bluuebunny/crossref_metadata_2025 huggingface dataset:
Emerging potential of transposons for gene therapy and generation of induced pluripotent stem cells
Authors: VandenDriessche Thierry , Ivics Zoltán , Izsvák Zsuzsanna , Chuah Marinee K. L.
Published: May 2009

Effective gene therapy requires robust delivery of the desired genes into the relevant target cells, long-term gene expression, and minimal risks of secondary effects. The development of efficient and safe nonviral vectors would greatly facilitate clinical gene therapy studies. However, nonviral gene transfer approaches typically result in only limited stable gene transfer efficiencies in most primary cells. The use of nonviral gene delivery approaches in conjunction with the latest generation transposon technology based on Sleeping Beauty (SB) or piggyBac transposons may potentially overcome some of these limitations. In particular, a large-scale genetic screen in mammalian cells yielded a novel hyperactive SB transposase, resulting in robust and stable gene marking in vivo after hematopoietic reconstitution with CD34+ hematopoietic stem/progenitor cells in mouse models. Moreover, the first-in-man clinical trial has recently been approved to use redirected T cells engineered with SB for gene therapy of B-cell lymphoma. Finally, induced pluripotent stem cells could be generated after genetic reprogramming with piggyBac transposons encoding reprogramming factors. These recent developments underscore the emerging potential of transposons in gene therapy applications and induced pluripotent stem generation for regenerative medicine.
GAGE: generally applicable gene set enrichment for pathway analysis
Authors: Luo Weijun , Friedman Michael S , Shedden Kerby , Hankenson Kurt D , Woolf Peter J
Published: May 2009

Background

Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene analyses, including greater robustness, sensitivity and biological relevance. However, previous GSA methods have limited usage as they cannot handle datasets of different sample sizes or experimental designs.

Results

To address these limitations, we present a new GSA method called Generally Applicable Gene-set Enrichment (GAGE). We successfully apply GAGE to multiple microarray datasets with different sample sizes, experimental designs and profiling techniques. GAGE shows significantly better results when compared to two other commonly used GSA methods of GSEA and PAGE. We demonstrate this improvement in the following three aspects: (1) consistency across repeated studies/experiments; (2) sensitivity and specificity; (3) biological relevance of the regulatory mechanisms inferred.

GAGE reveals novel and relevant regulatory mechanisms from both published and previously unpublished microarray studies. From two published lung cancer data sets, GAGE derived a more cohesive and predictive mechanistic scheme underlying lung cancer progress and metastasis. For a previously unpublished BMP6 study, GAGE predicted novel regulatory mechanisms for BMP6 induced osteoblast differentiation, including the canonical BMP-TGF beta signaling, JAK-STAT signaling, Wnt signaling, and estrogen signaling pathways–all of which are supported by the experimental literature.

Conclusion

GAGE is generally applicable to gene expression datasets with different sample sizes and experimental designs. GAGE consistently outperformed two most frequently used GSA methods and inferred statistically and biologically more relevant regulatory pathways. The GAGE method is implemented in R in the "gage" package, available under the GNU GPL fromhttp://sysbio.engin.umich.edu/~luow/downloads.php.
Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses
Authors: Slysz Gordon W , Baker Charles AH , Bozsa Benjamin M , Dang Anthony , Percy Andrew J , Bennett Melissa , Schriemer David C
Published: May 2009

Background

Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing data requires an automated solution, particularly when accommodating new tandem mass spectrometry modes for H/DX measurement. We sought to develop software that offers flexibility in defining workflows so as to support exploratory treatments of H/DX-MS data, with a particular focus on the analysis of very large protein systems and the mining of tandem mass spectrometry data.

Results

We present a software package ("Hydra") that supports both traditional and exploratory treatments of H/DX-MS data. Hydra's software architecture tolerates flexible data analysis procedures by allowing the addition of new algorithms without significant change to the underlying code base. Convenient user interfaces ease the organization of raw data files and input of peptide data. After executing a user-defined workflow, extracted deuterium incorporation values can be visualized in tabular and graphical formats. Hydra also automates the extraction and visualization of deuterium distribution values. Manual validation and assessment of results is aided by an interface that aligns extracted ion chromatograms and mass spectra, while providing a means of rapidly reprocessing the data following manual adjustment. A unique feature of Hydra is the automated processing of tandem mass spectrometry data, demonstrated on a large test data set in which 40,000 deuterium incorporation values were extracted from replicate analysis of approximately 1000 fragment ions in one hour using a typical PC.

Conclusion

The customizable workflows and user-friendly interfaces of Hydra removes a significant bottleneck in processing and visualizing H/DX-MS data and helps the researcher spend more time executing new experiments and interpreting results. This increased efficiency will encourage the analysis of larger protein systems. The ability to accommodate the tandem MS dimension supports alternative data collection and analysis strategies, as well as higher resolution localization of deuteration where permitted by the fragmentation mechanism.
Bos taurus genome sequence reveals the assortment of immunoglobulin and surrogate light chain genes in domestic cattle
Authors: Ekman Anna , Niku Mikael , Liljavirta Jenni , Iivanainen Antti
Published: May 2009

Background

The assortment of cattle immunoglobulin and surrogate light chain genes has been extracted from the version 3.1 ofBos taurusgenome sequence as a part of an international effort to sequence and annotate the bovine genome.

