Harker School

San Jose, CA, United States

Harker School

San Jose, CA, United States
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Ehteshami Bejnordi B.,Radboud University Nijmegen | Ehteshami Bejnordi B.,Beth Israel Deaconess Medical Center | Lin J.,Harker School | Glass B.,Beth Israel Deaconess Medical Center | And 6 more authors.
Proceedings - International Symposium on Biomedical Imaging | Year: 2017

Diagnosis of breast carcinomas has so far been limited to the morphological interpretation of epithelial cells and the assessment of epithelial tissue architecture. Consequently, most of the automated systems have focused on characterizing the epithelial regions of the breast to detect cancer. In this paper, we propose a system for classification of hematoxylin and eosin (H&E) stained breast specimens based on convolutional neural networks that primarily targets the assessment of tumor-associated stroma to diagnose breast cancer patients. We evaluate the performance of our proposed system using a large cohort containing 646 breast tissue biopsies. Our evaluations show that the proposed system achieves an area under ROC of 0.92, demonstrating the discriminative power of previously neglected tumor associated stroma as a diagnostic biomarker. © 2017 IEEE.


Yang L.,Peking University | Kirby E.N.,California Institute of Technology | Guhathakurta P.,University of California at Santa Cruz | Peng E.W.,Peking University | Cheng L.,Harker School
Astrophysical Journal | Year: 2013

The ability to measure metallicities and α-element abundances in individual red giant branch (RGB) stars using medium-resolution spectra (R ≈ 6000) is a valuable tool for deciphering the nature of Milky Way dwarf satellites and the history of the Galactic halo. Extending such studies to more distant systems like Andromeda is beyond the ability of the current generation of telescopes, but by co-adding the spectra of similar stars, we can attain the necessary signal-to-noise ratio (S/N) to make detailed abundance measurements. In this paper, we present a method to determine metallicities and α-element abundances using the co-addition of medium-resolution spectra. We test the method of spectral co-addition using high-S/N spectra of more than 1300 RGB stars from Milky Way globular clusters and dwarf spheroidal galaxies obtained with the Keck II telescope/DEIMOS spectrograph. We group similar stars using photometric criteria and compare the weighted ensemble average abundances ([Fe/H], [Mg/Fe], [Si/Fe], [Ca/Fe], and [Ti/Fe]) of individual stars in each group with the measurements made on the corresponding co-added spectrum. We find a high level of agreement between the two methods, which permits us to apply this co-added spectra technique to more distant RGB stars, like stars in the M31 satellite galaxies. This paper outlines our spectral co-addition and abundance measurement methodology and describes the potential biases in making these measurements. © 2013. The American Astronomical Society. All rights reserved.


Nalamachu S.,International Clinical Research Institute | Ruck D.,International Clinical Research Institute | Nalamasu R.,Harker School | Fasbinder S.,International Clinical Research Institute | Bansal R.,Texas A&M University
Journal of Opioid Management | Year: 2013

Objective: To assess the efficacy and safety of once-daily hydromorphone extended-release tablets (OROS [Alza Corporation, Mountain View, CA] hydromorphone ER) in patients with chronic neuropathic pain. Design: Single-center, open-label, 12-week study. Patients: Opioid-tolerant patients with chronic neuropathic pain for ≥6 months (N = 30). Interventions: Patients were converted from previous opioid therapy to OROS hydromorphone ER using a 5:1 morphine:hydromorphone equianalgesic dosing ratio, with an initial 50 percent reduction of the calculated equianalgesic dose, titrated every 3-4 days to adequate analgesia over 2 weeks. Outcome measures: The primary efficacy measure was change from baseline to week 12 (end of study) on question #5 ("average pain") of the Brief Pain Inventory (BPI). Secondary measures included least pain, worst pain, current pain, and sleep interference on the BPI, as well as the Pain Quality Assessment Scale (PQAS) and patient global assessment of treatment satisfaction. Results: Thirty patients were enrolled and received >1 dose of OROS hydromorphone ER, titrated to a final mean dose of 26.4 mg/d. Mean (SE) BPI change from baseline to end of study was-1.3 (0.59) for current pain (p < 0.05) and -1.8 (0.61) for worst pain (p < 0.01). Mean (SE) change from baseline was also significant for BPI scores for sleep interference (-1.7[0.61]; p < 0.01) and PQAS scores (-24.8[7.9], p < 0.01). The majority (81 percent) of patients were satisfied or very satisfied with treatment. The most common treatment-related adverse events were dizziness, headache, and nausea (two patients each). Conclusions: Patients with chronic neuropathic pain were safely and effectively converted to and maintained on OROS hydromorphone ER. © 2013 Journal of Opioid Management, All Rights Reserved.


