717 research outputs found
Toward Interpretable Deep Reinforcement Learning with Linear Model U-Trees
Deep Reinforcement Learning (DRL) has achieved impressive success in many
applications. A key component of many DRL models is a neural network
representing a Q function, to estimate the expected cumulative reward following
a state-action pair. The Q function neural network contains a lot of implicit
knowledge about the RL problems, but often remains unexamined and
uninterpreted. To our knowledge, this work develops the first mimic learning
framework for Q functions in DRL. We introduce Linear Model U-trees (LMUTs) to
approximate neural network predictions. An LMUT is learned using a novel
on-line algorithm that is well-suited for an active play setting, where the
mimic learner observes an ongoing interaction between the neural net and the
environment. Empirical evaluation shows that an LMUT mimics a Q function
substantially better than five baseline methods. The transparent tree structure
of an LMUT facilitates understanding the network's learned knowledge by
analyzing feature influence, extracting rules, and highlighting the
super-pixels in image inputs.Comment: This paper is accepted by ECML-PKDD 201
Radiation dose differences between thoracic radiotherapy planning CT and thoracic diagnostic CT scans
Purpose: To compare the absorbed dose from computed tomography (CT) in radiotherapy planning (RP CT) against those from diagnostic CT (DG CT) examinations and to explore the possible reasons for any dose differences.
Method: Two groups of patients underwent CT-scans of the thorax with either DG-CT (n=55) or RP-CT (n=55). Patients from each group had similar weight and body mass index (BMI) and were divided into low (25). Parameters including CTDIvol, DLP and scan length were compared.
Results: The mean CTDIvol and DLP values from RP-CT (38.1 mGy, 1472 mGy·cm) are approximately four times higher than for DG-CT (9.63 mGy, 376.5 mGy·cm). For low BMI group, the CTDIvol in the RP-CT scans (36.4 mGy) is 6.3 times higher than the one in the DG-CT scans (5.8 mGy). For high BMI group, the CTDIvol in the RP-CT (39.6 mGy) is 2.5 times higher than the one in the DG-CT scans (15.8 mGy). In the DG-CT scans a strong negative linear correlation between noise index (NI) and mean CTDIvol was observed (r =-0.954, p=0.004); the higher NI, the lower CTDIvol. This was not the case in the RP-DG scans.
Conclusion: The absorbed radiation dose is significantly higher and less BMI dependent for RP-CT scans compared to DG-CT. Image quality requirements of the examinations should be researched to ensure that radiation doses are not unnecessarily high
Traditional Roles in a Non‐Traditional Setting: Genetic Counseling in Precision Oncology
Next generation sequencing technology is increasingly utilized in oncology with the goal of targeting therapeutics to improve response and reduce side effects. Interpretation of tumor mutations requires sequencing of paired germline DNA, raising questions about incidental germline findings. We describe our experiences as part of a research team implementing a protocol for whole genome sequencing (WGS) of tumors and paired germline DNA known as the Michigan Oncology Sequencing project (MI‐ONCOSEQ) that includes options for receiving incidental germline findings. Genetic counselors (GCs) discuss options for return of results with patients during the informed consent process and document family histories. GCs also review germline findings and actively participate in the multi‐disciplinary Precision Medicine Tumor Board (PMTB), providing clinical context for interpretation of germline results and making recommendations about disclosure of germline findings. GCs have encountered ethical and counseling challenges with participants, described here. Although GCs have not been traditionally involved in molecular testing of tumors, our experiences with MI‐ONCOSEQ demonstrate that GCs have important applicable skills to contribute to multi‐disciplinary care teams implementing precision oncology. Broader use of WGS in oncology treatment decision making and American College of Medical Genetics and Genomics (ACMG) recommendations for active interrogation of germline tissue in tumor‐normal dyads suggests that GCs will have future opportunities in this area outside of research settings.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147078/1/jgc40655.pd
A screen to identify drug resistant variants to target-directed anti-cancer agents
The discovery of oncogenes and signal transduction pathways important for mitogenesis has triggered the development of target-specific small molecule anti-cancer compounds. As exemplified by imatinib (Gleevec), a specific inhibitor of the Chronic Myeloid Leukemia (CML)-associated Bcr-Abl kinase, these agents promise impressive activity in clinical trials, with low levels of clinical toxicity. However, such therapy is susceptible to the emergence of drug resistance due to amino acid substitutions in the target protein. Defining the spectrum of such mutations is important for patient monitoring and the design of next-generation inhibitors. Using imatinib and BCR/ABL as a paradigm for a drug-target pair, we recently reported a retroviral vector-based screening strategy to identify the spectrum of resistance-conferring mutations. Here we provide a detailed methodology for the screen, which can be generally applied to any drug-target pair
Genetic dissection of quantitative and qualitative traits using a minimum set of barley Recombinant Chromosome Substitution Lines
BACKGROUND:Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar 'Harrington' as the recurrent parent, and a wild barley accession from the Fertile Crescent 'Caesarea 26-24', as the donor parent (Matus et al. Genome 46:1010-23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. METHODS:Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388-92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. RESULTS:We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. CONCLUSION:This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.Carla De la Fuente Cantó, Joanne Russell, Christine A. Hackett, Allan Booth, Siobhan Dancey, Timothy S. George and Robbie Waug
Footprints- In the Footprints of Squier and Davis: Archeological Fieldwork in Ross County, Ohio
TABLE OF CONTENTS
Acknowledgements....................................................................iList of Tables...................................................................vii List of Figures...................................................................ix Contributors .........................................................................xiii
Chapter 1
In the Footprints of Squier and Davis : Archeological
Fieldwork in Ross County, Ohio
Mark J. Lynott................................................................................1 Previous Studies in Ohio ...................................................1 Hopewell Studies Today ................................................................4 Recent Field Research ..........................................................................6 Goal of this Volume ................................................................................12
Chapter 2
In Non-mound Space at the Hopewell Mound Group
