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Andrew Jackson, PhD
Senior Editor
Kyushu University Department of Agriculture
Session 2 – Reviewing the literature
Kyushu University
30 October 2014
Groups…
Team A (9.5) Mitsudome Takumi
Khansawanh Sisopha Arif Hamed
Sie Thu Minn Truong Tuan Linh
(Eiko Megan Uchida)
Team B (7) Vila Laokom
Ayumi Koyanagi Thi Mar Win
Katsuto Shimizu Vo Hong Tu
Groups…
Team A (12.5) Mitsudome Takumi
Khansawanh Sisopha Arif Hamed
Sie Thu Minn Truong Tuan Linh
(Eiko Megan Uchida)
Team B (11) Vila Laokom
Ayumi Koyanagi Thi Mar Win
Katsuto Shimizu Vo Hong Tu
Activity
Effectiveness of an Unmanned Aerial Survey of Fallen Trees in Eastern Japan Forest
Mitsudome Takumi, Khansawanh Sisopha, Arif Hamed, Sie Thu Minn, Truong Tuan Linh
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Introduction
Knowing the distribution of fallen trees is useful to understand the nutrient and carbon cycling.
Ground based surveys are both time consuming and labor intensive.
CO2
photosynthesis
Sunlight
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Aims of this study
Unmanned aerial vehicles (UAV)
Photographs
Ground survey
Number of fallen trees
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Methods
Unmanned aerial vehicle equipped with a camera
Map of survey area
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Results
211 aerial photographs
Mosaic of photos
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Effect of tree characteristics on identification
0
5
10
15
20
25
30
Ground-Surveryfallen trees
Visuallyidentifiedfallen trees
Maximum trunk width (m)
Nu
mb
er
of
falle
n t
ree
s id
en
tifi
ed
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Effect of tree characteristics on identification
Nu
mb
er o
f fa
llen
tre
es id
enti
fied
0
5
10
15
20
25
>10 5 to 10 0 to 5
Number ofground-Surveyedfallen trees
Number ofVisuallyIdentifiedfallen trees
Maximum trunk length (m)
Conclusions
Effective for identifying: • longer fallen trees • larger trunk width
Smaller fallen trees could not be clearly identified
Advances in imaging technology, could make this an attractive alternative to time consuming ground surveys.
Summary
Implications
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Activity
Effectiveness of an Unmanned Aerial Survey of Fallen Trees in Eastern Japan Forest
Vila Laokom, Ayumi Koyanagi, Thi Mar Win, Katsuto Shimizu, Vo Hong Tu
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Introduction
Knowing the distribution of fallen trees is useful to understand the nutrient and carbon cycling.
Ground based surveys are both time consuming and labor intensive.
CO2
photosynthesis
Sunlight
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Aims of this study
Unmanned aerial vehicles (UAV)
Photographs
Ground survey
Number of fallen trees
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Methods
Unmanned aerial vehicle equipped with a camera
Map of survey area
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Results
211 aerial photographs
Mosaic of photos
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Effect of tree characteristics on identification
0
5
10
15
20
25
30
Ground-Surveryfallen trees
Visuallyidentifiedfallen trees
Maximum trunk width (m)
Nu
mb
er
of
falle
n t
ree
s id
en
tifi
ed
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Effect of tree characteristics on identification
Nu
mb
er o
f fa
llen
tre
es id
enti
fied
0
5
10
15
20
25
>10 5 to 10 0 to 5
Number ofground-Surveyedfallen trees
Number ofVisuallyIdentifiedfallen trees
Maximum trunk length (m)
Conclusions
Effective for identifying: • longer fallen trees • larger trunk width
Smaller fallen trees could not be clearly identified
Advances in imaging technology, could make this an attractive alternative to time consuming ground surveys.
Summary
Implications
Inoue T, et al. (2014) PLoS ONE 9(10): e109881.
Journal club
1. Why does this study need to be done?
2. What did you do and what did you find?
3. How will this study help advance the field?
What are the three questions you need to answer when communicating your research?
Journal club
1. Is the topic scientifically relevant?
2. Is the study design appropriate and up-to-date?
3. Are the results significant?
4. Are the conclusions/interpretations logical and valid?
What are the four questions you need to answer when evaluating an article?
Transgene x environment interactions in genetically modified wheat
Zeller et al. PLoS One. 2010; 5: e11405.
Journal club
Journal club
• GM crops can increase food production • Regulatory authorities require assessment of risk
and performance • May be differences in phenotypic effects
between glasshouses and the field
Why this study needs to be done
No published studies on the ecological behavior of GM and control plants in glasshouse versus field environments.
Journal club
Are the aims topically relevant?
Does the ecological behavior of GM and control plants change in glasshouse versus field environments?