Kirby E.N.,California Institute of Technology | Guo M.,Irvington High School | Guo M.,Stanford University | Zhang A.J.,Harker School | And 6 more authors.
Astrophysical Journal | Year: 2015

We present carbon abundances of red giants in Milky Way (MW) globular clusters and dwarf spheroidal galaxies (dSphs). Our sample includes measurements of carbon abundances for 154 giants in the clusters NGC 2419, M68, and M15 and 398 giants in the dSphs Sculptor, Fornax, Ursa Minor, and Draco. This sample doubles the number of dSph stars with measurements of [C/Fe]. The [C/Fe] ratio in the clusters decreases with increasing luminosity above , which can be explained by deep mixing in evolved giants. The same decrease is observed in dSphs, but the initial [C/Fe] of the dSph giants is not uniform. Stars in dSphs at lower metallicities have larger [C/Fe] ratios. We hypothesize that [C/Fe] (corrected to the initial carbon abundance) declines with increasing [Fe/H] due to the metallicity dependence of the carbon yield of asymptotic giant branch stars and due to the increasing importance of SNe Ia at higher metallicities. We also identified 11 very carbon-rich giants (eight previously known) in three dSphs. However, our selection biases preclude a detailed comparison to the carbon-enhanced fraction of the MW stellar halo. Nonetheless, the stars with in dSphs follow a different [C/Fe] track with [Fe/H] than the halo stars. Specifically, [C/Fe] in dSphs begins to decline at lower [Fe/H] than in the halo. The difference in the metallicity of the [C/Fe] "knee" adds to the evidence from [α/Fe] distributions that the progenitors of the halo had a shorter timescale for chemical enrichment than the surviving dSphs. © 2015. The American Astronomical Society. All rights reserved..


Kirby E.N.,California Institute of Technology | Guhathakurta P.,University of California at Santa Cruz | Zhang A.J.,Harker School | Zhang A.J.,Stanford University | And 6 more authors.
Astrophysical Journal | Year: 2016

Although red giants deplete lithium on their surfaces, some giants are Li-rich. Intermediate-mass asymptotic giant branch (AGB) stars can generate Li through the Cameron-Fowler conveyor, but the existence of Li-rich, low-mass red giant branch (RGB) stars is puzzling. Globular clusters are the best sites to examine this phenomenon because it is straightforward to determine membership in the cluster and to identify the evolutionary state of each star. In 72 hours of Keck/DEIMOS exposures in 25 clusters, we found four Li-rich RGB and two Li-rich AGB stars. There were 1696 RGB and 125 AGB stars with measurements or upper limits consistent with normal abundances of Li. Hence, the frequency of Li-richness in globular clusters is (0.2 ±0.1)% for the RGB, (1.6 ±1.1)% for the AGB, and (0.3 ±0.1)% for all giants. Because the Li-rich RGB stars are on the lower RGB, Li self-generation mechanisms proposed to occur at the luminosity function bump or He core flash cannot explain these four lower RGB stars. We propose the following origin for Li enrichment: (1) All luminous giants experience a brief phase of Li enrichment at the He core flash. (2) All post-RGB stars with binary companions on the lower RGB will engage in mass transfer. This scenario predicts that 0.1% of lower RGB stars will appear Li-rich due to mass transfer from a recently Li-enhanced companion. This frequency is at the lower end of our confidence interval. © 2016. The American Astronomical Society. All rights reserved..


Pushparaj V.,Rensselaer Polytechnic Institute | Mahadevan L.,Harvard University | Sreekala S.,Rensselaer Polytechnic Institute | Ci L.,Rice University | And 2 more authors.
Carbon | Year: 2012

Brushes with nanoscale bristles, such as nanotube arrays held together by van der Waals forces, have applications as compliant electrical switches, probes and micro-scale cleaning tools. Repeated use exposes the brushes to contact and impact at high strains resulting in the bristles undergoing exfoliation, deformation and damage. We show that the damages incurred can be nearly recovered by capillary evaporation of solvents from the free standing aligned nanotube brushes. © 2012 Elsevier Ltd. All rights reserved.


Kirby E.N.,University of California at Irvine | Kirby E.N.,Center for Galaxy Evolution Fellow | Cohen J.G.,California Institute of Technology | Guhathakurta P.,University of California at Santa Cruz | And 5 more authors.
Astrophysical Journal | Year: 2013

We present spectroscopic metallicities of individual stars in seven gas-rich dwarf irregular galaxies (dIrrs), and we show that dIrrs obey the same massmetallicity relation as the dwarf spheroidal (dSph) satellites of both the Milky Way and M31: Z* σ M*0.30±0. 02 . The uniformity of the relation is in contradiction to previous estimates of metallicity based on photometry. This relationship is roughly continuous with the stellar massstellar metallicity relation for galaxies as massive asM* = 1012M⊙. Although the average metallicities of dwarf galaxies depend only on stellar mass, the shapes of their metallicity distributions depend on galaxy type. The metallicity distributions of dIrrs resemble simple, leaky box chemical evolution models, whereas dSphs require an additional parameter, such as gas accretion, to explain the shapes of their metallicity distributions. Furthermore, the metallicity distributions of the more luminous dSphs have sharp, metal-rich cut-offs that are consistent with the sudden truncation of star formation due to ram pressure stripping. © 2013. The American Astronomical Society. All rights reserved.


