Multiple Instance Learning for Heterogeneous Images: Training a CNN for Histopathology

Multiple instance (MI) learning with a convolutional neural network enables end-to-end training in the presence of weak image-level labels. We propose a new method for aggregating predictions from smaller regions of the image into an image-level classification by using the quantile function. The quantile function provides a more complete description of the heterogeneity within each image, improving image-level classification. We also adapt image augmentation to the MI framework by randomly selecting cropped regions on which to apply MI aggregation during each epoch of training. This provides a mechanism to study the importance of MI learning. We validate our method on five different classification tasks for breast tumor histology and provide a visualization method for interpreting local image classifications that could lead to future insights into tumor heterogeneity

Lessons Learned During Turbulent Times to Weather and Thrive in the Storm of COVID-19

This article describes the lessons learned by our university during the global healthcare crisis of COVID-19. It highlights the agile solutions employed to continue learning under extraordinary circumstances. While we have captured the stories that allowed our students to power through this tumultuous period if they so desired, these lessons may also provide guidance to other higher education institutions not only for the current turbulent times, but also enhance their ability to pause and pivot by utilizing agile management to weather this and future storms

Does mass drug administration for the integrated treatment of neglected tropical diseases really work? Assessing evidence for the control of schistosomiasis and soil-transmitted helminths in Uganda

This paper was one of four papers commissioned to review the role of social sciences in NTD control by TDR, the Special Programme for Research and Training on Tropical Diseases, which is executed by WHO and co-sponsored by UNICEF, UNDP, the World Bank and WHO.This article has been made available through the Brunel Open Access Publishing Fund.Background: Less is known about mass drug administration [MDA] for neglected tropical diseases [NTDs] than is suggested by those so vigorously promoting expansion of the approach. This paper fills an important gap: it draws upon local level research to examine the roll out of treatment for two NTDs, schistosomiasis and soil-transmitted helminths, in Uganda. Methods: Ethnographic research was undertaken over a period of four years between 2005-2009 in north-west and south-east Uganda. In addition to participant observation, survey data recording self-reported take-up of drugs for schistosomiasis, soil-transmitted helminths and, where relevant, lymphatic filariasis and onchocerciasis was collected from a random sample of at least 10% of households at study locations. Data recording the take-up of drugs in Ministry of Health registers for NTDs were analysed in the light of these ethnographic and social survey data. Results: The comparative analysis of the take-up of drugs among adults revealed that although most long term residents have been offered treatment at least once since 2004, the actual take up of drugs for schistosomiasis and soil-transmitted helminths varies considerably from one district to another and often also within districts. The specific reasons why MDA succeeds in some locations and falters in others relates to local dynamics. Issues such as population movement across borders, changing food supply, relations between drug distributors and targeted groups, rumours and conspiracy theories about the 'real' purpose of treatment, subjective experiences of side effects from treatment, alternative understandings of affliction, responses to social control measures and historical experiences of public health control measures, can all make a huge difference. The paper highlights the need to adapt MDA to local circumstances. It also points to specific generalisable issues, notably with respect to health education, drug distribution and more effective use of existing public health legislation. Conclusion: While it has been an achievement to have offered free drugs to so many adults, current standard practices of monitoring, evaluation and delivery of MDA for NTDs are inconsistent and inadequate. Efforts to integrate programmes have exacerbated the difficulties. Improved assessment of what is really happening on the ground will be an essential step in achieving long-term overall reduction of the NTD burden for impoverished communities.This article is available through the Brunel Open Access Publishing Fund

Social media and teacher professional learning communities

peer-reviewed.Background: An extensive and international evidence base positions professional learning communities (PLCs) as an effective continued professional development (CPD) mechanism that can impact on teachers’ practices and, in turn, students’ learning. The landscape of teacher PLCs is continuously developing; notably through teachers’ uses of social media. Yet, there is limited robust evidence identifying the characteristics of social media PLCs that impact on teachers’ learning and practice. Purpose: This exploratory study examined the characteristics of a specific Twitter-based professional learning community – #pechat. The research questions were: (i) what is the nature of a Twitter-based professional learning community? and (ii) what characteristics of a Twitter-based professional learning community develop learning and practice? Methods: Data were generated from 901 tweets between 100 participants; and 18 in-depth semi-structured elicitation interviews with participants and moderators of the Twitter-based professional learning community. Data were analysed through a process of deliberation, and a relativist approach informed quality. Findings: Two themes are reported to explain the nature of the Twitter-based professional learning community and the different types of characteristics of #pechat that developed learning and practice. The first theme engagement shows how different participants of #pechat engaged with discussions and how moderators played a key role in facilitating discussions between participants. The second theme shared practices shows how discussions between participants of #pechat led to the development of new practices that some teachers were able to use to accomplish particular objectives in their physical education lessons. Conclusion: The analysis of the data provided evidence to suggest that #pechat is a PLC and is representative of an established group of practitioners. These characteristics should be considered in the design of future online professional development experiences. Facilitator or moderator training could support the development of social media based PLCs that subsequently and positively impact on teachers’ practices.ACCEPTEDpeer-reviewe

A framework for conceptualizing how narratives from health-care consumers might improve or impede the use of information about provider quality

