encapsulation and sustained release of poly(ethylene imine)-poly(ethylene glycol) copolymers complexed to oligonucleotides
Authors: Sirsi Shashank R , Schray Rebecca C , Wheatley Margaret A , Lutz Gordon J
Published: April 2009

Antisense oligonucleotides (AOs) have been shown to induce dystrophin expression in muscles cells of patients with Duchenne Muscular Dystrophy (DMD) and in the mdx mouse, the murine model of DMD. However, ineffective delivery of AOs limits their therapeutic potential. Copolymers of cationic poly(ethylene imine) (PEI) and non-ionic poly(ethylene glycol) (PEG) form stable nanoparticles when complexed with AOs, but the positive surface charge on the resultant PEG-PEI-AO nanoparticles limits their biodistribution. We adapted a modified double emulsion procedure for encapsulating PEG-PEI-AO polyplexes into degradable polylactide-co-glycolic acid (PLGA) nanospheres. Formulation parameters were varied including PLGA molecular weight, ester end-capping, and sonication energy/volume. Our results showed successful encapsulation of PEG-PEI-AO within PLGA nanospheres with average diameters ranging from 215 to 240 nm. Encapsulation efficiency ranged from 60 to 100%, and zeta potential measurements confirmed shielding of the PEG-PEI-AO cationic charge. Kinetic measurements of 17 kDa PLGA showed a rapid burst release of about 20% of the PEG-PEI-AO, followed by sustained release of up to 65% over three weeks. To evaluate functionality, PEG-PEI-AO polyplexes were loaded into PLGA nanospheres using an AO that is known to induce dystrophin expression in dystrophic mdx mice. Intramuscular injections of this compound into mdx mice resulted in over 300 dystrophin-positive muscle fibers distributed throughout the muscle cross-sections, approximately 3.4 times greater than for injections of AO alone. We conclude that PLGA nanospheres are effective compounds for the sustained release of PEG-PEI-AO polyplexes in skeletal muscle and concomitant expression of dystrophin, and may have translational potential in treating DMD.
Scoring and psychometric validation of the Perception of Anticoagulant Treatment Questionnaire (PACT-Q©)
Authors: Prins MH , Guillemin I , Gilet H , Gabriel S , Essers B , Raskob G , Kahn SR
Published: April 2009

Background

The 'Perception of Anti-Coagulant Treatment Questionnaire' (PACT-Q) was developed to assess patients' expectations of, and satisfaction with their anticoagulant treatment. This questionnaire needs to be finalised and psychometrically validated.

Methods

The PACT-Q was included in the United States, the Netherlands and France into three phase III multinational clinical trials conducted to evaluate efficacy and safety of a new long-acting anticoagulant drug (idraparinux) compared to vitamin K antagonist (VKA). PACT-Q was administered to patients with deep venous thrombosis (DVT), atrial fibrillation (AF) or pulmonary embolism (PE) at Day 1, to assess patients' expectations, and at 3 and 6 months to assess patients' satisfaction and treatment convenience and burden. The final structure of the PACT-Q (Principal Component Analysis – PCA – with Varimax Rotation) was first determined and its psychometric properties were then measured with validity of the structure (Multitrait analysis), internal consistency reliability (Cronbach's alpha coefficients) and known-group validity.

Results

PCA and multitrait analyses showed the multidimensionality of the "Treatment Expectations" dimension, comprising 7 items that had to be scored independently. The "Convenience" and "Burden of Disease and Treatment" dimensions of the hypothesised original structure of the questionnaire were combined, thus resulting in 13 items grouped into the single dimension "Convenience". The "Anticoagulant Treatment Satisfaction" dimension remained unchanged and included 7 items. All items of the "Convenience" and "Anticoagulant Treatment Satisfaction" dimensions displayed good convergent and discriminant validity. The internal consistency reliability was good, with a Cronbach's alpha of 0.84 for the "Convenience" dimension, and 0.76 for the "Anticoagulant Treatment Satisfaction" dimension. Known-group validity was good, especially with regard to occurrence of thromboembolic events within 3 months from randomisation.

Conclusion

The PACT-Q is a valid and reliable instrument that allows the assessment of patients' expectations and satisfaction regarding anticoagulant treatment, as well as their opinion about treatment convenience of use. Its two-part structure – assessment of expectations at baseline in the first part, and of convenience, burden and treatment satisfaction in the second – was validated and displays good and stable psychometric properties. These results are not sufficient to recommend the use of satisfaction as primary endpoint in clinical trials; further validation work is needed to support the interpretation of PACT-Q dimension scores. However, this first validation makes the PACT-Q an appropriate measure for use in clinical and pharmacoepidemiological research, as well as in real-life studies.