Jennifer Pederson Weinberger .........................................13 Geophysical Survey .......................................................15Western Village Area.....................................................................16 Near the East Village .....................................................................18 Central Area ............................................................................19 Discussion .......................................................................................19
Chapter 3
Field Studies of the Octagon and Great Circle, High Bank Earthworks Ross County, Ohio
N’omi B. Greber and Orrin C. Shane III ..............................................23 Excavations at the Octagon ............................................................25 Geophysics at the Great Circle ............................................................30 Excavations at the Great Circle ..........................................................33 Radiocarbon Assays ...........................................................................41 Comments ....................................................................................44 Addendum ..........................................................................................46
Chapter 4
Spruce Hill Earthworks: The 1995-1996 National Park Service Investigations
Bret J. Ruby .............................................................................................49 Background .......................................................................................49 The Spruce Hill Earthworks .......................................................................49 Spruce Hill Revisited ......................................................................53 The 1995-1996 National Park Service Investigations ............................53 Discussion and Conclusions ..............................................................61
Chapter 5
Falling Through a Crack in the Core: The Surprise and Demise of Anderson Earthwork
William H. Pickard and Jeffrey W. Weinberger ........................................ 67 History and Setting ..................................................................................68 1993 Excavations ..................................................................................70 Discussion ..............................................................................................72 Conclusion ............................................................................................74
Chapter 6
Middle Woodland and Other Settlement Remains in the Overly Tract Near The Hopeton Earthwork, Ross County, Ohio
William S. Dancey .....................................................................................................77 Research Design.............................................................................77 Artifact Categories and their Distributions..............................................80 Discussion............................................................................................92
Chapter 7
Hopewell Occupation at the Hopeton Earthworks: Large Scale Surface Survey Using GPS Technology
Jarrod Burks and Dawn Walter Gagliano................................................97 The Survey Area ................................................................................98 Survey Methodology .............................................................................99 Survey Results ...................................................................................99 The Surface Data: A Siteless Approach .................................................103 Discussion and Conclusion .........................................................................106 Notes ...................................................................................................107
Chapter 8
Hopewellian Centers in Context: Investigations In and Around the Hopeton Earthworks
Bret J. Ruby And Mark J. Lynott .................................................................109 Surface Survey ......................................................................................110 Redwing Site ...........................................................................................111 Comparisons .........................................................................................118 Conclusions ......................................................................................122
Chapter 9
Searching for Hopewell Settlements: The Triangle Site at the Hopeton Earthworks
Mark Lynott ...................................................................................... 125 Field Investigations ............................................................................127 Geophysical Survey ............................................................................128 1998 Season ....................................................................................128 Features, Artifacts and Radiocarbon Dating ........................................130 Animal Remains ...............................................................................137 Plant Remains ................................................................................138 Interpretations ..............................................................................139
Chapter 10
Geophysical Investigations at the Hopeton Earthworks
John Weymouth, Bruce Bevan, and Rinita Dalan ...............................145 The Cesium Gradiometer Survey ...........................................................146 Cesium Gradiometer Results ...................................................................146 Geoscan Instrument Surveys ..............................................................148 Comparison of Cesium Magnetic and Resistance Data ........................148 Small Circles...........................................................................................149 Trench Excavations ...................................................................................149 Discussion ................................................................................................152 Conclusions ......................................................................................157
Chapter 11
Archeological and Geoarcheological Study of the Rectangular Enclosure at the Hopeton Works
Mark J. Lynott and Rolfe D. Mandel ......................................................159 The Study of the Rectangular Earthwork ................................................161 Geophysical Survey ..............................................................................163 Trench Excavations .............................................................................164 Chronology ........................................................................................170 Geoarcheological Analysis of Trench 1 .................................................172 Interpretations ................................................................................174
Chapter 12
Ohio Hopewell Ritual Craft Production
Katherine A. Spielmann ............................................................ 179Raw Material Procurement ....................................................................180 Hopewell Crafting ................................................................................181 Deposition ...........................................................................................186 Conclusions ....................................................................................188
References Cited .....................................................................................................18
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