Digital image analysis in breast pathology-from image processing techniques to artificial intelligence

Breast cancer is the most common malignant disease in women worldwide. In recent decades, earlier diagnosis and better adjuvant therapy have substantially improved patient outcome. Diagnosis by histopathology has proven to be instrumental to guide breast cancer treatment, but new challenges have emerged as our increasing understanding of cancer over the years has revealed its complex nature. As patient demand for personalized breast cancer therapy grows, we face an urgent need for more precise biomarker assessment and more accurate histopathologic breast cancer diagnosis to make better therapy decisions. The digitization of pathology data has opened the door to faster, more reproducible, and more precise diagnoses through computerized image analysis. Software to assist diagnostic breast pathology through image processing techniques have been around for years. But recent breakthroughs in artificial intelligence (AI) promise to fundamentally change the way we detect and treat breast cancer in the near future. Machine learning, a subfield of AI that applies statistical methods to learn from data, has seen an explosion of interest in recent years because of its ability to recognize patterns in data with less need for human instruction. One technique in particular, known as deep learning, has produced groundbreaking results in many important problems including image classification and speech recognition. In this review, we will cover the use of AI and deep learning in diagnostic breast pathology, and other recent developments in digital image analysis.

Prognostic value of Ki67 analysed by cytology or histology in primary breast cancer

Aims

The accuracy of biomarker assessment in breast pathology is vital for therapy decisions. The therapy predictive and prognostic biomarkers oestrogen receptor (ER), progesterone receptor, HER2 and Ki67 may act as surrogates to gene expression profiling of breast cancer. The aims of this study were to investigate the concordance of consecutive biomarker assessment by immunocytochemistry on preoperative fine-needle aspiration cytology versus immunohistochemistry (IHC) on the corresponding resected breast tumours. Further, to investigate the concordance with molecular subtype and correlation to stage and outcome.

Methods

Two retrospective cohorts comprising 385 breast tumours with clinicopathological data including gene expression-based subtype and up to 10-year overall survival data were evaluated.

Results

In both cohorts, we identified a substantial variation in Ki67 index between cytology and histology and a switch between low and high proliferation within the same tumour in 121/360 cases. ER evaluations were discordant in only 1.5% of the tumours. From cohort 2, gene expression data with PAM50 subtype were used to correlate surrogate subtypes. IHC-based surrogate classification could identify the correct molecular subtype in 60% and 64% of patients by cytology (n=63) and surgical resections (n=73), respectively. Furthermore, high Ki67 in surgical resections but not in cytology was associated with poor overall survival and higher probability for axillary lymph node metastasis.

Conclusions

This study shows considerable differences in the prognostic value of Ki67 but not ER in breast cancer depending on the diagnostic method. Furthermore, our findings show that both methods are insufficient in predicting true molecular subtypes.

Relationship between speaking English as a second language and agitation in people with dementia living in care homes: Results from the MARQUE (Managing Agitation and Raising Quality of life) English national care home survey

OBJECTIVE

As not speaking English as a first language may lead to increased difficulties in communication with staff and other residents, we (1) tested our primary hypotheses that care home residents with dementia speaking English as a second language experience more agitation and overall neuropsychiatric symptoms, and (2) explored qualitatively how staff consider that residents' language, ethnicity, and culture might impact on how they manage agitation.

METHODS

We interviewed staff, residents with dementia, and their family carers from 86 care homes (2014-2015) about resident's neuropsychiatric symptoms, agitation, life quality, and dementia severity. We qualitatively interviewed 25 staff.

RESULTS

Seventy-one out of 1420 (5%) of care home residents with dementia interviewed spoke English as a second language. After controlling for dementia severity, age, and sex, and accounting for care home and staff proxy clustering, speaking English as a second language compared with as a first language was associated with significantly higher Cohen-Mansfield Agitation Inventory (adjusted difference in means 8.3, 95% confidence interval 4.1 to 12.5) and Neuropsychiatric inventory scores (4.1, 0.65 to 7.5). Staff narratives described how linguistic and culturally isolating being in a care home where no residents or staff share your culture or language could be for people with dementia, and how this sometimes caused or worsened agitation.

CONCLUSIONS

Considering a person with dementia's need to be understood when selecting a care home and developing technology resources to enable dementia-friendly translation services could be important strategies for reducing distress of people with dementia from minority ethnic groups who live in care homes.