Trial Registration

(ClinicalTrials.gov numbers, NCT00067093, NCT00062803 and NCT00070655).
Expression of the calcium-activated potassium channel in upper and lower segment human myometrium during pregnancy and parturition
Authors: Gao Lu , Cong Binghai , Zhang Lanmei , Ni Xin
Published: April 2009

Background

Large conductance calcium-activated potassium channel (BKCa) plays an important role in the control of uterine contractility during pregnancy. The change from uterine quiescence to enhanced contractile activity may be associated with the spatial and temporal expression of BKCa within myometrium. The objectives of this study were to examine the expression of BKCa alpha- and beta-subunit in upper segment (US) and lower segment (LS) regions of uterus, and to investigate for the possibly differential expression of these proteins in US and LS myometrium obtained from three functional states: (1) non-pregnant (NP); (2) term pregnant not in labour (TNL) and (3) term pregnant in labour (TL).

Methods

Myometrial biopsies were collected from non-pregnant women at hysterectomy and pregnant women at either elective caesarean section or emergency caesarean section. Protein expression level and cellular localization of BKCa alpha- and beta-subunit in US and LS myometrium were determined by Western blot analysis and immunohistochemistry, respectively.

Results

BKCa alpha- and beta-subunit were predominantly localized to myometrial smooth muscle in both US and LS myometrium obtained from non-pregnant and pregnant patients. The level of BKCa alpha-subunit in US but not in LS was significantly higher in NP myometrium than those measured in myometrium obtained during pregnancy. Lower expression of BKCa alpha-subunit in both US and LS was found in TL than in TNL biopsies. Expression of beta-subunit in both US and LS myometrium was significantly reduced in TL group compared with those measured in TNL group. There was no significant difference in BKCa beta-subunit expression in either US or LS between NP and TNL group.

Conclusion

Our results suggest that expression of BKCa alpha- and beta-subunit in pregnant myometrium is reduced during labour, which is consistent with the myometrial activity at the onset of parturition.
Cost-effectiveness model comparing olanzapine and other oral atypical antipsychotics in the treatment of schizophrenia in the United States
Authors: Furiak Nicolas M , Ascher-Svanum Haya , Klein Robert W , Smolen Lee J , Lawson Anthony H , Conley Robert R , Culler Steven D
Published: April 2009

Background

Schizophrenia is often a persistent and costly illness that requires continued treatment with antipsychotics. Differences among antipsychotics on efficacy, safety, tolerability, adherence, and cost have cost-effectiveness implications for treating schizophrenia. This study compares the cost-effectiveness of oral olanzapine, oral risperidone (at generic cost, primary comparator), quetiapine, ziprasidone, and aripiprazole in the treatment of patients with schizophrenia from the perspective of third-party payers in the U.S. health care system.

Methods

A 1-year microsimulation economic decision model, with quarterly cycles, was developed to simulate the dynamic nature of usual care of schizophrenia patients who switch, continue, discontinue, and restart their medications. The model captures clinical and cost parameters including adherence levels, relapse with and without hospitalization, quality-adjusted life years (QALYs), treatment discontinuation by reason, treatment-emergent adverse events, suicide, health care resource utilization, and direct medical care costs. Published medical literature and a clinical expert panel were used to develop baseline model assumptions. Key model outcomes included mean annual total direct cost per treatment, cost per stable patient, and incremental cost-effectiveness values per QALY gained.

Results

The results of the microsimulation model indicated that olanzapine had the lowest mean annual direct health care cost ($8,544) followed by generic risperidone ($9,080). In addition, olanzapine resulted in more QALYs than risperidone (0.733 vs. 0.719). The base case and multiple sensitivity analyses found olanzapine to be the dominant choice in terms of incremental cost-effectiveness per QALY gained.

Conclusion

The utilization of olanzapine is predicted in this model to result in better clinical outcomes and lower total direct health care costs compared to generic risperidone, quetiapine, ziprasidone, and aripiprazole. Olanzapine may, therefore, be a cost-effective therapeutic option for patients with schizophrenia.
Accuracy estimation of foamy virus genome copying
Authors: Gärtner Kathleen , Wiktorowicz Tatiana , Park Jeonghae , Mergia Ayalew , Rethwilm Axel , Scheller Carsten
Published: April 2009

Background

Foamy viruses (FVs) are the most genetically stable viruses of the retrovirus family. This is in contrast to the in vitro error rate found for recombinant FV reverse transcriptase (RT). To investigate the accuracy of FV genome copying in vivo we analyzed the occurrence of mutations in HEK 293T cell culture after a single round of reverse transcription using a replication-deficient vector system. Furthermore, the frequency of FV recombination by template switching (TS) and the cross-packaging ability of different FV strains were analyzed.