Results

63 variable lambda chain and 22 variable kappa chain genes were identified and phylogenetically assigned to 8 and 4 subgroups, respectively. The specified phylogenetic relationships are compatible with the established ruminant light chain variable gene families or subgroups. Because of gaps and uncertainties in the assembled genome sequence, the number of genes might change in the future versions of the genome sequence. In addition, three bovine surrogate light chain genes were identified. The corresponding cDNAs were cloned and the expression of the surrogate light chain genes was demonstrated from fetal material.

Conclusion

The bovine kappa gene locus is compact and simple which may reflect the preferential use of the lambda chain in cattle. The relative orientation of variable and joining genes in both loci are consistent with a deletion mechanism in VJ joining. The orientation of some variable genes cannot be determined from the data available. The number of functional variable genes is moderate when compared to man or mouse. Thus, post-recombinatorial mechanisms might contribute to the generation of the bovine pre-immune antibody repertoire. The heavy chains probably contribute more to recombinational immunoglobulin repertoire diversity than the light chains but the heavy chain locus could not be annotated from the version 3.1 ofBos taurusgenome.
Efficient isolation of highly purified tonsil B lymphocytes using RosetteSep with allogeneic human red blood cells
Authors: Zuccolo Jonathan , Unruh Tammy L , Deans Julie P
Published: May 2009

Background

Human tonsils are a rich source of B lymphocytes exhibiting a variety of phenotypes and activation states. Existing methods of purification are time consuming or costly. The aim of the present study was to optimize conditions to isolate large numbers of highly purified primary B lymphocytes from tonsils in a short and cost-effective single step, using a commercially available reagent designed for purifying cells from whole blood (RosetteSep). This technique relies on the presence of the large excess of red blood cells in whole blood for the formation of immunorosettes, whereas single cell suspensions from tonsils contain relatively few red blood cells.

Results

B cell enrichment from tonsils was achieved using RosetteSep with no modification to the whole blood procedure; however, the degree of purity depended on the extent of red blood cell contamination of the starting tonsil cell suspension. Addition of a 50-fold excess of allogeneic human red blood cells, but not sheep red blood cells, reproducibly resulted in high levels of purity. Depletion of mononuclear cells from the donor red blood cells eliminated potential contamination with allogeneic B cells.

Conclusion

RosetteSep reagent can be used in combination with allogeneic human red blood cells to reproducibly isolate tonsil B lymphocytes to high levels of purity with no change in phenotype or loss of cells. This method provides considerable time and cost savings compared to other methods.
Breeding response of transcript profiling in developing seeds of Brassica napus
Authors: Hu Yaping , Wu Gang , Cao Yinglong , Wu Yuhua , Xiao Ling , Li Xiaodan , Lu Changming
Published: May 2009

Background

The upgrading of rapeseed cultivars has resulted in a substantial improvement in yield and quality in China over the past 30 years. With the selective pressure against fatty acid composition and oil content, high erucic acid- and low oil-content cultivars have been replaced by low erucic acid- and high oil-content cultivars. The high erucic acid cultivar Zhongyou 821 and its descendent, low erucic acid cultivar Zhongshuang 9, are representatives of two generations of the most outstanding Chinese rapeseed cultivars (B. napus) developed the past 2 decades. This paper compares the transcriptional profiles of Zhongshuang 9 and Zhongyou 821 for 32 genes that are principally involved in lipid biosynthesis during seed development in order to elucidate how the transcriptional profiles of these genes responded to quality improvement over the past 20 years.

Results

Comparison of the cultivar Zhongyou 821 with its descendent, Zhongshuang 9, shows that the transcriptional levels of seven of the 32 genes were upregulated by 30% to 109%, including FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC. Of the 32 genes, 10 (KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT and SUC1) were downregulated by at least 20% and most by 50%. The Napin gene alone accounted for over 75% of total transcription from all 32 genes assessed in both cultivars. Most of the genes showed significant correlation with fatty acid accumulation, but the correlation in ZS9 was significantly different from that in ZY821. Higher KCR2 activity is associated with higher C16:0, C18:0, and C18:2 in both cultivars, lower C22:1 and total fatty acid content in ZY821, and lower 18:1 in ZS9.

Conclusion

This paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the Napin gene predominantly transcribed. Selective pressure for zero erucic acid, low glucosinolate, high oleic acid and high oil content, as well as high yield, resulted in higher FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC expression levels and lower KAS3, β-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, α-CT and SUC1 expression levels. It also resulted in altered relationships between these genes during storage accumulation in seed development.
Combining the receptor tyrosine kinase inhibitor AEE788 and the mammalian target of rapamycin (mTOR) inhibitor RAD001 strongly inhibits adhesion and growth of renal cell carcinoma cells
Authors: Juengel Eva , Engler Johanna , Natsheh Iyad , Jones Jon , Mickuckyte Ausra , Hudak Lukasz , Jonas Dietger , Blaheta Roman A
Published: May 2009

Background

Treatment options for metastatic renal cell carcinoma (RCC) are limited due to resistance to chemo- and radiotherapy. The development of small-molecule multikinase inhibitors has now opened novel treatment options. We evaluated the influence of the receptor tyrosine kinase inhibitor AEE788, applied alone or combined with the mammalian target of rapamycin (mTOR) inhibitor RAD001, on RCC cell adhesion and proliferationin vitro.

