Critical review of key papers in biomedical imaging

Transcription

1 Critical review of key papers in biomedical imaging Organisers: Dr. Ivana Drobnjak, Dr. Tammy Kalber, Dr. Andrew Melbourne. journal_club/

2 Contents Course Aims Course Structure Course Assessment Course Papers Article writing Article reading Next week s article And finally an exercise

3 Website

4 Website

5 Aims and Objectives Reading and understanding scientific literature is a crucial skill for research The DTP Journal Club aims to equip students with the relevant skills to review the literature in their research field The DTP Journal Club will help improve Presentation Skills Critical thinking Scientific discussion Literature review skills Scientific reading and writing Raise awareness of biomedical imaging at UCL

6 Papers Key papers are chosen by Academic Staff members who will then lead the discussion In the first term we will have papers lead by: David Hawkes CMIC Sebastien Ourselin CMIC Erik Arstad Chemistry David Atkinson UCH Gary Zhang CMIC Dan Stoyanov CMIC Xavier Golay IoN Brian Hutton - UCH

7 Class Structure During the year there will be two rotations of presentations We encourage you to work together, for instance in pairs. Each week, one student will be asked to present a paper The presentation will be followed by discussion from the rest of the class contributing questions for discussion and their opinions. The academic staff member will be available to answer more technical questions..

8 Assessment 1) Class presentation (twice during the year) 2) Class contribution (throughout the year) 3) Individual paper review (twice during the year at the end of each rotation) Class contribution Presentation Written review

9 Assessment Class presentation (once per term) In the week that each student presents they will be assessed on: General presentation skills Understanding of the paper Understanding the context of the paper The strength of their conclusions Fielding of questions

10 Assessment Class contribution (throughout each term) Students are expected to contribute to discussion throughout the term: This will be primarily by providing questions for discussion and by providing opinions Discussion of other student s questions is strongly encouraged In addition you are asked to quickly summarise each paper in advance of the session Attendance will also form part of assessment

11 Assessment Class contribution (pre-session summary) You are asked to quickly summarise each paper in advance of the session: 1. What is the problem being solved 2. In your opinion, which previous work(s) were the most fundamental for this study (if any)? 3. How did this paper solve the problem? 4. Give two main limitations of the study? 5. How does their solution compare with others (if there are any)? 6. Is anyone using their solution today?

12 Assessment Individual paper review (once per term) Each student will submit a written review of one paper after each rotation: This can be any paper from that term Reviews should introduce the paper s key points and limitations and discuss the impact of the paper in relation to it s contemporary literature. We expect the reviews to be less than 1000 words!

13 Ivana s five law s of effective paper reading: 1. What are the key points? 2. What are the key limitations? 3. Why is the paper relevant? 4. Are the results plausible? 5. Are the conclusions supported by the results?

14 Course Papers Papers have been chosen by academic staff members for being key in their field. In general, the papers have been followed by a substantial body of work. Last year s paper choices were influenced by: Modality Style (technical/clinical/biological/review) Authorship Geography Citations

16 Course Papers: Modality

17 Course Papers: Geography

18 Course Papers: Geography & Modality

20 Article Writing What makes a good paper? How is a paper structured?

21 Article Writing What makes a good paper? Clarity (readers of multiple nationality and background), Reproducibility (fundamental), Predictivity (non-triviality). How is a paper structured?

22 Article Writing What makes a good paper? Clarity (readers of multiple nationality and background), Reproducibility (fundamental), Predictivity (non-triviality). How is a paper structured? Abstract, Introduction, Methods, Results, Conclusion, References.

23 Abstract Example

24 Abstract Example

25 Abstract Example

26 Abstract Example

27 Abstract Example

28 Reference Example

29 Reference Example

30 Article Writing Why do scientists write papers?

31 Article Writing Why do scientists write papers? Rapid communication of ideas, reading a paper quickly and assessing its worth is key, Types of paper, Consensus is established over time.

32 Article Writing Why do scientists write papers? Rapid communication of ideas, reading a paper quickly and assessing its worth is key, Types of paper, Consensus is established over time. Citations Why publish in journals?

33 Article Writing Why do scientists write papers? Rapid communication of ideas, reading a paper quickly and assessing its worth is key, Types of paper, Consensus is established over time. Citations Traceability, Continued peer review, Impact factor / citation counting / H-factor. Why publish in journals?