Liu C.,Harker School | Wang R.K.,University of Washington
Progress in Biomedical Optics and Imaging - Proceedings of SPIE | Year: 2014

Choroidal thickness (ChT), defined as the distance between the retinal pigment epithelium (RPE) and the choroid-sclera interface (CSI), is highly correlated with various ocular disorders like high myopia, diabetic retinopathy, and central serous chorioretinopathy. Long wavelength Optical Coherence Tomography (OCT) has the ability to penetrate deep to the CSI, making the measurement of the ChT possible. The ability to accurately segment the CSI and RPE is important in extracting clinical information. However, automated CSI segmentation is challenging due to the weak boundary in the lower choroid and inconsistent texture with varied blood vessels. We propose a K-means clustering based automated algorithm, which is effective in segmenting the CSI and RPE. The performance of the method was evaluated using 531 frames from 4 normal subjects. The RPE and CSI segmentation time was about 0.3 seconds per frame, and the average time was around 0.5 seconds per frame with correction among frames, which is faster than reported algorithms. The results from the proposed method are consistent with the manual segmentation results. Further investigation includes the optimization of the algorithm to cover more OCT images captured from patients and the increase of the processing speed and robustness of the segmentation method. © 2014 SPIE.


Trump J.R.,University of California at Santa Cruz | Hsu A.D.,Harker School | Fang J.J.,University of California at Santa Cruz | Faber S.M.,University of California at Santa Cruz | And 2 more authors.
Astrophysical Journal | Year: 2013

We present the first quantified, statistical map of broad-line active galactic nucleus (AGN) frequency with host galaxy color and stellar mass in nearby (0.01 < z < 0.11) galaxies. Aperture photometry and z-band concentration measurements from the Sloan Digital Sky Survey are used to disentangle AGN and galaxy emission, resulting in estimates of uncontaminated galaxy rest-frame color, luminosity, and stellar mass. Broad-line AGNs are distributed throughout the blue cloud and green valley at a given stellar mass, and are much rarer in quiescent (red sequence) galaxies. This is in contrast to the published host galaxy properties of weaker narrow-line AGNs, indicating that broad-line AGNs occur during a different phase in galaxy evolution. More luminous broad-line AGNs have bluer host galaxies, even at fixed mass, suggesting that the same processes that fuel nuclear activity also efficiently form stars. The data favor processes that simultaneously fuel both star formation activity and rapid supermassive black hole accretion. If AGNs cause feedback on their host galaxies in the nearby universe, the evidence of galaxy-wide quenching must be delayed until after the broad-line AGN phase. © 2013. The American Astronomical Society. All rights reserved..


Deming C.P.,University of California at Santa Cruz | Mercado R.,University of California at Santa Cruz | Gadiraju V.,Harker School | Sweeney S.W.,University of California at Santa Cruz | And 2 more authors.
ACS Sustainable Chemistry and Engineering | Year: 2015

Graphene quantum dots (GQDs)-supported palladium nanoparticles were synthesized by thermolytic reduction of PdCl2 in 1,2-propanediol at 80 °C in the presence of GQDs and then were subject to hydrothermal treatment at an elevated temperature within the range of 140 to 200 °C. Transmission electron microscopic measurements showed a raspberry-like morphology for the samples before and after hydrothermal treatment at temperatures ≤160 °C, where nanoparticles of ca. 8 nm in diameter formed large aggregates in the range of 50 to 100 nm in diameter, and at higher hydrothermal temperatures (180 and 200 °C), chain-like nanostructures were formed instead. X-ray photoelectron and Raman spectroscopic measurements revealed that the GQD structural defects were readily removed by hydrothermal treatments, and the defect concentrations exhibited a clear diminishment with increasing hydrothermal temperature, as indicated by the loss of oxygenated carbons in XPS and a drop in the D to G band ratio in Raman measurements. Voltammetric studies showed apparent electrocatalytic activity toward oxygen reduction, with a volcano-shaped variation of the activity with GQD defect concentration, and the peak activity was observed for the sample prepared at 180 °C with a mass activity of 23.9 A/gPd and specific activity of 1.08 A/m2 at +0.9 V vs RHE. This peak activity is attributed to optimal interactions between Pd and GQD where the GQD defects promoted charge transfer from metal to GQDs and hence weakened interactions with oxygenated intermediates, leading to enhanced ORR activity. The corresponding defect concentration was higher than that identified with the platinum counterparts due to the stronger affinity of oxygen to palladium. © 2015 American Chemical Society.

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