Characterization of a reference material for BCR-ABL (M-BCR) mRNA quantitation by real-time amplification assays:towards new standards for gene expression measurements

Monitoring of BCR-ABL transcripts has become established practice in the management of chronic myeloid leukemia. However, nucleic acid amplification techniques are prone to variations which limit the reliability of real-time quantitative PCR (RQ-PCR) for clinical decision making, highlighting the need for standardization of assays and reporting of minimal residual disease (MRD) data. We evaluated a lyophilized preparation of a leukemic cell line (K562) as a potential quality control reagent. This was found to be relatively stable, yielding comparable respective levels of ABL, GUS and BCR-ABL transcripts as determined by RQ-PCR before and after accelerated degradation experiments as well as following 5 years storage at -20 degrees C. Vials of freeze-dried cells were sent at ambient temperature to 22 laboratories on four continents, with RQ-PCR analyses detecting BCR-ABL transcripts at levels comparable to those observed in primary patient samples. Our results suggest that freeze-dried cells can be used as quality control reagents with a range of analytical instrumentations and could enable the development of urgently needed international standards simulating clinically relevant levels of MRD.

Interleukin-8 is associated with proliferation, migration, angiogenesis and chemosensitivity in vitro and in vivo in colon cancer cell line models

Interleukin-8 (IL-8), a chemokine with a defining CXC amino acid motif, is known to possess tumorigenic and proangiogenic properties. Overexpression of IL-8 has been detected in many human tumors, including colorectal cancer (CRC), and is associated with poor prognosis. The goal of our study was to determine the role of IL-8 overexpression in CRC cells in vitro and in vivo. We stably transfected the IL-8 cDNA into two human colon cancer cell lines, HCT116 and Caco2, and selected IL-8-secreting transfectants. Real-time RT-PCR confirmed that IL-8 mRNA was overexpressed in IL-8 transfectants with 45- to 85-fold higher than parental cells. The IL-8-transfected clones secreted 19- to 28-fold more IL-8 protein than control and parental cells as detected by ELISA. The IL-8 transfectants demonstrated increased cellular proliferation, cell migration and invasion based on functional assays. Growth inhibition studies showed that IL-8 overexpression lead to a significant resistance to oxaliplatin (p < 0.0001). Inhibition of IL-8 overexpression with small interfering RNA reversed the observed increases in tumorigenic functions and oxaliplatin resistance, suggesting that IL-8 not only provides a proliferative advantage but also promotes the metastatic potential of colon cancer cells. Using a tumor xenograft model, IL-8-expressing cells formed significantly larger tumors than the control cells with increased microvessel density. Together, these findings indicate that overexpression of IL-8 promotes tumor growth, metastasis, chemoresistance and angiogenesis, implying IL-8 to be an important therapeutic target in CRC.

Selecting the best targeted agent in first-line treatment of unresectable liver metastases from colorectal cancer:does the bench have the answers?

For physicians facing patients with organ-limited metastases from colorectal cancer, tumor shrinkage and sterilization of micrometastatic disease is the main goal, giving the opportunity for secondary surgical resection. At the same time, for the majority of patients who will not achieve a sufficient tumor response, disease control remains the predominant objective. Since FOLFOX or FOLFIRI have similar efficacies, the challenge is to define which could be the most effective targeted agent (anti-EGFR or anti-VEGF) to reach these goals. Therefore, a priori molecular identification of patients that could benefit from anti-EGFR or anti-VEGF monoclonal antibodies (i.e. the currently approved targeted therapies for metastatic colorectal cancer) is of critical importance. In this setting, the KRAS mutation status was the first identified predictive marker of response to anti-EGFR therapy. Since it has been demonstrated that tumors with KRAS mutation do not respond to anti-EGFR therapy, KRAS status must be determined prior to treatment. Thus, for KRAS wild-type patients, the choices that remain are either anti-VEGF or anti-EGFR. In this review, we present the most updated data from translational research programs dealing with the identification of biomarkers for response to targeted therapies.

