Normalized ghost imaging

We present an experimental comparison between different iterative ghost imaging algorithms. Our experimental setup utilizes a spatial light modulator for generating known random light fields to illuminate a partially-transmissive object. We adapt the weighting factor used in the traditional ghost imaging algorithm to account for changes in the efficiency of the generated light field. We show that our normalized weighting algorithm can match the performance of differential ghost imaging

Transformed Dissipation in Superconducting Quantum Circuits

Superconducting quantum circuits must be designed carefully to avoid dissipation from coupling to external control circuitry. Here we introduce the concept of current transformation to quantify coupling to the environment. We test this theory with an experimentally-determined impedance transformation of $\sim 10^5$ and find quantitative agreement better than a factor of 2 between this transformation and the reduced lifetime of a phase qubit coupled to a tunable transformer. Higher-order corrections from quantum fluctuations are also calculated with this theory, but found not to limit the qubit lifetime. We also illustrate how this simple connection between current and impedance transformation can be used to rule out dissipation sources in experimental qubit systems.Comment: 4 pages, 4 figure

Effect of the Deepening of the Tasman Gateway on the Global Ocean

We examine the effect of the deepening of the Tasman Seaway at the end of the Eocene in a climate model with realistic late Eocene bathymetry and winds. For this, we have constructed an Eocene numerical model based on the University of Victoria climate model with wind forcing derived from a fully coupled Eocene simulation. The model climate state is characterized by an oceanic meridional overturning circulation (MOC) involving Southern Hemisphere sinking and a northward atmospheric moisture transport across the equator. The deepening of the Tasman Seaway in the presence of an open Drake Passage and the associated establishment of the Antarctic Circumpolar Current (ACC) have a limited climatic impact on Antarctica. Nonetheless, the Antarctic deep sinking regions cool sufficiently to lead to a global deep ocean cooling of 3°C. No initiation of Northern Component Water is found, indicating that this may require the development of a more mature ACC. Previous studies suggest that the Ross Sea gyre cools the east coast of Australia, and expected the deepening of the Tasman Seaway to lead to a warming east of Australia due to the introduction of warmer water from the Australo-Antarctic Gulf. We here find that this warming is limited to close to the Australian coast, and that widespread cooling prevails further off shore

DeepGauge: Multi-Granularity Testing Criteria for Deep Learning Systems

Deep learning (DL) defines a new data-driven programming paradigm that constructs the internal system logic of a crafted neuron network through a set of training data. We have seen wide adoption of DL in many safety-critical scenarios. However, a plethora of studies have shown that the state-of-the-art DL systems suffer from various vulnerabilities which can lead to severe consequences when applied to real-world applications. Currently, the testing adequacy of a DL system is usually measured by the accuracy of test data. Considering the limitation of accessible high quality test data, good accuracy performance on test data can hardly provide confidence to the testing adequacy and generality of DL systems. Unlike traditional software systems that have clear and controllable logic and functionality, the lack of interpretability in a DL system makes system analysis and defect detection difficult, which could potentially hinder its real-world deployment. In this paper, we propose DeepGauge, a set of multi-granularity testing criteria for DL systems, which aims at rendering a multi-faceted portrayal of the testbed. The in-depth evaluation of our proposed testing criteria is demonstrated on two well-known datasets, five DL systems, and with four state-of-the-art adversarial attack techniques against DL. The potential usefulness of DeepGauge sheds light on the construction of more generic and robust DL systems.Comment: The 33rd IEEE/ACM International Conference on Automated Software Engineering (ASE 2018

A novel method for RNA extraction from FFPE samples reveals significant differences in biomarker expression between orthotopic and subcutaneous pancreatic cancer patient-derived xenografts.

Next-generation sequencing (NGS) can identify and validate new biomarkers of cancer onset, progression and therapy resistance. Substantial archives of formalin-fixed, paraffin-embedded (FFPE) cancer samples from patients represent a rich resource for linking molecular signatures to clinical data. However, performing NGS on FFPE samples is limited by poor RNA purification methods. To address this hurdle, we developed an improved methodology for extracting high-quality RNA from FFPE samples. By briefly integrating a newly-designed micro-homogenizing (mH) tool with commercially available FFPE RNA extraction protocols, RNA recovery is increased by approximately 3-fold while maintaining standard A260/A280 ratios and RNA quality index (RQI) values. Furthermore, we demonstrate that the mH-purified FFPE RNAs are longer and of higher integrity. Previous studies have suggested that pancreatic ductal adenocarcinoma (PDAC) gene expression signatures vary significantly under in vitro versus in vivo and in vivo subcutaneous versus orthotopic conditions. By using our improved mH-based method, we were able to preserve established expression patterns of KRas-dependency genes within these three unique microenvironments. Finally, expression analysis of novel biomarkers in KRas mutant PDAC samples revealed that PEAK1 decreases and MST1R increases by over 100-fold in orthotopic versus subcutaneous microenvironments. Interestingly, however, only PEAK1 levels remain elevated in orthotopically grown KRas wild-type PDAC cells. These results demonstrate the critical nature of the orthotopic tumor microenvironment when evaluating the clinical relevance of new biomarkers in cells or patient-derived samples. Furthermore, this new mH-based FFPE RNA extraction method has the potential to enhance and expand future FFPE-RNA-NGS cancer biomarker studies