Abstract P2-03-07: Digital image analysis of Ki67 in hot spots is superior to alternative proliferation associated markers in breast cancer

INTRODUCTION

Proliferative activity is one of the most important prognostic parameters in cancer. During the pathological examination of breast tumors, it is routinely evaluated by a count of the number of mitoses. Adding immunohistochemical stains of the nuclear protein Ki67 provides extra prognostic and predictive information. However, the currently used methods for both of these evaluations battle imperfections, primarily in reproducibility. In this study, we make an equally broad and detailed evaluation of mitoses, Ki67 and the more recently described Phosphohistone H3 (PHH3) in primary breast cancer using digital image analysis (DIA). Furthermore, we aim to investigate the prognostic and predictive value of proliferation-associated biomarkers in breast cancer stromal cells in relation to patient outcome.

MATERIALS AND METHODS

Two cohorts of primary breast cancer specimens (total n=297) with clinicopathological data including >10 years survival data, were sectioned and stained for Ki67, PHH3 and pancytokeratin (CKMNF116) and all glass slides were digitally scanned at x20. The DIA software used was the Visiopharm Integrator System (VIS) by Visiopharm A/S, Hoersholm, Denmark. VIS operates by a 'digital fusion' method that automatically excludes non-epithelial tissue restricting the analysis of the biomarkers (Ki67 and PHH3) to CKMNF116 positive cells. Both manual and DIA scores were compared for sensitivity and specificity for the gene expression based Luminal B versus A subtype, for high versus low transcriptomic grade as well as for their prognostic value in terms of Cox regression hazard ratios and breast cancer specific and overall survival. Further, we investigated whether the expression of Ki67 in the tumors' hot spots, invasive edges or as an average across all regions should be assessed for maximum power in relation to these outcomes. In addition, by inverting the DIA algorithm run by the VIS on the same cohorts, the expression of Ki67 and PHH3 was evaluated in the tumor stromal compartment.

RESULTS

Regardless of tumor region, DIA of Ki67 outperformed the other markers in sensitivity and specificity for gene expression subtypes and transcriptomic grade. In contrast to mitotic counts, tumors with high expression of Ki67 as defined by DIA, had significantly increased hazard ratio for all-cause mortality within 10 years from diagnosis. DIA of Ki67 was superior to manual Ki67 and PHH3 evaluations as well as to mitotic counts in terms of separation of patients with poor versus relatively good survival. Finally, we replaced the manual mitotic counts with DIA of Ki67 in hot spots as the marker for proliferation when determining histological grade. This increased the differences in estimated mean overall survival between the highest and lowest grades and added significantly more prognostic information to the classic Nottingham histological grade.

CONCLUSIONS

We conclude that digital image analysis of Ki67 in hot spots should be suggested as the marker of choice for proliferative activity in breast cancer.

Citation Format: Robertson S, Stålhammar G, Wedlund L, Gholizadeh S, Lippert M, Rantaleinen M, Bergh J, Hartman J. Digital image analysis of Ki67 in hot spots is superior to alternative proliferation associated markers in breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-07.

Collection and determinants of patient reported outcome measures in haemodialysis patients in Scotland

BACKGROUND/INTRODUCTION

Patient reported outcome measures (PROMs) can evaluate the quality of health in patients with established renal failure. There is limited experience of their use within national renal registries.

AIM

To describe the Scottish Renal Registry's (SRR) experience of collecting PROMS in the haemodialysis population and correlate PROMS to demographic and clinical parameters.

DESIGN

Retrospective observational cross-sectional study.

METHODS

Haemodialysis patients in Scotland were invited to complete the KDQOL™-36 questionnaire on the day of the annual SRR census in 2015 and 2016. Questionnaires were linked to census demographic and clinical variables.

RESULTS

In 2016, 738 questionnaires were linked to census data (39% of prevalent haemodialysis population). Response rates differed with age (≥ 65 years 42%, < 65 years 36%) [χ2P = 0.006]; duration of renal replacement therapy (<1 year 46%, ≥1 < 5 years 38%, ≥ 5 years 33%) [χ2P = 0.002] and social class (Scottish Index of Multiple Deprivation (SIMD) Class 1 32%, Class 2 41%, Class 3 40%, Class 4 48%, Class 5 40%) [χ2P < 0.001]. There were significant differences in PROMs with age, SIMD quintile and primary renal diagnosis. Achieving a urea reduction ratio of >65% and dialysing through arteriovenous access were associated with significantly higher PROMs. PROMs were not affected by haemoglobin or phosphate concentration.