Research problem
Investigated if a transgene could influence disease resistance and overall fitness in
an environment-dependent manner
Objectives
Journal club
What did they do? Are their methods appropriate?
Inserted the transgene Pm3b (resists mildew infection) into four wheat lines
Glasshouse Field
Mildew infection Mildew/ergot infection
Overall fitness* Overall fitness*
80 days (different levels of fertilizer)
*Plant height, vegetative mass, seed number, & seed yield
Journal club
What did they find? Are their results significant?
Fig. S1: Semi-quantitative PCR expression
Pm3b expression
Mlo expression
GM GM GM GM C C C C
1 2 3 4
Lines 2 & 4 show the highest expression of Pm3b
Journal club
What did they find? Are their results significant?
Fig. 1: Glasshouse – Effects of mildew infection and fungicide
• After 1 month, plants were naturally infected with mildew
• Sprayed with fungicide • Evaluated seed yield (80 d)
• GM had better seed yield • Fungicide decreased GM
seed yield • Fungicide improved control
seed yield?
“…the control lines benefited from the fungicide treatment…”
Journal club
What did they find? Are their results significant?
Effects of transgene on mildew infection
High fertilizer Medium fertilizer No fertilizer
GM had lower infection rate in both glasshouse and field environments
Glasshouse Field
Control GM Control GM
Journal club
What did they find? Are their results significant?
Effects of transgene on plant height
High fertilizer Medium fertilizer No fertilizer
GM plants had similar heights as controls in both glasshouse and field environments
Glasshouse Field
GM Control Control GM
Journal club
What did they find? Are their results significant?
Effects of transgene on seed yield
High fertilizer Medium fertilizer No fertilizer
GM plants had higher seed yield in glasshouses, but lower in fields
Glasshouse Field
Journal club
What did they find? Are their results significant? Individual differences in transgene lines
Transgene lines 2 & 4 were most resistant to mildew infection
Glasshouse
Field
1
1 2
2 3
3
4
4
Transgene lines 2 & 4 were most
susceptible to ergot infection
1 2 3 4
C C C C GM GM GM GM
Journal club
Are there conclusions logical?
“This study demonstrates that GM plants can differ in morphological fitness and pathogen-related traits from their control plants.”
Conclusion
GM plants grow better in glasshouse conditions…why?
• Environmental stress (drought, neighbor competition)
• Anything else?
Journal club
Are there conclusions logical?
Different levels of expression of Pm3b…why?
• Cell culture-mediated effects
• Position effect (where it inserted in the genome)
• Anything else?
Journal club
Are there conclusions logical?
Increased ergot infection in GM lines 2 & 4…why?
• Flowering time was different in these lines (data not shown)
• Increased chance that ergot spores could infect
• Anything else?
Journal club
How will this study advance the field?
• Most GM plants are first tested in glasshouses before moving to field testing
• Those that ‘fail’ in the glasshouse are no longer considered
• Implications of this study is that poor-performing GM plants in glasshouses may perform well in the field
• Field testing should always be considered
Journal club
Is this article structured well?
Introduction Okay, except that the research
problem is not clearly identified
Methods Clear, except not clear about damaged
field plants (vandals)
Results
• Statistical tests unclear • Figure S1 wrong online • Mildew infection is higher in
glasshouses is not presented
Journal club
Is this article structured well?
Discussion Terrible!
Well-structured
• Conclusion • Summary of findings • Relevance of findings • Unexpected results • Limitations • Implications
This article
• Conclusion • Limitations • Unexpected results • Implications • Relevance of findings
Journal club
Thank you!
Journal Club Schedule
October 23
October 30 Andrew Jackson (example)
November 6 Vila Laokom, Ayumi Koyanagi
November 13 Mitsudome Takumi, Khansawanh Sisopha
November 20 Thi Mar Win, Katsuto Shimizu
November 27 Arif Hamed, Sie Thu Minn
December 4 Vo Hong Tu, to be confirmed
December 8 Truong Tuan Linh, Eiko Megan Uchida
Seminar series
October 23 Effective presentations
October 30 Reviewing the literature
November 6 Academic publishing
November 13 Research and publication ethics
November 20 Effective writing
November 27 Manuscript structure
December 4 Communicating with journals
December 8 Peer review and revisions
Today’s presentation
October 23 Effective presentations
October 30 Reviewing the literature
November 6 Academic publishing
November 13 Research and publication ethics
November 20 Effective writing
November 27 Manuscript structure
December 4 Communicating with journals
December 8 Peer review and revisions
Finding the information you want
Section 1
Coverage and Staffing Plan Searching for
literature What do you want to
know?