Methods

RCC cell lines Caki-1, KTC-26 or A498 were treated with various concentrations of RAD001 or AEE788 and tumor cell proliferation, tumor cell adhesion to vascular endothelial cells or to immobilized extracellular matrix proteins (laminin, collagen, fibronectin) evaluated. The anti-tumoral potential of RAD001 combined with AEE788 was also investigated. Both, asynchronous and synchronized cell cultures were used to subsequently analyze drug induced cell cycle manipulation. Analysis of cell cycle regulating proteins was done by western blotting.

Results

RAD001 or AEE788 reduced adhesion of RCC cell lines to vascular endothelium and diminished RCC cell binding to immobilized laminin or collagen. Both drugs blocked RCC cell growth, impaired cell cycle progression and altered the expression level of the cell cycle regulating proteins cdk2, cdk4, cyclin D1, cyclin E and p27. The combination of AEE788 and RAD001 resulted in more pronounced RCC growth inhibition, greater rates of G0/G1 cells and lower rates of S-phase cells than either agent alone. Cell cycle proteins were much more strongly altered when both drugs were used in combination than with single drug application. The synergistic effects were observed in an asynchronous cell culture model, but were more pronounced in synchronous RCC cell cultures.

Conclusion

Potent anti-tumoral activitites of the multikinase inhibitors AEE788 or RAD001 have been demonstrated. Most importantly, the simultaneous use of both AEE788 and RAD001 offered a distinct combinatorial benefit and thus may provide a therapeutic advantage over either agent employed as a monotherapy for RCC treatment.
The 14-3-3σ gene promoter is methylated in both human melanocytes and melanoma
Authors: Liu Suhu , Howell Paul , Ren Suping , Fodstad Oystein , Riker Adam I
Published: May 2009

Background

Recent evidence demonstrates that 14-3-3σ acts as a tumor suppressor gene inactivated by methylation of its 5' CpG islands in epithelial tumor cells, while remaining un-methylated in normal human epithelia. The methylation analysis of 14-3-3σ has been largely overlooked in melanoma.

Methods

The methylation status of 14-3-3σ CpG island in melanocytes and melanoma cells was analyzed by methylation-specific sequencing (MSS) and quantitative methylation-specific PCR (Q-MSP). 14-3-3σ mRNA and protein expression in cell lines was detected by real-time RT-PCR and western blot. Melanoma cells were also treated by 5-aza-2'-deoxycytidine (DAC), a demethylating agent, and/or histone deacetylase inhibitor, Trichostatin A (TSA), to evaluate their effects on 14-3-3σ gene expression.

Results

14-3-3σ is hypermethylated in both human melanocytes and most melanoma cells in a lineage-specific manner, resulting in the silencing of 14-3-3σ gene expression and the active induction of 14-3-3σ mRNA and protein expression following treatment with DAC. We also observed a synergistic effect upon gene expression when DAC was combined with TSA. The promoter methylation status of 14-3-3σ was analyzed utilizing Q-MSP in 20 melanoma tissue samples and 10 cell lines derived from these samples, showing that the majority of melanoma samples maintain their hypermethylation status of the 14-3-3σ gene.

Conclusion

14-3-3σ is hypermethylated in human melanoma in a cell-linage specific manner. Spontaneous demethylation and re-expression of 14-3-3σ is a rare event in melanoma, indicating 14-3-3σ might have a tentative role in the pathogenesis of melanoma.
Journeys to tuberculosis treatment: a qualitative study of patients, families and communities in Jogjakarta, Indonesia
Authors: Rintiswati N , Mahendradhata Y , Suharna  , Susilawati  , Purwanta  , Subronto Y , Varkevisser CM , van der Werf MJ
Published: May 2009

Background

Many tuberculosis (TB) patients in Indonesia are diagnosed late. We seek to document patient journeys toward TB diagnosis and treatment and factors that influence health care seeking behavior.

Methods

TB patients in Jogjakarta municipality (urban) and Kulon Progo district (rural) were recruited from health care facilities participating in the DOTS strategy and health care facilities not participating in the DOTS strategy, using purposive sampling methods. Data were collected through in-depth interviews with TB patients and members of their family and through Focus Group Discussions (FGD) with community members.

Results

In total, 67 TB patients and 22 family members were interviewed and 6 FGDs were performed. According to their care seeking behavior patients were categorized into National TB program's (NTP) dream cases (18%), 'slow-but-sure patients' (34%), 'shopaholics' (45%), and the NTP's nightmare case (3%). Care seeking behavior patterns did not seem to be influenced by gender, place of residence and educational level. Factors that influenced care seeking behavior include income and advice from household members or friends. Family members based their recommendation on previous experience and affordability. FGD results suggest that the majority of people in the urban area preferred the hospital or chest clinic for diagnosis and treatment of TB whereas in the rural area private practitioners were preferred. Knowledge about TB treatment being free of charge was better in the urban area. Many community members from the rural area doubted whether TB treatment would be available free of charge.

Conclusion

Most TB patients took over a month to reach a DOTS facility after symptoms appeared and had consulted a number of providers. Their income and advice from household members and friends were factors that influenced their care seeking behavior most.
Treatment with lamivudine versus lamivudine and thymosin alpha-1 for e antigen-positive chronic hepatitis B patients: a meta-analysis
Authors: Zhang Yuan-Yuan , Chen En-Qiang , Yang Jin , Duan Yu-Rong , Tang Hong
Published: May 2009

Background

Currently, there is no evidence on the combination of lamivudine and thymosin alpha-1 on chronic hepatitis B patients. The aim of this study was to compare the effect of lamivudine monotherapy with that of lamivudine and thymosin alpha-1 combination therapy for the treatment of hepatitis B e antigen (HBeAg)-positive hepatitis B patients.