DISCUSSION/CONCLUSIONS

Routine collection of PROMs is feasible and can identify potentially under-recognized and treatable determinants to quality of life. The association between attaining recommended standards of care and improved PROMs is striking. Individual and population-wide strategies are required to improve PROMs.

Measurement of the ν μ energy spectrum with IceCube-79: IceCube Collaboration

IceCube is a neutrino observatory deployed in the glacial ice at the geographic South Pole. The ν μ energy unfolding described in this paper is based on data taken with IceCube in its 79-string configuration. A sample of muon neutrino charged-current interactions with a purity of 99.5% was selected by means of a multivariate classification process based on machine learning. The subsequent unfolding was performed using the software Truee. The resulting spectrum covers an E ν -range of more than four orders of magnitude from 125 GeV to 3.2 PeV. Compared to the Honda atmospheric neutrino flux model, the energy spectrum shows an excess of more than 1.9 σ in four adjacent bins for neutrino energies E ν ≥ 177.8 TeV . The obtained spectrum is fully compatible with previous measurements of the atmospheric neutrino flux and recent IceCube measurements of a flux of high-energy astrophysical neutrinos.

Waiting times for cancer patients in Sweden: A nationwide population-based study

AIMS

The reported long waiting times for cancer patients have mostly been related to prognostic outcome and less to patient-related experience to outcome. We assessed waiting times for patients with cancer of the breast, prostate, colon or rectum in Sweden.

METHODS

The median time from referral to start of treatment was assessed using data from clinical cancer registers for patients who received curative treatment during 2011, 2012 and 2013.

RESULTS

The median overall waiting time in different counties ranged from 7 to 28 days for breast cancer, from 117 to 280 days for prostate cancer, from 27 to 64 days for colon cancer and from 48 to 80 days for rectal cancer. For the entire nation, the median time from referral to start of treatment remained unchanged from 2011 to 2013 for each cancer diagnosis.

CONCLUSIONS

Large variations were found in waiting times between different counties in Sweden and between different types of cancer. The long waiting times identified in this study emphasize the need to improve national programmes for more rapid diagnosis and treatment.

Abstract P6-12-11: A randomized, double-blind, placebo-controlled window of opportunity trial evaluating clinical effects of high dose vitamin D in patients with breast cancer

This abstract was withdrawn by the authors.

Unscreened older men diagnosed with prostate cancer are at increased risk of aggressive disease

BACKGROUND

To evaluate the relationship between PSA testing history and high-risk disease among older men diagnosed with prostate cancer.

METHODS

Records from 1993 to 2014 were reviewed for men who underwent radiotherapy for prostate cancer at age 75 years or older. Patients were classified into one of four groups based on PSA-testing history: (1) no PSA testing; (2) incomplete/ineffective PSA testing; (3) PSA testing; or (4) cannot be determined. Outcomes of interest were National Comprehensive Cancer Network (NCCN) risk group (that is, low, intermediate or high risk) and biopsy grade at diagnosis. Multivariable logistic regression was used to determine the association between PSA testing history and high-risk cancer.

RESULTS

PSA-testing history was available in 274 (94.5%) of 290 subjects meeting study criteria. In total, 148 men (54.0%) underwent PSA testing with follow-up biopsy, 72 (26.3%) underwent PSA testing without appropriate follow-up, and 54 men (19.7%) did not undergo PSA testing. Patients who underwent PSA testing were significantly less likely to be diagnosed with NCCN high-risk cancer (23.0% vs 51.6%, P<0.001). On multivariable analysis, men with no/incomplete PSA testing had more than three-fold increased odds of high-risk disease at diagnosis (odds ratio 3.39, 95% confidence interval 1.96-5.87, P<0.001) as compared to the tested population.

CONCLUSIONS

Older men who underwent no PSA testing or incomplete testing were significantly more likely to be diagnosed with high-risk prostate cancer than those who were previously screened. It is reasonable to consider screening in healthy older men likely to benefit from early detection and treatment.