Specific question about familiar topic
Want to understand a new topic
Find a reported method
Find evidence to support a theory
General background reading
Compare your findings
1-1
Coverage and Staffing Plan Searching for
literature Where can I find it?
Online Databases
1-2
Coverage and Staffing Plan Searching for
literature Searching google
Quotes “…” “wheat genetically modified”
Exclude - genetically modified -wheat
Blank * genetically modified *
Related: Related: pubs.acs.org/journal/jafcau
Site: Site: pubs.acs.org/journal/jafcau
Range X..Y wheat genetically modified 2010..2014
1-3
Coverage and Staffing Plan Searching for
literature Navigating databases
1-4
Coverage and Staffing Plan Searching for
literature How to choose an article
– Online databases
1-5
Coverage and Staffing Plan Searching for
literature How to choose an article
Review articles
1-6
Coverage and Staffing Plan Searching for
literature How to choose an article
– Review articles
1-7
Coverage and Staffing Plan Searching for
literature Journal websites
1-8
Stay up to date
Most viewed
Most cited
Coverage and Staffing Plan Searching for
literature Sign up for alerts
Email alerts
Follow on social network sites
1-9
Coverage and Staffing Plan Searching for
literature Social networks
Facebook Twitter
1-10
Coverage and Staffing Plan Searching for
literature Reading Abstracts
What are you looking for?
Where is it found?
What are the key words?
Aims, key findings, implications
Introduction, Results, and Discussion
1-11
Coverage and Staffing Plan Searching for
literature
Background
Aims
Methods
Results
Conclusions
What are the 5 parts of an abstract?
Reading abstracts
Why the study was done
Objectives/hypothesis
Approach/methodology
Most important findings
Implications for the field
1-12
Coverage and Staffing Plan Searching for
literature
Five-year outcomes in living donor kidney transplants with a positive crossmatch
Renal transplant candidates with high levels of donor-specific anti-HLA antibodies have low transplantation rates and high mortality rates on dialysis. Using desensitization protocols, good short-term outcomes are possible in “positive crossmatch kidney transplants (+XMKTx)”, but long-term outcome data are lacking. The aim of the current study was to determine actual 5-year graft outcomes of +XMKTx. We compared graft survival and the functional and histologic status of 102 +XMKTx to 204 −XMKTx matched for age and sex. Actual 5-year death-censored graft survival was lower in the +XMKTx group (70.7% vs. 88.0%, p < 0.01) and chronic injury (glomerulopathy) was present in 54.5% of surviving grafts. Graft survival was higher in recipients with antibody against donor class I only compared with antibody against class II (either alone or in combination with class I) (85.3% vs. 62.6%, p = 0.05) and was similar to −XMKTx (85.3 vs. 88.0%, p = 0.64). Renal function and proteinuria ranged across a wide spectrum in all groups reflecting the different histological findings at 5 years. We conclude that when compared to −XMKTx, +XMKTx have inferior outcomes at 5 years, however, almost half of the surviving grafts do not have glomerulopathy and avoiding antibodies against donor class II may improve outcomes.
Bentall et al. Am J Transplant. 2013;13:76–85.
Finding information in abstracts
1-13
Coverage and Staffing Plan Searching for
literature
Five-year outcomes in living donor kidney transplants with a positive crossmatch
Renal transplant candidates with high levels of donor-specific anti-HLA antibodies have low transplantation rates and high mortality rates on dialysis. Using desensitization protocols, good short-term outcomes are possible in “positive crossmatch kidney transplants (+XMKTx)”, but long-term outcome data are lacking. The aim of the current study was to determine actual 5-year graft outcomes of +XMKTx. We compared graft survival and the functional and histologic status of 102 +XMKTx to 204 −XMKTx matched for age and sex. Actual 5-year death-censored graft survival was lower in the +XMKTx group (70.7% vs. 88.0%, p < 0.01) and chronic injury (glomerulopathy) was present in 54.5% of surviving grafts. Graft survival was higher in recipients with antibody against donor class I only compared with antibody against class II (either alone or in combination with class I) (85.3% vs. 62.6%, p = 0.05) and was similar to −XMKTx (85.3 vs. 88.0%, p = 0.64). Renal function and proteinuria ranged across a wide spectrum in all groups reflecting the different histological findings at 5 years. We conclude that when compared to −XMKTx, +XMKTx have inferior outcomes at 5 years, however, almost half of the surviving grafts do not have glomerulopathy and avoiding antibodies against donor class II may improve outcomes.
Bentall et al. Am J Transplant. 2013;13:76–85.
