Prediction of outcome in breast cancer patients using gene expression profiling

Breast cancer, the most common cancer diagnosed in women, is a complex and heterogeneous disease. In order to make the best treatment decision for a breast cancer patient, it is important to accurately determine that patient's risk of recurrence and the therapy to which that patient's tumor is most likely to respond. The prognostic and/or predictive factors currently accepted for use in primary breast cancer decision making (i.e. lymph node status, tumor size, nuclear grade, etc.) are not enough to accurately identify those patients who may require therapy and gives little information about what therapy they might best benefit from. Recent discoveries using gene expression profiling have greatly improved our understanding of the molecular pathogenesis of breast cancer. We believe that gene expression profiling may also improve the prognostication and/or prediction of breast cancer outcomes, and thus, the main objective of this work has been to develop and test gene expression-based predictors of outcome in breast cancer patients. First, we developed an expression-based predictor of outcome for Estrogen Receptor (ER) and/or Progesterone Receptor (PR)-positive breast cancer patients using biological differences among these tumors. Second, we developed a predictor for objectively classifying tumors into one of five intrinsic subtypes and validated this using multiple test sets. Next, using a single patient dataset, we determined the concordance in outcome predictions made by several different gene expression profiles (developed on different platforms by different laboratories). Lastly, we developed gene expression-based predictors for response to neoadjuvant chemotherapy. In summary, this work shows that gene expression profiling holds great promise in being clinically useful in the treatment decision-making process for breast cancer patients

Ultra-broadband wavelength-swept Tm-doped fiber laser using wavelength-combined gain stages

A wavelength-swept thulium-doped fiber laser system employing two parallel cavities with two different fiber gain stages is reported. The fiber gain stages were tailored to provide emission in complementary bands with external wavelength-dependent feedback cavities sharing a common rotating polygon mirror for wavelength scanning. The wavelength-swept laser outputs from the fiber gain elements were spectrally combined by means of a dichroic mirror and yielded over 500 mW of output with a scanning range from ~1740 nm to ~2070 nm for a scanning frequency of ~340 Hz

Wavelength-swept Tm-doped fiber laser operating in the two-micron wavelength band

A wavelength-swept thulium-doped silica fiber laser using an intracavity rotating slotted-disk wavelength scanning filter in combination with an intracavity solid etalon for passive control of temporal and spectral profiles is reported. The laser yielded a wavelength swept output in a step-wise fashion with each laser pulse separated from the previous pulse by a frequency interval equal to the free-spectral-range of the etalon and with an instantaneous linewidth of <0.05 nm. Scanning ranges from 1905 nm to 2049 nm for a cladding-pumping laser configuration, and from 1768 nm to 1956 nm for a core-pumping laser configuration were achieved at average output powers up to ~1 W

A Hard Look at NGC 5347: Revealing a Nearby Compton-thick AGN

Current measurements show that the observed fraction of Compton-thick (CT) active galactic nuclei (AGN) is smaller than the expected values needed to explain the cosmic X-ray background. Prior fits to the X-ray spectrum of the nearby Seyfert-2 galaxy NGC 5347 (z = 0.00792, D = 35.5 Mpc ) have alternately suggested a CT and Compton-thin source. Combining archival data from Suzaku, Chandra, and—most importantly—new data from NuSTAR, ... See full text for complete abstrac

An experimental observation of geometric phases for mixed states using NMR interferometry

Examples of geometric phases abound in many areas of physics. They offer both fundamental insights into many physical phenomena and lead to interesting practical implementations. One of them, as indicated recently, might be an inherently fault-tolerant quantum computation. This, however, requires to deal with geometric phases in the presence of noise and interactions between different physical subsystems. Despite the wealth of literature on the subject of geometric phases very little is known about this very important case. Here we report the first experimental study of geometric phases for mixed quantum states. We show how different they are from the well understood, noiseless, pure-state case.Comment: 4 pages, 3 figure

Direct and Simultaneous Observation of Ultrafast Electron and Hole Dynamics in Germanium