Results

We searched PUBMED (from 1966 onwards), EMBASE (from 1966), CBMdisk (Chinese Biomedical Database, from 1978), CNKI (National Knowledge Infrastructure, from 1980), the Cochrane Central Register of Controlled Trials and the Cochrane Database of Systematic Reviews. Eight trials (583 patients in total) were identified. The lamivudine and thymosin alpha-1 combination treatment was significantly superior to lamivudine treatment in terms of ALT normalization rate (80.2% vs. 68.8%, P = 0.01), virological response rate (84.7% vs. 74.9%, P = 0.002), and HBeAg seroconversion rate (45.1% vs. 15.2%, P < 0.00001).

Conclusion

Among HBeAg-positive patients, thymosin alpha-1 and lamivudine combination therapy may be more effective than lamivudine monotherapy, providing superior rates of biochemical response, virological response, and HBeAg seroconversion.
Maxillofacial trauma patient: coping with the difficult airway
Authors: Krausz Amir A , el-Naaj Imad Abu , Barak Michal
Published: May 2009

Establishing a secure airway in a trauma patient is one of the primary essentials of treatment. Any flaw in airway management may lead to grave morbidity and mortality. Maxillofacial trauma presents a complex problem with regard to the patient's airway. By definition, the injury compromises the patient's airway and it is, therefore, must be protected. In most cases, the patient undergoes surgery for maxillofacial trauma or for other, more severe, life-threatening injuries, and securing the airway is the first step in the introduction of general anaesthesia. In such patients, we anticipate difficult endotracheal intubation and, often, also difficult mask ventilation. In addition, the patient is usually regarded as having a "full stomach" and has not been cleared of a C-spine injury, which may complicate airway management furthermore. The time available to accomplish the task is short and the patient's condition may deteriorate rapidly. Both decision-making and performance are impaired in such circumstances. In this review, we discuss the complexity of the situation and present a treatment approach.
Prospective evaluation of serum biomarker levels and cartilage repair by autologous chondrocyte transplantation and subchondral drilling in a canine model
Authors: Nganvongpanit Korakot , Pothacharoen Peraphan , Chaochird Patama , Klunklin Kasisin , Warrit Kanawee , Settakorn Jongkolnee , Pattamapaspong Nuttaya , Luevitoonvechkij Sirichai , Arpornchayanon Olarn , Kongtawelert Prachya , Pruksakorn Dumnoensun
Published: May 2009

Introduction

The purpose of this study was to evaluate serum chondroitin sulfate (CS) and hyaluronic acid (HA) levels and the capability of cartilage repair of full-thickness cartilage defects after treatment with two different fundamental surgical techniques: autologous chondrocyte transplantation (AC) and subchondral drilling (SD).

Methods

A 4-mm-diameter full-thickness cartilage defect was created in each of 10 skeletally mature male outbred dogs. The dogs were randomly separated into two groups. Groups A and B were treated with AC and SD, respectively. An evaluation was made at the 24th week of the experiment. Serum was analyzed prospectively – preoperatively and at 6-week intervals – for CS and HA levels by enzyme-linked immunosorbent assay (ELISA) and ELISA-based assays, respectively.

Results

The cartilage repair assessment score (median ± standard deviation) of group A (9.5 ± 2.5) was significantly higher than that of group B (2.5 ± 1.3) (P < 0.05). Group A also demonstrated a better quality of hyaline-like cartilage repair. Prospective analysis of serum WF6 and HA levels between the two groups did not show any significant difference. Serum WF6 levels at the 24th week of the experiment had a negative correlation (r = -0.69, P < 0.05) with the cartilage repair assessment score, whereas serum HA levels tended to correlate positively (r = 0.46, 0.1 <P < 0.05).

Conclusions

AC treatment provides superior results to SD treatment, according to morphology, histology, and cartilage marker levels. AC treatment demonstrated a smoother surface, less fissure, better border integration, and a more reliable outcome of repairing cartilage. Moreover, a decreasing level of serum WF6, which correlated with good quality of the repairing tissue at the end of the follow-up period, was found predominantly in the AC group. Serum WF6 therefore should be further explored as a sensitive marker for the noninvasive therapeutic evaluation of cartilage repair procedures.
Prognostic Significance of Tumor Response at the End of Therapy in Group III Rhabdomyosarcoma: A Report From the Children's Oncology Group
Authors: Rodeberg David A. , Stoner Julie A. , Hayes-Jordan Andrea , Kao Simon C. , Wolden Suzanne L. , Qualman Steve J. , Meyer William H. , Hawkins Douglas S.
Published: May 2009

Purpose

Some patients with rhabdomyosarcoma (RMS) achieve less than a complete response (CR) despite receiving all planned therapy. We assessed the impact of best response at the completion of all therapy on patient outcome.

Patients and Methods

We studied 419 clinical group III participants who completed all protocol therapy without developing progressive disease for Intergroup Rhabdomyosarcoma Study (IRS) IV. Response (complete resolution [CR], partial response [PR; ≥ 50% decrease], or no response [NR; < 50% decrease and < 25% increase]) was determined by radiographic measurement and categorized by the best response.