34 Article Writing Why do scientists write papers? Rapid communication of ideas, reading a paper quickly and assessing its worth is key, Types of paper, Consensus is established over time. Citations Traceability, Continued peer review, Impact factor / citation counting / H-factor. Why publish in journals? Use of peer review

35 Article Writing Use of peer-review Why do we do it and what is in it for us?! Blinding, Poor quality work, plagiarism and fraud, The implications of poor peer review can be large: Sokal Hwang Wakefield

36 Contents Course Aims Course Structure Course Assessment Course Papers Article writing Article reading Next week s article (well two weeks time ) And finally an exercise

37 The First Paper (chaired by Gary Zhang) Modeling dendrite density from magnetic resonance diffusion measurements Sune N. Jespersen, a, Christopher D. Kroenke, b Leif Østergaard, a Joseph J.H. Ackerman, b,c,d and Dmitriy A. Yablonskiy b,e a Center of Functionally Integrative Neuroscience, Aarhus University Hospital Århus Sygehus, Nørrebrogade 44, Building 30, 8000 Århus C, Denmark b Department of Radiology, Washington University, St. Louis, Missouri 63110, USA c Department of Chemistry, Washington University, St. Louis, Missouri 63110, USA d Department of Internal Medicine, Washington University, St. Louis, Missouri 63110, USA e Department of Physics, Washington University, St. Louis, Missouri 63110, USA Received 15 September 2006; accepted 29 October 2006 Available online 22 December 2006 Diffusion-weighted imaging (DWI) provides a noninvasive tool to probe tissue microstructure. We propose a simplified model of neural cytoarchitecture intended to capture the essential features important for water diffusion as measured by NMR. Two components contribute to the NMR signal in this model: (i) the dendrites and axons, which are modeled as long cylinders with two diffusion coefficients, parallel (D L ) and perpendicular (D T ) to the cylindrical axis, and (ii) an isotropic monoexponential diffusion component describing water diffusion within and across all other structures, i.e., in extracellular space and glia cells. The model parameters are estimated from 153 diffusionweighted images acquired from a formalin-fixed baboon brain. A close correspondence between the data and the signal model is found, with the model parameters consistent with literature values. The model provides an estimate of dendrite density from noninvasive MR diffusion measurements, a parameter likely to be of value for understanding normal as well as abnormal brain development and function Elsevier Inc. All rights reserved. Keywords: Diffusion; Neural tissue; Cytoarchitectonics; Spherical harmonics

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40 Rapid paper reading exercise Cerebral organoids model human brain development and microcephaly Madeline A. Lancaster 1, Magdalena Renner 1, Carol-Anne Martin 2, Daniel Wenzel 1, Louise S. Bicknell 2, Matthew E. Hurles 3, Tessa Homfray 4, Josef M. Penninger 1, Andrew P. Jackson 2 & Juergen A. Knoblich 1 The complexity of the human brain has made it difficult to study many brain disorders in model organisms, highlighting the need for an in vitro model of human brain development. Here we have developed a human pluripotent stem cell-derived three-dimensional organoid culture system, termed cerebral organoids, that develop various discrete, although interdependent, brain regions. These include a cerebral cortex containing progenitor populations that organize and produce mature cortical neuron subtypes. Furthermore, cerebral organoids are shown to recapitulate features of human cortical development, namely characteristic progenitor zone organization with abundant outer radial glial stem cells. Finally, we use RNA interference and patient-specific induced pluripotent stem cells to model microcephaly, a disorder that has been difficult to recapitulate in mice. We demonstrate premature neuronal differentiation in patient organoids, a defect that could help to explain the disease phenotype. Together, these data show that three-dimensional organoids can recapitulate development and disease even in this most complex human tissue.

41 Rapid paper reading exercise First individually (10mins) Then in groups of three (10mins) Whole group discussion.

42 Ivana s five law s of effective paper reading: 1. What are the key points? 2. What are the key limitations? 3. Why is the paper relevant? 4. Are the results plausible? 5. Are the conclusions supported by the results?

43 Paper exercise summary 1. What is the problem being solved 2. In your opinion, which previous work(s) were the most fundamental for this study (if any)? 3. How did this paper solve the problem? 4. Give two main limitations of the study? 5. How does their solution compare with others (if there are any)? 6. Is anyone using their solution today?