WHIRLBOB, the Whirlpool Based Variant of STRIBOB: Lighter, Faster, and Constant Time

WHIRLBOB, also known as STRIBOBr2, is an AEAD (Authenticated Encryption with Associated Data) algorithm derived from STRIBOBr1 and the Whirlpool hash algorithm. WHIRLBOB/STRIBOBr2 is a second round candidate in the CAESAR competition. As with STRIBOBr1, the reduced-size Sponge design has a strong provable security link with a standardized hash algorithm. The new design utilizes only the LPS or ρ component of Whirlpool in flexibly domain-separated BLNK Sponge mode. The number of rounds is increased from 10 to 12 as a countermeasure against Rebound Distinguishing attacks. The 8 ×8 - bit S-Box used by Whirlpool and WHIRLBOB is constructed from 4 ×4 - bit “MiniBoxes”. We report on fast constant-time Intel SSSE3 and ARM NEON SIMD WHIRLBOB implementations that keep full miniboxes in registers and access them via SIMD shuffles. This is an efficient countermeasure against AES-style cache timing side-channel attacks. Another main advantage of WHIRLBOB over STRIBOBr1 (and most other AEADs) is its greatly reduced implementation footprint on lightweight platforms. On many lower-end microcontrollers the total software footprint of π+BLNK = WHIRLBOB AEAD is less than half a kilobyte. We also report an FPGA implementation that requires 4,946 logic units for a single round of WHIRLBOB, which compares favorably to 7,972 required for Keccak / Keyak on the same target platform. The relatively small S-Box gate count also enables efficient 64-bit bitsliced straight-line implementations. We finally present some discussion and analysis on the relationships between WHIRLBOB, Whirlpool, the Russian GOST Streebog hash, and the recent draft Russian Encryption Standard Kuznyechik.

Analysis of the early-time optical spectra of SN 2011fe in M101

The nearby Type Ia supernova SN 2011fe in M101 (cz=241 km s^-1) provides a unique opportunity to study the early evolution of a "normal" Type Ia supernova, its compositional structure, and its elusive progenitor system. We present 18 high signal-to-noise spectra of SN 2011fe during its first month beginning 1.2 days post-explosion and with an average cadence of 1.8 days. This gives a clear picture of how various line-forming species are distributed within the outer layers of the ejecta, including that of unburned material (C+O). We follow the evolution of C II absorption features until they diminish near maximum light, showing overlapping regions of burned and unburned material between ejection velocities of 10,000 and 16,000 km s^-1. This supports the notion that incomplete burning, in addition to progenitor scenarios, is a relevant source of spectroscopic diversity among SNe Ia. The observed evolution of the highly Doppler-shifted O I 7774 absorption features detected within five days post-explosion indicate the presence of O I with expansion velocities from 11,500 to 21,000 km s^-1. The fact that some O I is present above C II suggests that SN 2011fe may have had an appreciable amount of unburned oxygen within the outer layers of the ejecta.

Addition of docetaxel, zoledronic acid, or both to first-line long-term hormone therapy in prostate cancer (STAMPEDE): survival results from an adaptive, multiarm, multistage, platform randomised controlled trial

BACKGROUND: Long-term hormone therapy has been the standard of care for advanced prostate cancer since the 1940s. STAMPEDE is a randomised controlled trial using a multiarm, multistage platform design. It recruits men with high-risk, locally advanced, metastatic or recurrent prostate cancer who are starting first-line long-term hormone therapy. We report primary survival results for three research comparisons testing the addition of zoledronic acid, docetaxel, or their combination to standard of care versus standard of care alone.