Results

At the end of therapy, 341 participants (81%) achieved a best response of CR and 78 (19%) had a best response of PR/NR. Five-year failure-free survival was similar for participants achieving CR (80%) and PR/NR (78%). After adjustment for age, nodal status, primary site, and histology, there was no significant indication of lower risk of failure (hazard ratio [HR], 0.77; 95% CI, 0.46 to 1.27; P = .3) nor death (HR, 0.63; 95% CI, 0.36 to 1.09; P = .1) for CR versus PR/NR participants. Seventeen participants with a best response of PR/NR had surgical procedures; eight (50%) of 16 with available pathology reports had residual viable tumor and only three achieved a complete resection. Resection of residual masses was not associated with improved outcome.

Conclusion

CR status at the end of protocol therapy in clinical group III participants was not associated with a reduction of disease recurrence and death. Aggressive alternative therapy may not be warranted for RMS patients with a residual mass at the end of planned therapy.
Metastatic Renal Cell Carcinoma: Many Treatment Options, One Patient
Authors: Rini Brian I.
Published: May 2009

There has been a recent expansion of therapeutic options in metastatic renal cell carcinoma (RCC) targeted at the vascular endothelial growth factor and mammalian target of rapamycin pathways, which are fundamental to the biology of RCC. These treatment options have similarities in antitumor effect but also important differences in regards to clinical effects, toxicity and patient populations in which they have been investigated. Further, issues regarding the role of debulking nephrectomy, timing of therapy, and appropriate sequencing of agents have emerged as clinically relevant. There are thus potentially many different treatment approaches to each metastatic RCC patient. This review discusses how to integrate the available data regarding targeted therapy in metastatic RCC into personalized cancer care.
Selective Inhibition of CYP17 With Abiraterone Acetate Is Highly Active in the Treatment of Castration-Resistant Prostate Cancer
Authors: Attard Gerhardt , Reid Alison H.M. , A'Hern Roger , Parker Christopher , Oommen Nikhil Babu , Folkerd Elizabeth , Messiou Christina , Molife L. Rhoda , Maier Gal , Thompson Emilda , Olmos David , Sinha Rajesh , Lee Gloria , Dowsett Mitch , Kaye Stan B. , Dearnaley David , Kheoh Thian , Molina Arturo , de Bono Johann S.
Published: May 2009

Purpose

It has been postulated that castration-resistant prostate cancer (CRPC) commonly remains hormone dependent. Abiraterone acetate is a potent, selective, and orally available inhibitor of CYP17, the key enzyme in androgen and estrogen biosynthesis.

Patients and Methods

This was a phase I/II study of abiraterone acetate in castrate, chemotherapy-naive CRPC patients (n = 54) with phase II expansion at 1,000 mg (n = 42) using a two-stage design to reject the null hypothesis if more than seven patients had a prostate-specific antigen (PSA) decline of ≥ 50% (null hypothesis = 0.1; alternative hypothesis = 0.3; α = .05; β = .14). Computed tomography scans every 12 weeks and circulating tumor cell (CTC) enumeration were performed. Prospective reversal of resistance at progression by adding dexamethasone 0.5 mg/d to suppress adrenocorticotropic hormone and upstream steroids was pursued.

Results

A decline in PSA of ≥ 50% was observed in 28 (67%) of 42 phase II patients, and declines of ≥ 90% were observed in eight (19%) of 42 patients. Independent radiologic evaluation reported partial responses (Response Evaluation Criteria in Solid Tumors) in nine (37.5%) of 24 phase II patients with measurable disease. Decreases in CTC counts were also documented. The median time to PSA progression (TTPP) on abiraterone acetate alone for all phase II patients was 225 days (95% CI, 162 to 287 days). Exploratory analyses were performed on all 54 phase I/II patients; the addition of dexamethasone at disease progression reversed resistance in 33% of patients regardless of prior treatment with dexamethasone, and pretreatment serum androgen and estradiol levels were associated with a probability of ≥ 50% PSA decline and TTPP on abiraterone acetate and dexamethasone.

Conclusion

CYP17 blockade by abiraterone acetate results in declines in PSA and CTC counts and radiologic responses, confirming that CRPC commonly remains hormone driven.
Latent Epstein-Barr Virus Infection of Tumor Cells in Classical Hodgkin's Lymphoma Predicts Adverse Outcome in Older Adult Patients
Authors: Diepstra Arjan , van Imhoff Gustaaf W. , Schaapveld Michael , Karim-Kos Henrike , van den Berg Anke , Vellenga Edo , Poppema Sibrand
Published: May 2009

Purpose

In classical Hodgkin's lymphoma (cHL), the impact of tumor cell Epstein-Barr virus (EBV) status on clinical outcome is controversial.

Patients and Methods

We assessed failure-free survival (FFS) and relative survival (RS) in 412 patients with cHL and age-defined subgroups in a population-based study in the northern Netherlands. Tumor cell EBV status was positive in 34%, and the median follow-up time was 7.1 years. Patients' median age at diagnosis was 35 years (range, 7 to 91 years), and 63% had Ann Arbor stage I or II, 24% had stage III, and 12% had stage IV disease.

Results

EBV status influenced 5-year FFS and RS only in patients from the age group 50 to 74 years. Five-year FFS was 60% in patients with EBV-positive versus 85% in EBV-negative tumors (P = .01). Five-year RS was 69% in patients with EBV-positive versus 82% in EBV-negative tumors (P = .03). After adjusting for histology, HLA class II expression by tumor cells, stage, presence of extranodal localizations and treatment, and the effect of positive EBV tumor status remained significant in FFS multivariate analysis (hazard ratio, 3.11; 95% CI, 1.28 to 7.53; P = .01).