Constraints on Ultrahigh-Energy Cosmic-Ray Sources from a Search for Neutrinos above 10 PeV with IceCube

We report constraints on the sources of ultrahigh-energy cosmic rays (UHECRs) above 10^{9}  GeV, based on an analysis of seven years of IceCube data. This analysis efficiently selects very high- energy neutrino-induced events which have deposited energies from 5×10^{5}  GeV to above 10^{11}  GeV. Two neutrino-induced events with an estimated deposited energy of (2.6±0.3)×10^{6}  GeV, the highest neutrino energy observed so far, and (7.7±2.0)×10^{5}  GeV were detected. The atmospheric background-only hypothesis of detecting these events is rejected at 3.6σ. The hypothesis that the observed events are of cosmogenic origin is also rejected at >99% CL because of the limited deposited energy and the nonobservation of events at higher energy, while their observation is consistent with an astrophysical origin. Our limits on cosmogenic neutrino fluxes disfavor the UHECR sources having a cosmological evolution stronger than the star formation rate, e.g., active galactic nuclei and γ-ray bursts, assuming proton-dominated UHECRs. Constraints on UHECR sources including mixed and heavy UHECR compositions are obtained for models of neutrino production within UHECR sources. Our limit disfavors a significant part of parameter space for active galactic nuclei and new-born pulsar models. These limits on the ultrahigh-energy neutrino flux models are the most stringent to date.

Searches for Sterile Neutrinos with the IceCube Detector

The IceCube neutrino telescope at the South Pole has measured the atmospheric muon neutrino spectrum as a function of zenith angle and energy in the approximate 320 GeV to 20 TeV range, to search for the oscillation signatures of light sterile neutrinos. No evidence for anomalous ν_{μ} or ν[over ¯]_{μ} disappearance is observed in either of two independently developed analyses, each using one year of atmospheric neutrino data. New exclusion limits are placed on the parameter space of the 3+1 model, in which muon antineutrinos experience a strong Mikheyev-Smirnov-Wolfenstein-resonant oscillation. The exclusion limits extend to sin^{2}2θ_{24}≤0.02 at Δm^{2}∼0.3  eV^{2} at the 90% confidence level. The allowed region from global analysis of appearance experiments, including LSND and MiniBooNE, is excluded at approximately the 99% confidence level for the global best-fit value of |U_{e4}|^{2}.

A phase 2 trial exploring the clinical and correlative effects of combining doxycycline with bone-targeted therapy in patients with metastatic breast cancer

Background

Bone-targeting agents (BTAs), such as bisphosphonates and denosumab, have demonstrated no discernable effects on tumour response or disease free/overall survival in patients with bone metastases from breast cancer. Doxycycline is both osteotropic and has anti-cancer effects. When combined with zoledronate in animal models, doxycycline showed significantly increased inhibition of tumour burden and increased bone formation. We evaluated the effects of adding doxycycline to ongoing anti-cancer therapy in patients with metastatic breast cancer.

Methods

Breast cancer patients with bone metastases and ≥3 months of BTA use, entered this single-arm study. Patients received doxycycline 100 mg orally, twice a day for 12 weeks. The co-primary endpoints were; effect on validated pain scores (FACT-Bone pain and Brief Pain Inventory) and bone resorption markers (serum C-telopeptide, [sCTx]). All endpoints (pain scores, sCTx, bone-specific alkaline phosphatase, skeletal-related events, toxicity) were evaluated at baseline, 4, 8 and 12 weeks. Bone marrow was sampled at baseline and week 12 for exploratory biomarker analysis.

Results

Out of 37 enroled patients, 27 (73%) completed 12 weeks of therapy. No significant changes were seen in pain scores or bone turnover markers. Failure to complete treatment: drug toxicity (70%) and disease progression (30%). Sixteen (43%) patients had GI adverse events.

Conclusions

Doxycycline 100 mg twice daily for 12 weeks had no significant effects on either bone pain or bone turnover markers. Its toxicity profile in this patient population would make further evaluation challenging.

Integrative veterinary medical education and consensus guidelines for an integrative veterinary medicine curriculum within veterinary colleges

Integrative veterinary medicine (IVM) describes the combination of complementary and alternative therapies with conventional care and is guided by the best available evidence. Veterinarians frequently encounter questions about complementary and alternative veterinary medicine (CAVM) in practice, and the general public has demonstrated increased interest in these areas for both human and animal health. Consequently, veterinary students should receive adequate exposure to the principles, theories, and current knowledge supporting or refuting such techniques. A proposed curriculum guideline would broadly introduce students to the objective evaluation of new veterinary treatments while increasing their preparation for responding to questions about IVM in clinical practice. Such a course should be evidence-based, unbiased, and unaffiliated with any particular CAVM advocacy or training group. All IVM courses require routine updating as new information becomes available. Controversies regarding IVM and CAVM must be addressed within the course and throughout the entire curriculum. Instructional honesty regarding the uncertainties in this emerging field is critical. Increased training of future veterinary professionals in IVM may produce an openness to new ideas that characterizes the scientific method and a willingness to pursue and incorporate evidence-based medicine in clinical practice with all therapies, including those presently regarded as integrative, complementary, or alternative.