METHODS: Standard of care was hormone therapy for at least 2 years; radiotherapy was encouraged for men with N0M0 disease to November, 2011, then mandated; radiotherapy was optional for men with node-positive non-metastatic (N+M0) disease. Stratified randomisation (via minimisation) allocated men 2:1:1:1 to standard of care only (SOC-only; control), standard of care plus zoledronic acid (SOC + ZA), standard of care plus docetaxel (SOC + Doc), or standard of care with both zoledronic acid and docetaxel (SOC + ZA + Doc). Zoledronic acid (4 mg) was given for six 3-weekly cycles, then 4-weekly until 2 years, and docetaxel (75 mg/m(2)) for six 3-weekly cycles with prednisolone 10 mg daily. There was no blinding to treatment allocation. The primary outcome measure was overall survival. Pairwise comparisons of research versus control had 90% power at 2·5% one-sided α for hazard ratio (HR) 0·75, requiring roughly 400 control arm deaths. Statistical analyses were undertaken with standard log-rank-type methods for time-to-event data, with hazard ratios (HRs) and 95% CIs derived from adjusted Cox models. This trial is registered at ClinicalTrials.gov (NCT00268476) and ControlledTrials.com (ISRCTN78818544).

FINDINGS: 2962 men were randomly assigned to four groups between Oct 5, 2005, and March 31, 2013. Median age was 65 years (IQR 60-71). 1817 (61%) men had M+ disease, 448 (15%) had N+/X M0, and 697 (24%) had N0M0. 165 (6%) men were previously treated with local therapy, and median prostate-specific antigen was 65 ng/mL (IQR 23-184). Median follow-up was 43 months (IQR 30-60). There were 415 deaths in the control group (347 [84%] prostate cancer). Median overall survival was 71 months (IQR 32 to not reached) for SOC-only, not reached (32 to not reached) for SOC + ZA (HR 0·94, 95% CI 0·79-1·11; p=0·450), 81 months (41 to not reached) for SOC + Doc (0·78, 0·66-0·93; p=0·006), and 76 months (39 to not reached) for SOC + ZA + Doc (0·82, 0·69-0·97; p=0·022). There was no evidence of heterogeneity in treatment effect (for any of the treatments) across prespecified subsets. Grade 3-5 adverse events were reported for 399 (32%) patients receiving SOC, 197 (32%) receiving SOC + ZA, 288 (52%) receiving SOC + Doc, and 269 (52%) receiving SOC + ZA + Doc.

INTERPRETATION: Zoledronic acid showed no evidence of survival improvement and should not be part of standard of care for this population. Docetaxel chemotherapy, given at the time of long-term hormone therapy initiation, showed evidence of improved survival accompanied by an increase in adverse events. Docetaxel treatment should become part of standard of care for adequately fit men commencing long-term hormone therapy.

FUNDING: Cancer Research UK, Medical Research Council, Novartis, Sanofi-Aventis, Pfizer, Janssen, Astellas, NIHR Clinical Research Network, Swiss Group for Clinical Cancer Research.

Non-equilibrium modeling of the FE XVII 3C/3D Line Ratio in an Intense X-ray Free-electron Laser Excited Plasma

Recent measurements using an X-ray Free Electron Laser (XFEL) and an Electron Beam Ion Trap at the Linac Coherent Light Source facility highlighted large discrepancies between the observed and theoretical values for the Fe XVII 3C/3D line intensity ratio. This result raised the question of whether the theoretical oscillator strengths may be significantly in error, due to insufficiencies in the atomic structure calculations. We present time-dependent spectral modeling of this experiment and show that non-equilibrium effects can dramatically reduce the predicted 3C/3D line intensity ratio, compared with that obtained by simply taking the ratio of oscillator strengths. Once these non-equilibrium effects are accounted for, the measured line intensity ratio can be used to determine a revised value for the 3C/3D oscillator strength ratio, giving a range from 3.0 to 3.5. We also provide a framework to narrow this range further, if more precise information about the pulse parameters can be determined. We discuss the implications of the new results for the use of Fe XVII spectral features as astrophysical diagnostics and investigate the importance of time-dependent effects in interpreting XFEL-excited plasmas.