Conclusion

This study indicates that treatment failure in older adult patients with cHL is associated with positive tumor cell EBV status.
Determinants of Medical Care for Young Women with Turner Syndrome
Authors: Devernay Marie , Ecosse Emmanuel , Coste Joël , Carel Jean-Claude
Published: May 2009

Context: Turner syndrome is associated with reduced life expectancy. Lifelong follow-up is strongly recommended, but follow-up during the transition between pediatric and adult care has been little evaluated.

Objective: Our objective was to evaluate the medical follow-up of a population-based cohort of young adult patients.

Design, Setting, and Patients: A questionnaire study was conducted with a national cohort of 568 women, aged 22.6 ± 2.6 yr (range, 18.3–31.2), a mean of 6 yr after stopping GH treatment (StaTur cohort).

Main Outcome Measures: We assessed the proportion of patients with adequate follow-up at seven medical assessments over 4 yr and its determinants.

Results: Most participants were followed by gynecologists or general practitioners. Medical assessments were performed in 16% (audiometry) to 68% (lipid level determinations) of participants, with little consistency in individual patients. Only 20 of 568 patients (3.5%) underwent all assessments in the 4-yr period. Multivariate analysis identified the type of physician as the only factor consistently associated with follow-up, which was more adequate with endocrinologists than with other physicians. Other variables associated with at least one adequate follow-up assessment were paternal socioeconomic class, education level, number of Turner syndrome disease components, size of the medical center following the patient in childhood, and physical health dimensions of Short Form 36 questionnaire.

Conclusions: By contrast with the intensive medical follow-up in childhood, follow-up was grossly inadequate during the transition phase. During this phase, patients should be sent to physicians specializing in Turner syndrome and particular attention should be paid to patients with lower levels of education and from families of low socioeconomic status.

This study finds adherence to recommended follow-up for young adult women with Turner syndrome is incomplete even when there is good access to care.
A novel genetic mechanism regulates dorsolateral hinge-point formation during zebrafish cranial neurulation
Authors: Nyholm Molly K. , Abdelilah-Seyfried Salim , Grinblat Yevgenya
Published: May 2009

During neurulation, vertebrate embryos form a neural tube (NT), the rudiment of the central nervous system. In mammals and birds, a key step in cranial NT morphogenesis is dorsolateral hinge-point (DLHP) bending, which requires an apical actomyosin network. The mechanism of DLHP formation is poorly understood, although several essential genes have been identified, among them Zic2, which encodes a zinc-finger transcription factor. We found that DLHP formation in the zebrafish midbrain also requires actomyosin and Zic function. Given this conservation, we used the zebrafish to study how genes encoding Zic proteins regulate DLHP formation. We demonstrate that the ventral zic2a expression border predicts DLHP position. Using morpholino (MO) knockdown, we show zic2a and zic5 are required for apical F-actin and active myosin II localization and junction integrity. Furthermore, myosin II activity can function upstream of junction integrity during DLHP formation, and canonical Wnt signaling, an activator of zic gene transcription, is necessary for apical active myosin II localization, junction integrity and DLHP formation. We conclude that zic genes act downstream of Wnt signaling to control cytoskeletal organization, and possibly adhesion, during neurulation. This study identifies zic2a and zic5 as crucial players in the genetic network linking patterned gene expression to morphogenetic changes during neurulation, and strengthens the utility of the zebrafish midbrain as a NT morphogenesis model.
MER3 is required for normal meiotic crossover formation, but not for presynaptic alignment in rice
Authors: Wang Kejian , Tang Ding , Wang Mo , Lu Jufei , Yu Hengxiu , Liu Jiafan , Qian Baoxiang , Gong Zhiyun , Wang Xin , Chen Jianmin , Gu Minghong , Cheng Zhukuan
Published: May 2009

MER3, a ZMM protein, is required for the formation of crossovers in Saccharomyces cerevisiae and Arabidopsis. Here, MER3, the first identified ZMM gene in a monocot, is characterized by map-based cloning in rice (Oryza sativa). The null mutation of MER3 results in complete sterility without any vegetative defects. Cytological analyses show that chiasma frequency is reduced dramatically in mer3 mutants and the remaining chiasmata distribute randomly among different pollen mother cells, implying possible coexistence of two kinds of crossover in rice. Immunocytological analyses reveal that MER3 only exists as foci in prophase I meiocytes. In addition, MER3 does not colocalize with PAIR2 at the beginning of prophase I, but locates on one end of PAIR2 fragments at later stages, whereas MER3 foci merely locate on one end of REC8 fragments when signals start to be seen in early prophase I. The normal loading of PAIR2 and REC8 in mer3 implies that their loading is independent of MER3. On the contrary, the absence of MER3 signal in pair2 mutants indicates that PAIR2 is essential for the loading and further function of MER3.
Drug–Drug Interaction Between Clopidogrel and the Proton Pump Inhibitors
Authors: Norgard Nicholas B , Mathews Kathryn D , Wall Geoffrey C
Published: May 2009

Objective:

To evaluate the interaction between clopidogrel and proton pump inhibitors (PPIs).

Data Sources:

Literature retrieval was accessed through PubMed (1980–January 2009), abstracts from 2008 American Heart Association and 2009 Society of Cardiovascular Angiography and Interventions Scientific Sessions, and media press releases using the terms clopidogrel, proton pump inhibitors, cytochrome 2C19, genetic cytochrome P450 polymorphisms, and drug interaction. In addition, reference citations from publications identified in the search were reviewed.