Evidence for Astrophysical Muon Neutrinos from the Northern Sky with IceCube

Results from the IceCube Neutrino Observatory have recently provided compelling evidence for the existence of a high energy astrophysical neutrino flux utilizing a dominantly Southern Hemisphere data set consisting primarily of ν(e) and ν(τ) charged-current and neutral-current (cascade) neutrino interactions. In the analysis presented here, a data sample of approximately 35,000 muon neutrinos from the Northern sky is extracted from data taken during 659.5 days of live time recorded between May 2010 and May 2012. While this sample is composed primarily of neutrinos produced by cosmic ray interactions in Earth's atmosphere, the highest energy events are inconsistent with a hypothesis of solely terrestrial origin at 3.7σ significance. These neutrinos can, however, be explained by an astrophysical flux per neutrino flavor at a level of Φ(E(ν))=9.9(-3.4)(+3.9)×10(-19)  GeV(-1) cm(-2) sr(-1) s(-1)(E(ν)/100  TeV(-2), consistent with IceCube's Southern-Hemisphere-dominated result. Additionally, a fit for an astrophysical flux with an arbitrary spectral index is performed. We find a spectral index of 2.2(-0.2)(+0.2), which is also in good agreement with the Southern Hemisphere result.

Neoadjuvant endocrine therapy and window of opportunity trials: new standards in the treatment of breast cancer?

Until recently, the use of neoadjuvant endocrine therapy was mainly restricted to those patients whose general frailty or comorbidities were contraindications to surgery. There is now increased evidence that certain patient populations (i.e. older patients with hormone-receptor positive disease) can gain as good a pathologic response, with considerably less toxicity, from neoadjuvant endocrine therapy than from neoadjuvant chemotherapy. Optimization of neoadjuvant endocrine therapy is therefore an important therapeutic goal. However, possibly of greater importance in the overall management of breast cancer, is the increased interest in exploring the effects of brief periods of endocrine therapy on in vivo biomarkers, in so called window of opportunity trials. These trials can not only be used to identify the mechanisms of action of novel agents but also to predict optimal subsequent adjuvant therapy for individual patients. While this paper will briefly review the history of neoadjuvant endocrine therapy, more emphasis will be on the evaluation of pivotal window of opportunity trials that will likely lead to a long awaited paradigm shift in the management of breast cancer.

Flavor Ratio of Astrophysical Neutrinos above 35 TeV in IceCube

A diffuse flux of astrophysical neutrinos above 100 TeV has been observed at the IceCube Neutrino Observatory. Here we extend this analysis to probe the astrophysical flux down to 35 TeV and analyze its flavor composition by classifying events as showers or tracks. Taking advantage of lower atmospheric backgrounds for showerlike events, we obtain a shower-biased sample containing 129 showers and 8 tracks collected in three years from 2010 to 2013. We demonstrate consistency with the (fe:fμ:fτ)⊕≈(1:1:1)⊕ flavor ratio at Earth commonly expected from the averaged oscillations of neutrinos produced by pion decay in distant astrophysical sources. Limits are placed on nonstandard flavor compositions that cannot be produced by averaged neutrino oscillations but could arise in exotic physics scenarios. A maximally tracklike composition of (0:1:0)⊕ is excluded at 3.3σ, and a purely showerlike composition of (1:0:0)⊕ is excluded at 2.3σ.

Validation of a Trunk-mounted Accelerometer to Measure Peak Impacts during Team Sport Movements

This study assessed the validity of an accelerometer to measure impacts in team sports. 76 participants completed a team sport circuit. Accelerations were collected concurrently at 100 Hz using an accelerometer and a 36-camera motion analysis system. The largest peak accelerations per movement were compared in 2 ways: i) pooled together and filtered at 13 different cut-off frequencies (range 6-25 Hz) to identify the optimal filtering frequency, and ii) the optimal cut-off frequency split into the 7 movements performed (n=532). Raw and 25-16 Hz filtering frequencies significantly overestimated and 6 Hz underestimated motion analysis peak accelerations (P <0.007). The 12 Hz filtered accelerometer data revealed the strongest relationship with motion analysis data (accuracy - 0.01±0.27 g, effect size - 0.01, agreement - 0.55 to 0.53 g, precision 0.27 g, and relative error 5.5%; P=1.00). The accelerometer underestimated peak accelerations during tackling and jumping, and overestimated during walking, jogging, sprinting and change of direction. Lower agreement and reduced precision were associated with sprinting, jumping and tackling. The accelerometer demonstrated an acceptable level of concurrent validity compared to a motion analysis system when filtered at a cut-off frequency of 12 Hz. The results advocate the use of accelerometers to measure movements in team sport.