Implementation of a new atomic basis for the He i equilibrium line ratio technique for electron temperature and density diagnostic in the SOL for H-mode plasmas in DIII-D

Evaluating the ratio of selected helium lines allows for measurement of electron densities and temperatures. This technique is applied for L-mode plasmas at TEXTOR (O. Schmitz et al., Plasma Phys. Control. Fusion 50 (2008) 115004). We report our first efforts to extend it to H-mode plasma diagnostics in DIII-D. This technique depends on the accuracy of the atomic data used in the collisional radiative model (CRM). We present predictions for the electron temperatures and densities by using recently calculated R-Matrix With Pseudostates (RMPS) and Convergent Close-Coupling (CCC) electron-impact excitation and ionization data. We include contributions from higher Rydberg states by means of the projection matrix. These effects become significant for high electron density conditions, which are typical in H-mode. We apply a non-equilibrium model for the time propagation of the ionization balance to predict line emission profiles from experimental H-mode data from DIII-D. © 2010 Elsevier B.V. All rights reserved.

A Fast Analysis Method for the Groove Gap Waveguide Using Transmission Line Theory

The Groove Gap Waveguide (GGW) shows a behavior similar to the classical rectangular waveguide (RWG), but it is formed by two pieces which do not require metal contact. This feature suggests the GGW as a suitable alternative to the RGW for mm-wave frequencies, where ensuring the proper metal contact according to the wavelength size results challenging. Nevertheless, there is a lack of effective analysis tools for the complex GGW topology, and assuming a direct equivalence between the RGW and the GGW is too rough, so that dilatory full-wave simulations are required. This work presents a fast analysis method based on transmission line theory, which establishes the proper correspondence between the GGW and the RWG. In addition, below cutoff behavior of the GGW is studied for the first time. Several numerical tests and two manufactured prototypes validate the proposed method, which seems very adequate to optimize future GGW structures.

The VLT-FLAMES Tarantula survey: XX. The nature of the X-ray bright emission-line star VFTS 399

Context: The stellar population of the 30 Doradus star-forming region in the Large Magellanic Cloud contains a subset of apparently single, rapidly rotating O-type stars. The physical processes leading to the formation of this cohort are currently uncertain. 

Aims: One member of this group, the late O-type star VFTS 399, is found to be unexpectedly X-ray bright for its bolometric luminosity-in this study we aim to determine its physical nature and the cause of this behaviour. 

Methods: To accomplish this we performed a time-resolved analysis of optical, infrared and X-ray observations. 

Results: We found VFTS 399 to be an aperiodic photometric variable with an apparent near-IR excess. Its optical spectrum demonstrates complex emission profiles in the lower Balmer series and select He i lines-taken together these suggest an OeBe classification. The highly variable X-ray luminosity is too great to be produced by a single star, while the hard, non-thermal nature suggests the presence of an accreting relativistic companion. Finally, the detection of periodic modulation of the X-ray lightcurve is most naturally explained under the assumption that the accretor is a neutron star. 

Conclusions: VFTS 399 appears to be the first high-mass X-ray binary identified within 30 Dor, sharing many observational characteristics with classical Be X-ray binaries. Comparison of the current properties of VFTS 399 to binary-evolution models suggests a progenitor mass 25 M_⊙ for the putative neutron star, which may host a magnetic field comparable in strength to those of magnetars. VFTS 399 is now the second member of the cohort of rapidly rotating "single" O-type stars in 30 Dor to show evidence of binary interaction resulting in spin-up, suggesting that this may be a viable evolutionary pathway for the formation of a subset of this stellar population.

Searching for swept-up hydrogen and helium in the late-time spectra of 11 nearby Type Ia supernovae