Study Selection and Data Extraction:

Relevant original research articles and review articles were evaluated. Articles were selected if they were published in English and focused on any of the key words or appeared to have substantial content addressing the drug interaction.

Data Synthesis:

Recent attention has been placed on a potential interaction observed between clopidogrel and the widely used PPIs. Preliminary evidence suggests that omeprazole interacts with clopidogrel, reducing clopidogrel's antiplatelet effects as measured by various laboratory tests. Most data indicate that the interaction involves the competitive inhibition of the CYP2C19 isoenzyme. The interaction appears to be clinically significant, as several retrospective analyses have shown an increase in adverse cardiovascular outcomes when PPIs and clopidogrel are used concomitantly. However, this may not be a class effect.

Conclusions:

Available data suggest that omeprazole is the PPI most likely to have a significant interaction with clopidogrel. Further studies are needed to determine that an interaction between the other PPIs and clopidogrel does not exist. In situations in which both clopidogrel and a PPI are indicated, pantoprazole should be used since it is the PPI least likely to interact with clopidogrel.
Design of a Robot and Test Procedure for the Dynamic Testing of Anchorages in a Geotechnical Centrifuge
Authors: Hao J. , Neilson R. D. , Ivanović A. , Li J. , Starkey A. J. , Rodger A. A. , Davies M. C. R.
Published: May 2009

The design of a novel robot for the dynamic testing of ground anchorages in a geotechnical centrifuge is presented. The structure tested comprises nine pretensioned anchorages in a 3×3 array, installed in dry sand, supporting a retaining wall. The anchorages are partially threaded and have washers and nuts installed so that the amount of load can be varied by tightening the nuts against the wall. The purpose of the robot is to move to the head of anchorage during operation of the centrifuge, locate onto the nut, rotate it by a prescribed amount to change the load, disengage from the nut, and then apply an impulse to the end of the length of anchorage protruding from the wall. The resulting vibration response is measured by an accelerometer and captured by a data acquisition system for processing to investigate the effect of load on the dynamic response of the anchorage. The robot has four degrees of freedom, three linear motions, and one rotation and includes a solenoid operated impulse-generating device. The design specification and detailed structure of the robot are presented along with commissioning tests to prove the effectiveness of the system before deployment on an extensive test program.
Relationship among Brain and Blood Glucose Levels and Spontaneous and Glucoprivic Feeding
Authors: Dunn-Meynell Ambrose A. , Sanders Nicole M. , Compton Douglas , Becker Thomas C. , Eiki Jun-ichi , Zhang Bei B. , Levin Barry E.
Published: May 2009

Although several studies implicate small declines in blood glucose levels as stimulus for spontaneous meal initiation, no mechanism is known for how these dips might initiate feeding. To assess the role of ventromedial hypothalamus (VMH) (arcuate plus ventromedial nucleus) glucosensing neurons as potential mediators of spontaneous and glucoprivic feeding, meal patterns were observed, and blood and VMH microdialysis fluid were sampled in 15 rats every 10 min for 3.5 h after dark onset and 2 h after insulin (5 U/kg, i.v.) infusion. Blood glucose levels declined by 11% beginning ∼5 min before 65% of all spontaneous meals, with no fall in VMH levels. After insulin, blood and VMH glucose reached nadirs by 30–40 min, and the same rats ate 60% faster and spent 84% more time eating during the ensuing hypoglycemia. Although 83% of first hypoglycemic meals were preceded by 5 min dips in VMH (but not blood) glucose levels, neither blood nor VMH levels declined before second meals, suggesting that low glucose, rather than changing levels, was the stimulus for glucoprivic meals. Furthermore, altering VMH glucosensing by raising or lowering glucokinase (GK) activity failed to affect spontaneous feeding, body or adipose weights, or glucose tolerance. However, chronic depletion by 26–70% of VMH GK mRNA reduced glucoprivic feeding. Thus, although VMH glucosensing does not appear to be involved in either spontaneous feeding or long-term body-weight regulation, it does participate in glucoprivic feeding, similar to its role in the counter-regulatory neurohumoral responses to glucoprivation.
Hippocampal Place Cell Firing Patterns Can Induce Long-Term Synaptic PlasticityIn Vitro
Authors: Isaac John T. R. , Buchanan Katherine A. , Muller Robert U. , Mellor Jack R.
Published: May 2009

In the hippocampus, synaptic strength between pyramidal cells is modifiable by NMDA receptor (NMDAR)-dependent long-term potentiation (LTP) and long-term depression (LTD), both of which require coincident presynaptic and postsynaptic activity.In vivo, many pyramidal cells exhibit location-specific activity patterns and are known as “place cells.” The combination of these factors suggests that synaptic plasticity will be induced at synapses connecting place cells with overlapping firing fields, because such cells fire coincidentally when the rat is in a specific part of the environment. However, this prediction, which is important for models of how long-term synaptic plasticity can be used to encode space in the hippocampal network, has not been tested. To investigate this, action potential time series recorded simultaneously from place cells in freely moving rats were replayed concurrently into postsynaptic CA1 pyramidal cells and presynaptic inputs during perforated patch-clamp recordings from adult hippocampal slices. Place cell firing patterns induced large, pathway-specific, NMDAR-dependent LTP that was rapidly expressed within a few minutes. However, place-cell LTP was induced only if the two place cells had overlapping firing fields and if the cholinergic tone present in the hippocampus during exploration was restored by bath application of the cholinergic agonist carbachol. LTD was never observed in response to place cell firing patterns. Our findings demonstrate that spike patterns from hippocampal place cells can robustly induce NMDAR-dependent LTP, providing important evidence in support of a model in which spatial distance is encoded as the strength of synaptic connections between place cells.
HumanAPOEIsoform-Dependent Effects on Brain β-Amyloid Levels in PDAPP Transgenic Mice
Authors: Bales Kelly R. , Liu Feng , Wu Su , Lin Suizhen , Koger Deanna , DeLong Cynthia , Hansen Jeffrey C. , Sullivan Patrick M. , Paul Steven M.
Published: May 2009

