Learning Deep Neural Networks for Enhanced Prostate Histological Image Analysis

In recent years, deep convolutional neural networks (CNNs) have shown promise for improving prostate cancer diagnosis by enabling quantitative histopathology through digital pathology. However, there are a number of factors that limit the widespread adoption and clinical utility of deep learning for digital pathology. One of these limitations is the requirement for large labelled training datasets which are expensive to construct due to limited availability of the requisite expertise. Additionally, digital pathology applications typically require the digitisation of histological slides at high magnifications. This process can be challenging especially when digitising large histological slides such as prostatectomies. This work studies and addresses these issues in two important applications of digital pathology: prostate nuclei detection and cell type classification. We study the performance of CNNs at different magnifications and demonstrate that it is possible to perform nuclei detection in low magnification prostate histopathology using CNNs with minimal loss in accuracy. We then study the training of prostate nuclei detectors in the small data setting and demonstrate that although it is possible to train nuclei detectors with minimal data, the models will be sensitive to hyperparameter choice and therefore may not generalise well. Instead, we show that pre-training the CNNs with colon histology data makes them more robust to hyperparameter choice. We then study the CNN performance for prostate cell type classification using supervised, transfer and semi-supervised learning in the small data setting. Our results show that transfer learning can be detrimental to performance but semi-supervised learning is able to provide significant improvements to the learning curve, allowing the training of neural networks with modest amounts of labelled data. We then propose a novel semi-supervised learning method called Deeply-supervised Exemplar CNNs and demonstrate their ability to improve the cell type classifier learning curves at a much better rate than previous semi-supervised neural network methods

Why did they do that?: the methodology of reasons for action

‘Why did they do that?’ is one of the most common questions in International Relations. However, we cannot access other people’s reasons for action the same way that we perceive our own; we cannot introspect the reasons of other actors. This paper provides a unifying framework that delineates different types of knowledge claims regarding reason attribution. There are three possible methodological responses: (1) assume a possible reason and explain behavior in terms of that reason; (2) avoid the direct attribution of reason to individuals and locate explanatory leverage at an analytical level beyond the individual actor reason; and (3) use empirical evidence to adjudicate between possible reasons. Excessive skepticism of evidence of reasons lessens our understanding of the causes of action. When using empirical evidence, contrary to existing arguments, the paper shows that private settings do not systematically favor the true revelation of reasons. The paper also proposes a general principle, consilience, that allows evaluation of empirical claims of reason attribution that subsumes several existing methodological considerations, organizes them, and gives a consistent means of choosing between alternative reason attributions

Portraying the nature of corruption: Using an explorative case-study design

What is the nature of corruption in Western democracies? To answer this research question, the authors study 10 Dutch corruption cases in depth, looking at confidential criminal files. The cases allow them to sketch a general profile of a corruption case. The authors offer nine propositions to portray the nature of corruption. They conclude that corruption usually takes place within enduring relationships, that the process of becoming corrupt can be characterized as a slippery slope, and that important motives for corruption, aside from material gain, include friendship or love, status, and the desire to impress others. The explorative multiple case study methodology helps to expand our understanding of the way in which officials become corrupt. © 2008 The American Society for Public Administration

TESS hunt for young and maturing exoplanets (THYME). III. A two-planet system in the 400 Myr Ursa major group

A.W.M. was supported through NASA's Astrophysics Data Analysis Program (80NSSC19K0583). M.L.W. was supported by a grant through NASA's K2 GO program (80NSSC19K0097). This material is based on work supported by the National Science Foundation Graduate Research Fellowship Program under grant No. DGE-1650116 to P.C.T. A.V.'s work was performed under contract with the California Institute of Technology/Jet Propulsion Laboratory funded by NASA through the Sagan Fellowship Program executed by the NASA Exoplanet Science Institute. D.D. acknowledges support from NASA through Caltech/JPL grant RSA-1006130 and through the TESS Guest Investigator Program grant 80NSSC19K1727.Exoplanets can evolve significantly between birth and maturity, as their atmospheres, orbits, and structures are shaped by their environment. Young planets (<1 Gyr) offer an opportunity to probe the critical early stages of this evolution, where planets evolve the fastest. However, most of the known young planets orbit prohibitively faint stars. We present the discovery of two planets transiting HD 63433 (TOI 1726, TIC 130181866), a young Sun-like (M∗=0.99±0.03) star. Through kinematics, lithium abundance, and rotation, we confirm that HD 63433 is a member of the Ursa Major moving group (τ=414±23 Myr). Based on the TESS light curve and updated stellar parameters, we estimate the planet radii are 2.15±0.10R⊕ and 2.67±0.12R⊕, the orbital periods are 7.11 and 20.55 days, and the orbital eccentricities are lower than about 0.2. Using HARPS-N velocities, we measure the Rossiter-McLaughlin signal of the inner planet, demonstrating that the orbit is prograde. Since the host star is bright (V=6.9), both planets are amenable to transmission spectroscopy, radial velocity measurements of their masses, and more precise determination of the stellar obliquity. This system is therefore poised to play an important role in our understanding of planetary system evolution in the first billion years after formation.PostprintPeer reviewe