The direct detection of a stellar system that explodes as a Type Ia supernova (SN Ia) has not yet been successful. Various indirect methods have been used to investigate SN Ia progenitor systems but none have produced conclusive results. A prediction of single-degenerate models is that H- (or He-) rich material from the envelope of the companion star should be swept up by the SN ejecta in the explosion. Seven SNe Ia have been analysed to date looking for signs of H-rich material in their late-time spectra and none were detected. We present results from new late-time spectra of 11 SNe Ia obtained at the Very Large Telescope using XShooter and FORS2. We present the tentative detection of Hα emission for SN 2013ct, corresponding to ∼0.007 M_⊙ of stripped/ablated companion star material (under the assumptions of the spectral modelling). This mass is significantly lower than expected for single-degenerate scenarios, suggesting that >0.1 M_⊙ of H-rich is present but not observed. We do not detect Hα emission in the other 10 SNe Ia. This brings the total sample of normal SNe Ia with non-detections (<0.001–0.058 M_⊙) of H-rich material to 17 events. The simplest explanation for these non-detections is that these objects did not result from the explosion of a CO white dwarf accreting matter from a H-rich companion star via Roche lobe overflow or symbiotic channels. However, further spectral modelling is needed to confirm this. We also find no evidence of He-emission features, but models with He-rich companion stars are not available to place mass limits.

Time-dependent Suppression of Oscillatory Power in Evolving Solar Magnetic Fields

Oscillation amplitudes are generally smaller within magnetically active regions like sunspots and plage when compared to their surroundings. Such magnetic features, when viewed in spatially resolved power maps, appear as regions of suppressed power due to reductions in the oscillation amplitudes. Employing high spatial- and temporal-resolution observations from the Dunn Solar Telescope (DST) in New Mexico, we study the power suppression in a region of evolving magnetic fields adjacent to a pore. By utilizing wavelet analysis, we study for the first time how the oscillatory properties in this region change as the magnetic field evolves with time. Image sequences taken in the blue continuum, G-band, Ca ii K, and Hα filters were used in this study. It is observed that the suppression found in the chromosphere occupies a relatively larger area, confirming previous findings. Also, the suppression is extended to structures directly connected to the magnetic region, and is found to get enhanced as the magnetic field strength increased with time. The dependence of the suppression on the magnetic field strength is greater at longer periods and higher formation heights. Furthermore, the dominant periodicity in the chromosphere was found to be anti-correlated with increases in the magnetic field strength.

A Phase II Biomarker-Embedded Study of Lapatinib plus Capecitabine as First-line Therapy in Patients with Advanced or Metastatic Gastric Cancer

An exploratory phase II biomarker-embedded trial (LPT109747; NCT00526669) designed to determine the association of lapatinib-induced fluoropyrimidine gene changes with efficacy of lapatinib plus capecitabine as first-line treatment for advanced gastric cancer or gastroesophageal junction adenocarcinoma independent of tumor HER2 status. Tumor biopsies obtained before and after 7-day lapatinib (1,250 mg) to analyze changes in gene expression, followed by a 14-day course of capecitabine (1,000 mg/m(2) twice daily, 14/21 days) plus lapatinib 1,250 mg daily. Blood samples were acquired for pharmacokinetic analysis. Primary clinical objectives were response rate (RR) and 5-month progression-free survival (PFS). Secondary objectives were overall survival (OS), PFS, time to response, duration of response, toxicity, and identification of associations between lapatinib pharmacokinetics and biomarker endpoints. Primary biomarker objectives were modulation of 5-FU-pathway genes by lapatinib, effects of germline SNPs on treatment outcome, and trough steady-state plasma lapatinib concentrations. Sixty-eight patients were enrolled; (75% gastric cancer, 25% gastroesophageal junction). Twelve patients (17.9%) had confirmed partial response, 31 (46.3%) had stable disease, and 16 (23.9%) had progressive disease. Median PFS and OS were 3.3 and 6.3 months, respectively. Frequent adverse events included diarrhea (45%), decreased appetite (39%), nausea (36%), and fatigue (36%). Lapatinib induced no changes in gene expression from baseline and no significant associations were found for SNPs analyzed. Elevated baseline HER3 mRNA expression was associated with a higher RR (33% vs. 0%; P = 0.008). Lapatinib plus capecitabine was well tolerated, demonstrating modest antitumor activity in patients with advanced gastric cancer. The association of elevated HER3 and RR warrants further investigation as an important player for HER-targeted regimens in combination with capecitabine