Results

We initially sequenced 90,000 nucleotides and detected 39 mutations, corresponding to an in vivo error rate of approximately 4 × 10-4 per site per replication cycle. Surprisingly, all mutations were transitions from G to A, suggesting that APOBEC3 activity is the driving force for the majority of mutations detected in our experimental system. In line with this, we detected a late but significant APOBEC3G and 3F mRNA by quantitative PCR in the cells. We then analyzed 170,000 additional nucleotides from experiments in which we co-transfected the APOBEC3-interfering foamy viral bet gene and observed a significant 50% drop in G to A mutations, indicating that APOBEC activity indeed contributes substantially to the foamy viral replication error rate in vivo. However, even in the presence of Bet, 35 out of 37 substitutions were G to A, suggesting that residual APOBEC activity accounted for most of the observed mutations. If we subtract these APOBEC-like mutations from the total number of mutations, we calculate a maximal intrinsic in vivo error rate of 1.1 × 10-5 per site per replication. In addition to the point mutations, we detected one 49 bp deletion within the analyzed 260000 nucleotides.

Analysis of the recombination frequency of FV vector genomes revealed a 27% probability for a template switching (TS) event within a 1 kilobase (kb) region. This corresponds to a 98% probability that FVs undergo at least one additional TS event per replication cycle. We also show that a given FV particle is able to cross-transfer a heterologous FV genome, although at reduced efficiency than the homologous vector.

Conclusion

Our results indicate that the copying of the FV genome is more accurate than previously thought. On the other hand recombination among FV genomes appears to be a frequent event.
The histone 3 lysine 4 methyltransferase, Mll2, is only required briefly in development and spermatogenesis
Authors: Glaser Stefan , Lubitz Sandra , Loveland Kate L , Ohbo Kazu , Robb Lorraine , Schwenk Frieder , Seibler Jost , Roellig Daniela , Kranz Andrea , Anastassiadis Konstantinos , Stewart A Francis
Published: April 2009

Background

Histone methylation is thought to be central to the epigenetic mechanisms that maintain and confine cellular identity in multi-cellular organisms. To examine epigenetic roles in cellular homeostasis, we conditionally mutated the histone 3 lysine 4 methyltransferase, Mll2, in embryonic stem (ES) cells, during development and in adult mice using tamoxifen-induced Cre recombination.

Results

In ES cells, expression profiling unexpectedly revealed that only one gene,Magoh2, is dependent upon Mll2 and few other genes were affected. Loss of Mll2 caused loss of H3K4me3 at theMagoh2promoter and concomitant gain of H3K27me3 and DNA methylation. Hence Mll2, which is orthologous toDrosophilaTrithorax, is required to prevent Polycomb-Group repression of theMagoh2promoter, and repression is further accompanied by DNA methylation. Early loss of Mll2in uterorecapitulated the embryonic lethality found inMll2-/- embryos. However, loss of Mll2 after E11.5 produced mice without notable pathologies. Hence Mll2 is not required for late development, stem cells or homeostasis in somatic cell types. However it is required in the germ cell lineage. Spermatogenesis was lost upon removal of Mll2, although spermatogonia A persisted.

Conclusion

These data suggest a bimodal recruit and maintain model whereby Mll2 is required to establish certain epigenetic decisions during differentiation, which are then maintained by redundant mechanisms. We also suggest that these mechanisms relate to the epigenetic maintenance of CpG island promoters.
Inflammation predicts accelerated brachial arterial wall changes in patients with recent-onset rheumatoid arthritis
Authors: Hannawi Suad , Marwick Thomas H , Thomas Ranjeny
Published: April 2009

Introduction

Patients with recent-onset rheumatoid arthritis (RA) have impaired brachial artery endothelial function compared with controls matched for age, sex and cardiovascular risk factors. The present study examined endothelium-dependent (flow-mediated dilatation (FMD)) and independent (glyceryl trinitrate (GTN)-mediated dilatation (GMD)) structural responses in early RA patients, and determined progress over one year.

Methods

Brachial artery FMD and GMD and carotid intima media thickness (cIMT) were studied using ultrasound in 20 patients diagnosed with early RA in whom symptoms had been present for less than 12 months, and in 20 control subjects matched for age, sex and established cardiovascular risk factors. FMD and GMD were re-assessed after 12 months in RA patients and the change in each parameter was calculated. Data were analysed by univariate regression.