Development of a general analysis and unfolding scheme and its application to measure the energy spectrum of atmospheric neutrinos with IceCube: IceCube Collaboration

We present the development and application of a generic analysis scheme for the measurement of neutrino spectra with the IceCube detector. This scheme is based on regularized unfolding, preceded by an event selection which uses a Minimum Redundancy Maximum Relevance algorithm to select the relevant variables and a random forest for the classification of events. The analysis has been developed using IceCube data from the 59-string configuration of the detector. 27,771 neutrino candidates were detected in 346 days of livetime. A rejection of 99.9999 % of the atmospheric muon background is achieved. The energy spectrum of the atmospheric neutrino flux is obtained using the TRUEE unfolding program. The unfolded spectrum of atmospheric muon neutrinos covers an energy range from 100 GeV to 1 PeV. Compared to the previous measurement using the detector in the 40-string configuration, the analysis presented here, extends the upper end of the atmospheric neutrino spectrum by more than a factor of two, reaching an energy region that has not been previously accessed by spectral measurements.

Reply to the comment by Harron on “Widespread declines in woodland caribou (Rangifer tarandus caribou) continue in Alberta”

Estimation of demographic trends from vital rates provides a powerful means to estimate population trends in cryptic or difficult to study species such as woodland caribou (Rangifer tarandus caribou (Gmelin, 1788)). Using such methods, Hervieux et al. (2013; Can. J. Zool. 91(12): 872–882) recently showed 11 of 14 woodland caribou populations in Alberta were declining at ∼8%/year following up to 18 years of monitoring. Harron (2015; Can. J. Zool. 93(2): 149–150) critiques our original study, claiming that negative biases in our demographic monitoring exaggerate our conclusions of widespread caribou declines. Here, we systematically review each of Harron’s claims of bias, rejecting each of his claims upon careful review of the mechanisms by which his purported claims would manifest in our population trend estimation. Therefore, we conclude that Harron’s scientific critique was superficial and misleading. Delays in conservation actions raised by Harron’s critique risk diminishing opportunities to conserve and recover this federally and provincially protected species.

Lead Identification to Clinical Candidate Selection

Chagas disease affects 8 million people worldwide and remains a main cause of death due to heart failure in Latin America. The number of cases in the United States is now estimated to be 300,000, but there are currently no Food and Drug Administration (FDA)–approved drugs available for patients with Chagas disease. To fill this gap, we have established a public-private partnership between the University of California, San Francisco and the Genomics Institute of the Novartis Research Foundation (GNF) with the goal of delivering clinical candidates to treat Chagas disease. The discovery phase, based on the screening of more than 160,000 compounds from the GNF Academic Collaboration Library, led to the identification of new anti-Chagas scaffolds. Part of the screening campaign used and compared two screening methods, including a colorimetric-based assay using Trypanosoma cruzi expressing β-galactosidase and an image-based, high-content screening (HCS) assay using the CA-I/72 strain of T. cruzi. Comparing molecules tested in both assays, we found that ergosterol biosynthesis inhibitors had greater potency in the colorimetric assay than in the HCS assay. Both assays were used to inform structure-activity relationships for antiparasitic efficacy and pharmacokinetics. A new anti– T. cruzi scaffold derived from xanthine was identified, and we describe its development as lead series.

Observation of high-energy astrophysical neutrinos in three years of IceCube data

A search for high-energy neutrinos interacting within the IceCube detector between 2010 and 2012 provided the first evidence for a high-energy neutrino flux of extraterrestrial origin. Results from an analysis using the same methods with a third year (2012-2013) of data from the complete IceCube detector are consistent with the previously reported astrophysical flux in the 100 TeV-PeV range at the level of 10(-8)  GeV cm-2 s-1 sr-1 per flavor and reject a purely atmospheric explanation for the combined three-year data at 5.7σ. The data are consistent with expectations for equal fluxes of all three neutrino flavors and with isotropic arrival directions, suggesting either numerous or spatially extended sources. The three-year data set, with a live time of 988 days, contains a total of 37 neutrino candidate events with deposited energies ranging from 30 to 2000 TeV. The 2000-TeV event is the highest-energy neutrino interaction ever observed.