To investigate the role of human apolipoprotein E (apoE) on Aβ depositionin vivo, we crossed PDAPP mice lacking mouseApoeto targeted replacement mice expressing human apoE (PDAPP/TRE2, PDAPP/TRE3, or PDAPP/TRE4). We then measured the levels of apoE protein and Aβ peptides in plasma, CSF, and brain homogenates in these mice at different ages. We also quantified the amount of brain Aβ and amyloid burden in 18-month-old mice. In young PDAPP/TRE4 mice that were analyzed at an age before brain Aβ deposition, we observed a significant decrease in the levels of apoE in CSF and brain when compared with age-matched mice expressing either human E2 or E3. The brain levels of Aβ42 in PDAPP/TRE4 mice were substantially elevated even at this very early time point. In older PDAPP/TRE4 mice, the levels of insoluble apoE protein increased in parallel to the dramatic rise in brain Aβ burden, and the majority of apoE was associated with Aβ. In TRE4 only mice, we also observed a significant decrease in the level of apoE in brain homogenates. Since the relative level of apoE mRNA was equivalent in PDAPP/TRE and TRE only mice, it appears that post-translational mechanisms influence the levels of apoE protein in brain (E4 < E3 ≪ E2), resulting in early and dramatic apoE isoform-dependent effects on brain Aβ levels (E4 ≫ E3 > E2) that increase with age. Therapeutic strategies aimed at increasing the soluble levels of apoE protein, regardless of isoform, may effectively prevent and (or) treat Alzheimer's disease.
TMEM16B, A Novel Protein with Calcium-Dependent Chloride Channel Activity, Associates with a Presynaptic Protein Complex in Photoreceptor Terminals
Authors: Stöhr Heidi , Heisig Julia B. , Benz Peter M. , Schöberl Simon , Milenkovic Vladimir M. , Strauss Olaf , Aartsen Wendy M. , Wijnholds Jan , Weber Bernhard H. F. , Schulz Heidi L.
Published: May 2009

Photoreceptor ribbon synapses release glutamate in response to graded changes in membrane potential evoked by vast, logarithmically scalable light intensities. Neurotransmitter release is modulated by intracellular calcium levels. Large Ca2+-dependent chloride currents are important regulators of synaptic transmission from photoreceptors to second-order neurons; the molecular basis underlying these currents is unclear. We cloned human and mouseTMEM16B, a member of the TMEM16 family of transmembrane proteins, and show that it is abundantly present in the photoreceptor synaptic terminals in mouse retina. TMEM16B colocalizes with adaptor proteins PSD95, VELI3, and MPP4 at the ribbon synapses and contains a consensus PDZ class I binding motif capable of interacting with PDZ domains of PSD95. Furthermore, TMEM16B is lost from photoreceptor membranes of MPP4-deficient mice. This suggests that TMEM16B is a novel component of a presynaptic protein complex recruited to specialized plasma membrane domains of photoreceptors. TMEM16B confers Ca2+-dependent chloride currents when overexpressed in mammalian cells as measured by halide sensitive fluorescent protein assays and whole-cell patch-clamp recordings. The compartmentalized localization and the electrophysiological properties suggest TMEM16B to be a strong candidate for the long sought-after Ca2+-dependent chloride channel in the photoreceptor synapse.
Realignment of Interaural Cortical Maps in Asymmetric Hearing Loss
Authors: Cheung Steven W. , Bonham Ben H. , Schreiner Christoph E. , Godey Benoit , Copenhaver David A.
Published: May 2009

Misalignment of interaural cortical response maps in asymmetric hearing loss evolves from initial gross divergence to near convergence over a 6 month recovery period. The evolution of left primary auditory cortex (AI) interaural frequency map changes is chronicled in squirrel monkeys with asymmetric hearing loss induced by overstimulating the right ear with a 1 kHz tone at 136 dB for 3 h. AI frequency response areas (FRAs), derived from tone bursts presented to the poorer or better hearing ears, are compared at 6, 12, and 24 weeks after acoustic overstimulation. Characteristic frequency (CF) and minimum threshold parameters are extracted from FRAs, and they are used to quantify interaural response map differences. A large interaural CF map misalignment of ΔCF ∼1.27 octaves at 6 weeks after overstimulation decreases substantially to ΔCF ∼0.62 octave at 24 weeks. Interaural cortical threshold map misalignment faithfully reflects peripheral asymmetric hearing loss at 6 and 12 weeks. However, AI threshold map misalignment essentially disappears at 24 weeks, primarily because ipsilateral cortical thresholds have become unexpectedly elevated relative to peripheral thresholds. The findings document that plastic change in central processing of sound stimuli arriving from the nominally better hearing ear may account for progressive realignment of both interaural frequency and threshold maps.