Results

Mean FMD and GMD were significantly lower in early RA patients at baseline than in controls, but each parameter significantly improved in one year. FMD and GMD responses were positively associated with each other. Patients' age, C-reactive protein (CRP) level and cIMT at baseline and CRP level at one year, were negatively associated with change in brachial responses in one year.

Conclusions

Patients with recent-onset RA have altered brachial artery responses signifying both functional and structural abnormalities. However, early control of inflammation may reduce arterial dysfunction and thus the tendency for atherosclerotic progression.
Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii
Authors: Mullapudi Nandita , Joseph Sandeep J , Kissinger Jessica C
Published: April 2009

Background

Toxoplasma gondii is a member of the phylum Apicomplexa, which consists entirely of parasitic organisms that cause several diseases of veterinary and human importance. Fundamental mechanisms of gene regulation in this group of protistan parasites remain largely uncharacterized. Owing to their medical and veterinary importance, genome sequences are available for several apicomplexan parasites. Their genome sequences reveal an apparent paucity of known transcription factors and the absence of canonical cis-regulatory elements. We have approached the question of gene regulation from a sequence perspective by mining the genomic sequence data to identify putative cis-regulatory elements using a de novo approach.

Results

We have identified putative cis-regulatory elements present upstream of functionally related groups of genes and subsequently characterized the function of some of these conserved elements using reporter assays in the parasite. We show a sequence-specific role in gene-expression for seven out of eight identified elements.

Conclusions

This work demonstrates the power of pure sequence analysis in the absence of expression data or a priori knowledge of regulatory elements in eukaryotic organisms with compact genomes.
Phase II Study of Eribulin Mesylate, a Halichondrin B Analog, in Patients With Metastatic Breast Cancer Previously Treated With an Anthracycline and a Taxane
Authors: Vahdat Linda T. , Pruitt Brian , Fabian Carol J. , Rivera Ragene R. , Smith David A. , Tan-Chiu Elizabeth , Wright Jonathan , Tan Antoinette R. , DaCosta Noshir A. , Chuang Ellen , Smith John , O'Shaughnessy Joyce , Shuster Dale E. , Meneses Nicole L. , Chandrawansa Kumari , Fang Fang , Cole Patricia E. , Ashworth Simon , Blum Joanne L.
Published: April 2009

Purpose

Eribulin mesylate (E7389), a nontaxane microtubule dynamics inhibitor, is a structurally simplified, synthetic analog of the marine natural product halichondrin B. This open-label, single-arm, phase II study evaluated efficacy and tolerability of eribulin in heavily pretreated patients with metastatic breast cancer (MBC).

Methods

MBC patients who were previously treated with an anthracycline and a taxane received eribulin mesylate (1.4 mg/m2) as a 2- to 5-minute intravenous (IV) infusion on days 1, 8, and 15 of a 28-day cycle. Because of neutropenia (at day 15), an alternative regimen of eribulin on days 1 and 8 of a 21-day cycle was administered. The primary end point was overall response rate.

Results

Of the 103 patients treated, the median number of prior chemotherapy regimens was four (range, one to 11 regimens). In the per-protocol population (n = 87), eribulin achieved an independently reviewed objective response rate (all partial responses [PRs]) of 11.5% (95% CI, 5.7 to 20.1) and a clinical benefit rate (PR plus stable disease ≥ 6 months) of 17.2% (95% CI, 10.0 to 26.8). The median duration of response was 171 days (5.6 months; range, 44 to 363 days), the median progression-free survival was 79 days (2.6 months; range, 1 to 453 days), and the median overall survival was 275 days (9.0 months; range, 15 to 826 days). The most common drug-related grades 3 to 4 toxicities were as follows: neutropenia, 64%; leukopenia, 18%; fatigue, 5%; peripheral neuropathy, 5%; and febrile neutropenia, 4%.

Conclusion

Eribulin demonstrated activity with manageable tolerability (including infrequent grade 3 and no grade 4 neuropathy) in heavily pretreated patients with MBC when dosed as a short IV infusion on days 1 and 8 of a 21-day cycle.
Dose-Intensified Compared With Standard Chemotherapy for Nonmetastatic Ewing Sarcoma Family of Tumors: A Children's Oncology Group Study
Authors: Granowetter Linda , Womer Richard , Devidas Meenakshi , Krailo Mark , Wang Chenguang , Bernstein Mark , Marina Neyssa , Leavey Patrick , Gebhardt Mark , Healey John , Shamberger Robert Cooper , Goorin Allen , Miser James , Meyer James , Arndt Carola A.S. , Sailer Scott , Marcus Karen , Perlman Elizabeth , Dickman Paul , Grier Holcombe E.
Published: April 2009