Preoperative Exercise during Neoadjuvant Therapy for Pancreatic Cancer: A Pilot Study

Exercise improves cancer treatment outcomes including health-related quality of life and physical functioning. Patients with pancreatic cancer are generally older adults, and frailty and cachexia are prevalent. Chemotherapy and chemoradiation are increasingly administered prior to pancreatic cancer surgery, and sarcopenia has been shown to accompany these therapies. Preoperative exercise may improve health, well-being, and perioperative outcomes among patients undergoing preoperative therapy for pancreatic cancer. The purpose of this pilot study was to determine the feasibility of exercise in this context. Feasibility was defined as patients completing, on average, 60% of recommended weekly exercise minutes. Twenty patients (M=64 years old, SD=9.9; 42% female) enrolled in a home-based exercise program during preoperative therapy (chemotherapy and/or chemoradiation and preoperative “rest”, M=21.2 weeks total, SD=16.4). Exercise recommendations included moderate-intensity walking for 20-30 minutes/day on ≥3 days/week and moderate-intensity resistance exercises for 30-45 minutes/day on ≥2 days/week. Exercise recommendations (120 minutes of moderate-intensity activity/week) were based on American College of Sports Medicine and American Cancer Society recommendations (150 minutes of moderate-intensity activity/week), but reduced due to patients’ older age and concurrent preoperative therapy. Resistance exercises targeted upper body, lower body, and abdominal muscles, and patients were instructed to perform 3 sets of 8-12 repetitions of multiple exercises for each region during each session. Patients received Yamax Digiwalker pedometers, graded resistance tube sets, and booklets and DVDs with instructions and safety tips. Research staff provided detailed instructions and resistance exercise demonstrations at enrollment and monitored and encouraged adherence with biweekly phone calls. Patients recorded minutes of walking and resistance exercise in daily logs. On average, patients reported 73.9 minutes of walking (\u3e100% of recommendation, SD=72.4) and 43.1 minutes of resistance exercise per week (71.8% of recommendation, SD=39.0). Patients reported the most walking during chemoradiation (M=94.7 minutes/week, SD=104.3), followed by preoperative “rest” (M=77.4 minutes/week, SD=80.4), and chemotherapy (M=70.8 minutes/week, SD=75.2). Patients reported the most resistance exercise during the preoperative “rest” period (M=51.6 minutes/week, SD=52.3), followed by chemoradiation (M=38.0 minutes/week, SD=36.8), and chemotherapy (M=31.1 minutes/week, SD=38.1). Walking and resistance exercise are feasible for patients undergoing preoperative therapy for pancreatic cancer. Varying levels of fatigue and treatment-related side effects may affect exercise during different treatment phases

Impact of a non-therapeutic laparotomy in patients with locally advanced pancreatic cancer treated with induction (m)FOLFIRINOX:Trans-Atlantic Pancreatic Surgery (TAPS) Consortium study

Background: Surgery in selected patients with locally advanced pancreatic cancer after induction chemotherapy may have drawbacks related to surgical risks and breaks or delays in oncological treatment, in particular when curative intent resection is not possible (that is non-therapeutic laparotomy). The aim of this study was to assess the incidence and oncological impact of a non-therapeutic laparotomy in patients with locally advanced pancreatic cancer treated with induction (m)FOLFIRINOX chemotherapy. Methods : This was a retrospective international multicentre study including patients diagnosed with pathology-proven locally advanced pancreatic cancer treated with at least one cycle of (m)FOLFIRINOX (2012–2019). Patients undergoing a non-therapeutic laparotomy (group A) were compared with those not undergoing surgery (group B) and those undergoing resection (group C). Results : Overall, 663 patients with locally advanced pancreatic cancer were included (67 patients (10.1%) in group A, 425 patients (64.1%) in group B, and 171 patients (25.8%) in group C). A non-therapeutic laparotomy occurred in 28.2% of all explorations (67 of 238), with occult metastases in 30 patients (30 of 67, 44.8%) and a 90-day mortality rate of 3.0% (2 of 67). Administration of palliative therapy (65.9% versus 73.1%; P = 0.307) and median overall survival (20.4 [95% c.i. 15.9 to 27.3] versus 20.2 [95% c.i. 19.1 to 22.7] months; P = 0.752) did not differ between group A and group B respectively. The median overall survival in group C was 36.1 (95% c.i. 30.5 to 41.2) months. The 5-year overall survival rates were 11.4%, 8.7%, and 24.7% in group A, group B, and group C, respectively. Compared with group B, non-therapeutic laparotomy (group A) was not associated with reduced overall survival (HR = 0.88 [95% c.i. 0.61 to 1.27]). Conclusion: More than a quarter of surgically explored patients with locally advanced pancreatic cancer after induction (m) FOLFIRINOX did not undergo a resection. Such non-therapeutic laparotomy does not appear to substantially impact oncological outcomes.</p