Male breast cancer in BRCA1 and BRCA2 mutation carriers : pathology data from the Consortium of Investigators of Modifiers of BRCA1/2

Background: BRCA1 and, more commonly, BRCA2 mutations are associated with increased risk of male breast cancer (MBC). However, only a paucity of data exists on the pathology of breast cancers (BCs) in men with BRCA1/2 mutations. Using the largest available dataset, we determined whether MBCs arising in BRCA1/2 mutation carriers display specific pathologic features and whether these features differ from those of BRCA1/2 female BCs (FBCs). Methods: We characterised the pathologic features of 419 BRCA1/2 MBCs and, using logistic regression analysis, contrasted those with data from 9675 BRCA1/2 FBCs and with population-based data from 6351 MBCs in the Surveillance, Epidemiology, and End Results (SEER) database. Results: Among BRCA2 MBCs, grade significantly decreased with increasing age at diagnosis (P = 0.005). Compared with BRCA2 FBCs, BRCA2 MBCs were of significantly higher stage (P for trend = 2 x 10(-5)) and higher grade (P for trend = 0.005) and were more likely to be oestrogen receptor-positive [odds ratio (OR) 10.59; 95 % confidence interval (CI) 5.15-21.80] and progesterone receptor-positive (OR 5.04; 95 % CI 3.17-8.04). With the exception of grade, similar patterns of associations emerged when we compared BRCA1 MBCs and FBCs. BRCA2 MBCs also presented with higher grade than MBCs from the SEER database (P for trend = 4 x 10(-12)). Conclusions: On the basis of the largest series analysed to date, our results show that BRCA1/2 MBCs display distinct pathologic characteristics compared with BRCA1/2 FBCs, and we identified a specific BRCA2-associated MBC phenotype characterised by a variable suggesting greater biological aggressiveness (i.e., high histologic grade). These findings could lead to the development of gender-specific risk prediction models and guide clinical strategies appropriate for MBC management.Peer reviewe

ACC/AHA/ASE 2003 Guideline Update for the Clinical Application of Echocardiography: Summary Article: A Report of the American College of Cardiology/American HeartAssociation Task Force on Practice Guidelines (ACC/AHA/ASE Committee to Update the 1997 Guidelines for the Clinical Application of Echocardiography)

"The previous guideline for the use of echocardiography was published in March 1997. Since that time, there have been significant advances in the technology of echocardiography and growth in its clinical use and in the scientific evidence leading to recommendations for its proper use. Each section has been reviewed and updated in evidence tables, and where appropriate, changes have been made in recommendations. A new section on the use of intraoperative transesophageal echocardiography (TEE) is being added to update the guidelines published by the American Society of Anesthesiologists and the Society of Cardiovascular Anesthesiologists. There are extensive revisions, especially of the sections on ischemic heart disease; congestive heart failure, cardiomyopathy, and assessment of left ventricular (LV) function; and screening and echocardiography in the critically ill. There are new tables of evidence and extensive revisions in the ischemic heart disease evidence tables. Because of space limitations, only those sections and evidence tables with new recommendations will be printed in this summary article. Where there are minimal changes in a recommendation grouping, such as a change from Class IIa to Class I, only that change will be printed, not the entire set of recommendations. Advances for which the clinical applications are still being investigated, such as the use of myocardial contrast agents and three-dimensional echocardiography, will not be discussed.

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

American Gut: an Open Platform for Citizen Science Microbiome Research

McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3):e00031-18