Purpose

The Ewing sarcoma family of tumors (ESFT) is a group of malignant tumors of soft tissue and bone sharing a chromosomal translocation affecting the EWS locus. The Intergroup INT-0091 demonstrated the superiority of a regimen of vincristine, cyclophosphamide, doxorubicin (VDC), and dactinomycin alternating with ifosfamide and etoposide (IE) over VDC for patients with nonmetastatic ESFT of bone. The goal of this study was to determine whether a dose-intensified regimen of VDC alternating with IE would further improve the outcome for patients with nonmetastatic ESFT of bone or soft tissue.

Methods

Patients with previously untreated, nonmetastatic ESFT of bone or soft tissue were eligible. They were randomly assigned to receive standard doses of VDC/IE over 48 weeks or a dose-intensified regimen of VDC/IE over 30 weeks.

Results

Four hundred seventy-eight patients met eligibility requirements: 231 patients received the standard regimen; 247 patients received the intensified regimen. The 5-year event-free survival (EFS) and overall survival rates for all eligible patients were 71.1% (95% CI, 67.7% to 75.0%) and 78.6% (95% CI, 74.6% to 82.1%), respectively. There was no significant difference (P = .57) in EFS between patients treated with the standard (5-year EFS, 72.1%; 95% CI, 65.8% to 77.5%) or intensified regimen (5-year EFS, 70.1%; 63.9% to 75%). Patients with soft tissue tumors accounted for 20% of the study population; there was no difference in outcome between patients with soft tissue and bone primary sites.

Conclusion

Dose escalation of alkylating agents as tested in this trial did not improve the outcome for patients with nonmetastatic ESFT of bone or soft tissue.
High Prevalence of Vitamin D Deficiency Despite Supplementation in Premenopausal Women With Breast Cancer Undergoing Adjuvant Chemotherapy
Authors: Crew Katherine D. , Shane Elizabeth , Cremers Serge , McMahon Donald J. , Irani Dinaz , Hershman Dawn L.
Published: April 2009

Purpose

Vitamin D deficiency is associated with increased breast cancer risk and decreased breast cancer survival. The purpose of this study was to determine the prevalence of vitamin D deficiency, as measured by serum 25-hydroxyvitamin D (25-OHD), in premenopausal women at initiation of adjuvant chemotherapy for breast cancer and after 1 year of vitamin D supplementation.

Patients and Methods

The study included 103 premenopausal women from the northeastern United States with stages I to III breast cancer who received adjuvant chemotherapy and participated in a 1-year zoledronate intervention trial. All patients were prescribed vitamin D3 (cholecalciferol) 400 IU and calcium carbonate 1,000 mg daily. At baseline and at 6 and 12 months, bone mineral density (BMD) measurements were obtained and blood was collected and analyzed in batches for serum 25-OHD. Vitamin D deficiency was defined as serum 25-OHD less than 20 ng/mL, insufficiency as 20 to 29 ng/mL, and sufficiency as 30 ng/mL or greater.

Results

At baseline, 74% of women were vitamin D deficient (median, 17 ng/mL). Vitamin D deficiency was slightly less common in white women (66%) compared with black (80%) and Hispanic (84%) women. After vitamin D supplementation for 1 year, less than 15% of white and Hispanic women, and no black women, achieved sufficient 25-OHD levels. Vitamin D levels did not correlate with baseline BMD and were not altered by chemotherapy or bisphosphonate use.

Conclusion

Vitamin D deficiency is highly prevalent in women with breast cancer. The current recommended dietary allowance of vitamin D is too low to increase serum 25-OHD greater than 30 ng/mL. Optimal dosing for bone health and, possibly, improved survival has yet to be determined.
Comparison of Models to Predict Nonsentinel Lymph Node Status in Breast Cancer Patients With Metastatic Sentinel Lymph Nodes: A Prospective Multicenter Study
Authors: Coutant Charles , Olivier Camille , Lambaudie Eric , Fondrinier Eric , Marchal Fréderic , Guillemin François , Seince Nathalie , Thomas Véronique , Levêque Jean , Barranger Emmanuel , Darai Emile , Uzan Serge , Houvenaeghel Gilles , Rouzier Roman
Published: April 2009

Purpose

Several models have been developed to predict nonsentinel lymph node (non-SN) status in patients with breast cancer with sentinel lymph node (SN) metastasis. The purpose of our investigation was to compare available models in a prospective, multicenter study.