Understanding excited carrier dynamics in semiconductors is crucial for the development of photovoltaics and efficient photonic devices. However, overlapping spectral features in optical/NIR pump-probe spectroscopy often render assignments of separate electron and hole carrier dynamics ambiguous. Here, ultrafast electron and hole dynamics in germanium nanocrystalline thin films are directly and simultaneously observed by attosecond transient absorption spectroscopy (ATAS) in the extreme ultraviolet at the germanium M_{4,5}-edge (~30 eV). We decompose the ATAS spectra into contributions of electronic state blocking and photo-induced band shifts at a carrier density of 8*10^{20}cm^{-3}. Separate electron and hole relaxation times are observed as a function of hot carrier energies. A first order electron and hole decay of ~1 ps suggests a Shockley-Read-Hall recombination mechanism. The simultaneous observation of electrons and holes with ATAS paves the way for investigating few to sub-femtosecond dynamics of both holes and electrons in complex semiconductor materials and across junctions.Comment: Includes Supplementary Informatio

Effective Temperatures of Low-Mass Stars from High-Resolution H-band Spectroscopy

High-resolution, near-infrared spectra will be the primary tool for finding and characterizing Earth-like planets around low-mass stars. Yet, the properties of exoplanets can not be precisely determined without accurate and precise measurements of the host star. Spectra obtained with the Immersion GRating INfrared Spectrometer (IGRINS) simultaneously provide diagnostics for most stellar parameters, but the first step in any analysis is the determination of the effective temperature. Here we report the calibration of high-resolution H-band spectra to accurately determine effective temperature for stars between 4000-3000 K ($\sim$K8--M5) using absorption line depths of Fe I, OH, and Al I. The field star sample used here contains 254 K and M stars with temperatures derived using BT-Settl synthetic spectra. We use 106 stars with precise temperatures in the literature to calibrate our method with typical errors of about 140 K, and systematic uncertainties less than $\sim$120 K. For the broadest applicability, we present T$_{\rm eff}$--line-depth-ratio relationships, which we test on 12 members of the TW Hydrae Association and at spectral resolving powers between $\sim$10,000--120,000. These ratios offer a simple but accurate measure of effective temperature in cool stars that is distance and reddening independent.Comment: 19 pages, 11 figures and 3 tables. Accepted in Ap

Asymptomatic stenosis in the cervical and thoracic spines of patients with symptomatic lumbar stenosis

Study Design Retrospective study. Objective Studies on age-related degenerative changes causing concurrent stenoses in the cervical, thoracic, and lumbar spines (triple stenosis) are rare in the literature. Our objectives were to determine: (1) the incidence of asymptomatic radiologic cervical and thoracic stenosis in elderly patients with symptomatic lumbar stenosis, (2) the incidence of concurrent radiologic spinal stenosis in the cervical and thoracic spines, and (3) the radiologic features of cervical stenosis that might predict concurrent thoracic stenosis. Methods Whole-spine T2 sagittal magnetic resonance images of patients older than 80 and diagnosed with lumbar spinal stenosis between January 2003 and January 2012 were evaluated retrospectively. We included patients with asymptomatic spondylotic cervical and thoracic stenosis. We measured the anteroposterior diameters of the vertebral body, bony spinal canal, and spinal cord, along with the Pavlov ratio and anterior or posterior epidural stenosis at the level of the disk for each cervical and thoracic level. We compared the radiologic parameters between the subgroups of cervical stenosis with and without thoracic stenosis. Results Among the 460 patients with lumbar stenosis, 110 (23.9%) had concurrent radiologic cervical stenosis and 112 (24.3%) had concurrent radiologic thoracic stenosis. Fifty-six patients (12.1%) had combined radiologic cervical and thoracic stenosis in addition to their symptomatic lumbar stenosis (triple stenosis). Anterior epidural stenosis at C7–T1 was associated with a high prevalence of thoracic stenosis. Conclusions It appears that asymptomatic radiologic cervical and thoracic stenosis is common in elderly patients with symptomatic lumbar stenosis