Consumers choosing a health-care provider have access to diverse information including narratives by patients about their prior experiences. However, little research has examined how narratives might improve or impede the use of information about the quality of providers’ performance. This paper describes a conceptual framework for examining mechanisms by which narrative information might influence consumer judgments and decisions about providers. We conducted a conceptual review of risk communication and behavioral decision research. We synthesized the literature to form the foundation of a conceptual framework for assessing how narrative information about provider quality impacts consumer decisions about providers. We identified four key characteristics of narratives (convey emotion; explain logic; provide relational information; and capture naturalistic experience) that may address four consumer needs (avoid surprise and regret; recognize dominant options; motivate to act or not act; and make multi-attribute tradeoff decisions). We also identified three main functions of narratives (provide a simple, powerful cue; imbue quality information with meaning; and stimulate cognition and behavior) in four decision contexts (short-term treatments; external disruptions; chronic illness; problematic experiences). A rigorous research program can be derived from the conceptual framework to generate evidence-based recommendations about whether and how patient narratives might encourage: (1) more reasoned decisions; (2) consistency with a patient’s own values/preferences; and (3) engagement with provider quality information. Research results can be used then to develop robust guidance for health communicators reporting diverse and often incommensurate performance metrics

PREDICTION OF TOXICANT-SPECIFIC GENE EXPRESSION SIGNATURES FOLLOWING CHEMOTHERAPEUTIC TREATMENT OF BREAST CELL LINES

Global gene expression profiling has demonstrated that the predominant cellular response to a range of toxicants is a general stress response. This stereotyped environmental stress response commonly includes repression of protein synthesis and cell-cycle–regulated genes and induction of DNA damage and oxidative stress–responsive genes. Our laboratory recently characterized the general stress response of breast cell lines derived from basal-like and luminal epithelium after treatment with doxorubicin (DOX) or 5-fluorouracil (5FU) and showed that each cell type has a distinct response. However, we expected that some of the expression changes induced by DOX and 5FU would be unique to each compound and might reflect the underlying mechanisms of action of these agents. Therefore, we employed supervised analyses (significance analysis of microarrays) to identify genes that showed differential expression between DOX-treated and 5FU-treated cell lines. We then used cross-validation analyses and identified genes that afforded high predictive accuracy in classifying samples into the two treatment classes. To test whether these gene lists had good predictive accuracy in an independent data set, we treated our panel of cell lines with etoposide, a compound mechanistically similar to DOX. We demonstrated that using expression patterns of 100 genes we were able to obtain 100% predictive accuracy in classifying the etoposide samples as being more similar in expression to DOX-treated than to 5FU-treated samples. These analyses also showed that toxicant-specific gene expression patterns, similar to general stress responses, vary according to cell type

AAPM medical physics practice guideline 10.a.: Scope of practice for clinical medical physics.

The American Association of Physicists in Medicine (AAPM) is a nonprofit professional society whose primary purposes are to advance the science, education, and professional practice of medical physics. The AAPM has more than 8000 members and is the principal organization of medical physicists in the United States. The AAPM will periodically define new practice guidelines for medical physics practice to help advance the science of medical physics and to improve the quality of service to patients throughout the United States. Existing medical physics practice guidelines will be reviewed for the purpose of revision or renewal, as appropriate, on their fifth anniversary or sooner. Each medical physics practice guideline (MPPG) represents a policy statement by the AAPM, has undergone a thorough consensus process in which it has been subjected to extensive review, and requires the approval of the Professional Council. The medical physics practice guidelines recognize that the safe and effective use of diagnostic and therapeutic radiation requires specific training, skills, and techniques as described in each document. As the review of the previous version of AAPM Professional Policy (PP)-17 (Scope of Practice) progressed, the writing group focused on one of the main goals: to have this document accepted by regulatory and accrediting bodies. After much discussion, it was decided that this goal would be better served through a MPPG. To further advance this goal, the text was updated to reflect the rationale and processes by which the activities in the scope of practice were identified and categorized. Lastly, the AAPM Professional Council believes that this document has benefitted from public comment which is part of the MPPG process but not the AAPM Professional Policy approval process. The following terms are used in the AAPM's MPPGs: Must and Must Not: Used to indicate that adherence to the recommendation is considered necessary to conform to this practice guideline. Should and Should Not: Used to indicate a prudent practice to which exceptions may occasionally be made in appropriate circumstances

Impact of a Pharmacy Benefit Change on New Use of Mail Order Pharmacy among Diabetes Patients: The Diabetes Study of Northern California (DISTANCE)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110855/1/hesr12223-sup-0001-AuthorMatrix.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/110855/2/hesr12223.pd

Time evolution of the chiral phase transition during a spherical expansion

We examine the non-equilibrium time evolution of the hadronic plasma produced in a relativistic heavy ion collision, assuming a spherical expansion into the vacuum. We study the $O(4)$ linear sigma model to leading order in a large-$N$ expansion. Starting at a temperature above the phase transition, the system expands and cools, finally settling into the broken symmetry vacuum state. We consider the proper time evolution of the effective pion mass, the order parameter $\langle \sigma \rangle$, and the particle number distribution. We examine several different initial conditions and look for instabilities (exponentially growing long wavelength modes) which can lead to the formation of disoriented chiral condensates (DCCs). We find that instabilities exist for proper times which are less than 3 fm/c. We also show that an experimental signature of domain growth is an increase in the low momentum spectrum of outgoing pions when compared to an expansion in thermal equilibrium. In comparison to particle production during a longitudinal expansion, we find that in a spherical expansion the system reaches the ``out'' regime much faster and more particles get produced. However the size of the unstable region, which is related to the domain size of DCCs, is not enhanced.Comment: REVTex, 20 pages, 8 postscript figures embedded with eps