Patients and Methods

In a cohort of 561 positive-SN patients who underwent axillary lymph node dissection, we evaluated the areas under the receiver operating characteristic curves (AUCs), calibration, rates of false negatives (FN), and number of patients in the group at low risk for non-SN calculated from nine models. We also evaluated these parameters in the subgroup of patients with micrometastasis or isolated tumor cells (ITC) in the SN.

Results

At least one non-SN was metastatic in 147 patients (26.2%). Only two of nine models had an AUC greater than 0.75. Three models were well calibrated. Two models yielded an FN rate less than 5%. Three models were able to assign more than a third of patients in the low-risk group. Overall, the Memorial Sloan-Kettering Cancer Center nomogram and Tenon score outperform other methods for all patients, including the subgroup of patients with only SN micrometastases or ITC.

Conclusion

Our study suggests that all models do not perform equally, especially for the subgroup of patients with only micrometastasis or ITC in the SN. We point out available evaluation methods to assess their performance and provide guidance for clinical practice.
Prognosis After Ipsilateral Breast Tumor Recurrence and Locoregional Recurrences in Patients Treated by Breast-Conserving Therapy in Five National Surgical Adjuvant Breast and Bowel Project Protocols of Node-Negative Breast Cancer
Authors: Anderson Stewart J. , Wapnir Irene , Dignam James J. , Fisher Bernard , Mamounas Eleftherios P. , Jeong Jong-Hyeon , Geyer Charles E. , Wickerham D. Lawrence , Costantino Joseph P. , Wolmark Norman
Published: April 2009

Purpose

Locoregional failure (LRF) after breast-conserving therapy (BCT) is associated with increased risk of distant disease and death. The magnitude of this risk has not been adequately characterized in patients with lymph node-negative disease.

Patients and Methods

Our study population included 3,799 women randomly assigned to five National Surgical Adjuvant Breast and Bowel Project protocols of node-negative disease (ie, B-13, B-14, B-19, B-20, and B-23) who underwent lumpectomy and whole breast irradiation with or without adjuvant systemic therapy. Cumulative incidences of ipsilateral breast tumor recurrence (IBTR) and other locoregional recurrence (oLRR) were calculated, along with distant-disease–free interval (DDFI) and overall survival (OS) after these events. Cox models were employed to model mortality by using clinical and pathologic factors jointly with these events.

Results

Four hundred nineteen patients (11.0%) experienced LRF: 342 (9.0%) experienced IBTR, and 77 (2.0%) experienced oLRR. The 12-year cumulative incidences of IBTR and oLRR in patients treated with adjuvant systemic therapy were 6.6% and 1.8%, respectively. Overall, 37.1% of IBTRs and 72.7% of oLRRs occurred within 5 years of diagnosis. Older age, black race, higher body mass index (BMI), larger tumors, and occurrence of IBTR or oLRR were significantly associated with increased mortality. The 5-year OS after IBTR and oLRR were 76.6% and 34.9%, respectively. Adjusted hazard ratios for mortality associated with IBTR and oLRR were significantly higher in estrogen receptor (ER)–negative patients than in ER-positive patients (P = .002 and P < .0001, respectively). Patients with early LRF had worse OS and DDFI than those with later-occurring LRF.

Conclusion

Although LRF is uncommon in patients with node-negative breast cancer who are treated with lumpectomy, radiation, and adjuvant systemic therapy, those who do develop LRF have substantially worse OS and DDFI.
Effects of Chemotherapy in AIDS-Associated Non-Hodgkin's Lymphoma on Kaposi's Sarcoma Herpesvirus DNA in Blood
Authors: Lin Lan , Lee Jeannette Y. , Kaplan Lawrence D. , Dezube Bruce J. , Noy Ariela , Krown Susan E. , Levine Alexandra M. , Yu Yanxing , Hayward Gary S. , Ambinder Richard F.
Published: April 2009

Purpose

To determine the relative frequency with which Kaposi's sarcoma–associated herpesvirus/HHV-8 (KSHV) DNA is detected in peripheral-blood mononuclear cells (PBMCs) and in plasma of patients with AIDS-KS and AIDS-associated non-Hodgkin's lymphoma (NHL; AIDS-NHL); to determine whether the presence of viral DNA in plasma reflects lysis of tumor cells or reflects the presence of viremia (ie, virion-encapsidated DNA); and to determine the effect of lymphoma therapy on KSHV DNA.

Patients and Methods

Samples were obtained from patients enrolled in AIDS Malignancy Consortium clinical trials and from healthy donors. Real time PCR was used to quantify KSHV DNA in peripheral blood mononuclear cells (PBMC) and plasma. DNase digestion and fragment size determination studies were used to characterize the DNA detected.

Results

In patients with AIDS-KS, KSHV DNA was detected in PBMC (54%) and in plasma (62%). In patients with AIDS-NHL, KSHV DNA was detected in PBMC (19%) and in plasma (22%). Median copy numbers also differed. KSHV DNA in plasma appeared to be encapsidated. In six patients with AIDS-NHL who were treated with chemotherapy (with or without rituximab), KSHV copy number declined in PBMC and in plasma.

Conclusion

KSHV DNA is sometimes detected in PBMC or in plasma of patients with AIDS-NHL without KS. Among patients with KSHV DNA detected in PBMC or in plasma, copy number does not distinguish between patients with AIDS-NHL and AIDS-KS. KSHV DNA in plasma likely reflects viremia and not simply lysis of tumor or other KSHV-infected cells. KSHV DNA copy number in PBMC and in plasma declined with lymphoma-directed cytotoxic chemotherapy in each of the six patients studied.
Comprehensive Pharmacogenetic Analysis of Irinotecan Neutropenia and Pharmacokinetics
Authors: Innocenti Federico , Kroetz Deanna L. , Schuetz Erin , Dolan M. Eileen , Ramírez Jacqueline , Relling Mary , Chen Peixian , Das Soma , Rosner Gary L. , Ratain Mark J.
Published: April 2009

Purpose

We aim to identify genetic variation, in addition to the UGT1A1*28 polymorphism, that can explain the variability in irinotecan (CPT-11) pharmacokinetics and neutropenia in cancer patients.

Patients and Methods

Pharmacokinetic, genetic, and clinical data were obtained from 85 advanced cancer patients treated with single-agent CPT-11 every 3 weeks at doses of 300 mg/m2 (n = 20) and 350 mg/m2 (n = 65). Forty-two common variants were genotyped in 12 candidate genes of the CPT-11 pathway using several methodologies. Univariate and multivariate models of absolute neutrophil count (ANC) nadir and pharmacokinetic parameters were evaluated.

Results

Almost 50% of the variation in ANC nadir is explained by UGT1A1*93, ABCC1 IVS11 –48C>T, SLCO1B1*1b, ANC baseline levels, sex, and race (P < .0001). More than 40% of the variation in CPT-11 area under the curve (AUC) is explained by ABCC2 –24C>T, SLCO1B1*5, HNF1A 79A>C, age, and CPT-11 dose (P < .0001). Almost 30% of the variability in SN-38 (the active metabolite of CPT-11) AUC is explained by ABCC1 1684T>C, ABCB1 IVS9 –44A>G, and UGT1A1*93 (P = .004). Other models explained 17%, 23%, and 27% of the variation in APC (a metabolite of CPT-11), SN-38 glucuronide (SN-38G), and SN-38G/SN-38 AUCs, respectively. When tested in univariate models, pretreatment total bilirubin was able to modify the existing associations between genotypes and phenotypes.

Conclusion

On the basis of this exploratory analysis, common polymorphisms in genes encoding for ABC and SLC transporters may have a significant impact on the pharmacokinetics and pharmacodynamics of CPT-11. Confirmatory studies are required.
Inactivation of Drosophila Huntingtin affects long-term adult functioning and the pathogenesis of a Huntington’s disease model
Authors: Zhang Sheng , Feany Mel B. , Saraswati Sudipta , Littleton J. Troy , Perrimon Norbert
Published: April 2009

A polyglutamine expansion in the huntingtin (HTT) gene causes neurodegeneration in Huntington’s disease (HD), but the in vivo function of the native protein (Htt) is largely unknown. Numerous biochemical and in vitro studies have suggested a role for Htt in neuronal development, synaptic function and axonal trafficking. To test these models, we generated a null mutant in the putative Drosophila HTT homolog (htt, hereafter referred to asdhtt) and, surprisingly, found that dhtt mutant animals are viable with no obvious developmental defects. Instead, dhtt is required for maintaining the mobility and long-term survival of adult animals, and for modulating axonal terminal complexity in the adult brain. Furthermore, removing endogenous dhtt significantly accelerates the neurodegenerative phenotype associated with a Drosophila model of polyglutamine Htt toxicity (HD-Q93), providing in vivo evidence that disrupting the normal function of Htt might contribute to HD pathogenesis.
Ethanol induces embryonic malformations by competing for retinaldehyde dehydrogenase activity during vertebrate gastrulation
Authors: Kot-Leibovich Hadas , Fainsod Abraham
Published: April 2009

Human embryos exposed to alcohol (ethanol) develop a complex developmental phenotype known as fetal alcohol spectrum disorder (FASD). In Xenopus embryos, ethanol reduces the levels of retinoic acid (RA) signaling during gastrulation. RA, a metabolite of vitamin A (retinol), is required for vertebrate embryogenesis, and deviation from its normal levels results in developmental malformations. Retinaldehyde dehydrogenase 2 (RALDH2) is required to activate RA signaling at the onset of gastrulation. We studied the effect of alcohol on embryogenesis by manipulating retinaldehyde dehydrogenase activity in ethanol-treated embryos. In alcohol-treated embryos, we analyzed RA signaling levels, phenotypes induced and changes in gene expression. Developmental defects that were characteristic of high ethanol concentrations were phenocopied by a low ethanol concentration combined with partial RALDH inhibition, whereas Raldh2 overexpression rescued the developmental malformations induced by high ethanol. RALDH2 knockdown resulted in similar RA signaling levels when carried out alone or in combination with ethanol treatment, suggesting that RALDH2 is the main target of ethanol. The biochemical evidence that we present shows that, at the onset of RA signaling during early gastrulation, the ethanol effect centers on the competition for the available retinaldehyde dehydrogenase activity. In light of the multiple regulatory roles of RA, continued embryogenesis in the presence of abnormally low RA levels provides an etiological explanation for the malformations observed in individuals with FASD.
Effect of bioethanol as an alternative fuel on the emissions reduction characteristics and combustion stability in a spark ignition engine
Authors: Yoon S H , Ha S Y , Roh H G , Lee C S
Published: April 2009

An experimental investigation was performed on the combustion performance, reduction characteristics of exhaust emissions, and engine performance of a spark ignition engine fuelled with bioethanol, ethanol—gasoline blend, and gasoline fuel. The test fuels were an ethanol—gasoline blend (E85), which consists of 85 vol% bioethanol and 15vol% gasoline, pure bioethanol (E100), and gasoline fuel without any additives (G100). In this work, the combustion and exhaust emission characteristics, including the combustion pressure, brake mean effective pressure (BMEP), and maximum brake torque (MBT) timing of the ethanol—gasoline blend and pure ethanol, were compared with those obtained with gasoline fuel. For the comparison of combustion and emissions characteristics for bioethanol, ethanol blends, and gasoline, the experiments were carried out under various engine operating conditions and the results were compared with those obtained using conventional gasoline fuel.

The results of this study showed that an ethanol-blended fuel or pure ethanol led to a drastic decrease in exhaust emissions under all operating conditions. The exhaust emissions such as hydrocarbons, carbon monoxide, and nitrogen oxides were reduced when using the bioethanol-blended and undiluted ethanol fuel because of the highly oxygenated component of ethanol fuel. Because the ignition timing was advanced above MBT timing when the ethanol fuels were used, improved combustion stability and a better combustion phase were measured because of the high octane rating of the ethanol. Combustion performance such as the brake torque and BMEP remained nearly the same or increased over those found using conventional gasoline fuel under various spark ignition timings and throttle valve openings.
Influence of the initial clearance on the peak stress in connecting-rod small ends
Authors: Pioli A , Strozzi A , Baldini A , Giacopini M , Rosi R
Published: April 2009

The stress increase that is caused by the presence of an initial clearance within the small end of connecting rods for motorbike and car engines is investigated. Plane analytical and numerical modellings of the dry contact between the small-end and piston pin are adopted. Based upon a recent analytical result, a normalizing parameter is introduced, which allows the stress concentration factor at the small-end bore sides to be expressed as a function of a proper combination of the initial clearance between the small end and gudgeon pin, the applied load, and Young's modulus, for prescribed aspect ratios of the small end and hollow pin. Design diagrams summarizing the consequences of an initial clearance between the small-end bore and gudgeon pin on the eye peak stress are reported, which cover a wide range of geometries, clearances, and loadings. Selected comparisons between two-dimensional and three-dimensional models are carried out.
The design of a Formula Student race car: a case study
Authors: Mihailidis A , Samaras Z , Nerantzis I , Fontaras G , Karaoglanidis G
Published: April 2009

This paper presents the procedure followed in order to design the first Formula Student race car of the Aristotle University of Thessaloniki, Greece. Despite the restrictions imposed by the Formula SAE rules, the designer has a broad range of freedom in creativity and innovativeness. The design concept of the main vehicle parts, such as the frame and the suspension, is described and the design objectives and assumptions are analysed. The paper also focuses on several new features regarding the suspension adjustments, the steering system, and the engine modifications. Following this procedure, it was made possible to build a competitive and reliable car in a period of just 9 months.