Aims
Methods
Conclusions
Background
Results
Finding information in abstracts
1-14
Coverage and Staffing Plan Searching for
literature
Key words - objectives: aim, examined, explored, studied, investigated, but, however
Key words – results: showed, compared, identified, found, stronger, higher, lower
Five-year outcomes in living donor kidney transplants with a positive crossmatch
Renal transplant candidates with high levels of donor-specific anti-HLA antibodies have low transplantation rates and high mortality rates on dialysis. Using desensitization protocols, good short-term outcomes are possible in “positive crossmatch kidney transplants (+XMKTx)”, but long-term outcome data are lacking. The aim of the current study was to determine actual 5-year graft outcomes of +XMKTx. We compared graft survival and the functional and histologic status of 102 +XMKTx to 204 −XMKTx matched for age and sex. Actual 5-year death-censored graft survival was lower in the +XMKTx group (70.7% vs. 88.0%, p < 0.01) and chronic injury (glomerulopathy) was present in 54.5% of surviving grafts. Graft survival was higher in recipients with antibody against donor class I only compared with antibody against class II (either alone or in combination with class I) (85.3% vs. 62.6%, p = 0.05) and was similar to −XMKTx (85.3 vs. 88.0%, p = 0.64). Renal function and proteinuria ranged across a wide spectrum in all groups reflecting the different histological findings at 5 years. We conclude that when compared to −XMKTx, +XMKTx have inferior outcomes at 5 years, however, almost half of the surviving grafts do not have glomerulopathy and avoiding antibodies against donor class II may improve outcomes.
Key words – conclusions: conclusion, summary
Key words in abstracts
1-15
Activity 1
1. You are a medical student interested in this topic. Choose two keywords from this article that you might use to search for more information.
French nurse cured of Ebola contracted in Liberia
The first French national to be infected with the virus was airlifted back to France on September 19 and received experimental treatment at a military hospital. Ebola has killed more than 3,300 people in west Africa in the worst-ever outbreak of the disease. The first use of an experimental antiviral medicine, favipiravir, for the treatment of Ebola was authorized for the first time.
http://www.msn.com/en-in/news/world/french-nurse-cured-of-ebola-contracted-in-liberia/ar-BB7qOz9
Date range search
Activity 1
1. You are interested in using this drug to treat Ebola. You would like more specific details
2. You would like more general background about the situation in Africa.
3. You are concerned about how people might behave here, if there was an out break of Ebola
2. Choose one article that you think maybe interesting in the following situations.
Successful treatment of advanced Ebola virus infection with favipiravir
Ebola in west Africa
Ebola viral disease in Nigeria: The panic and cultural threat
Activity 1
3. Read the abstract of Successful treatment of advanced Ebola virus infection with favipiravir. A. Why is this study important? B. What did they do? C. What did they find? D. Would you use this drug to treat Ebola?
Paper management tools
Section 3
Paper management
Why use paper management tools?
Avoid trying to find an article like this!
2-1
Paper management Papers
Search by keywords, authors, journals, etc.
Sort articles by authors, titles, journals, or year
Read full screen, Email, or print your articles
Organize your articles in folders and “smart folders”
2-2
Paper management
Reference management software
Why should you use it?
Keeps your references organized Simplifies in-text citations Prepares the reference list in the ‘correct’ format Allows you change reference style easily if you
change journals
2-3
Paper management
Reference management software
EndNote Most established Styles easy to find on journal websites
Which one to use?
RefWorks Web-based Widely used
Mendeley Newer (and free!) Allows collaborations
Papers Easy-to-use interface (iTunes) Great for paper management
2-4
Paper management
Reference management software
Where to find ‘styles’?
Most have the journal styles pre-installed
Can often download up-to-date styles
But always double-check for formatting accuracy
ChemPhysChem
2-5
Reading strategies
Section 2
Reading strategies How often do you read?
Read often!
Learn how native English speakers write
Learn proper argument structure
Learn manuscript structure and style
Get new ideas, identify problems
Discuss with colleagues
3-1
Reading strategies
What are you looking for?
Where is it found?
What are the key words?
Key points
Aims, key findings, implications
Introduction, Results, and Discussion
3-2
Reading strategies How to read an article
From start to finish?
Section by
section? Not efficient!
What do you want to know?
Where can you find it?
3-3
Reading strategies
Read Figures and then Results
Read Discussion for interpretation
Self-assess knowledge of topic
Read Title and Abstract first
Refer to Introduction and Methods if necessary
Strategies for reading
Read last paragraph of introduction for hypothesis/objectives
3-4
Reading strategies Introduction
General introduction
Specific aims Aims
Current state of the field
Problem in the field
3-5
Reading strategies Results
What they found
Order of results is logical, tells a story
Each subsection often corresponds to one figure
1. Initial observation 2. Characterization 3. Application
3-6
Reading strategies Discussion
Summary of findings
Relevance of findings
Implications for the field
3-7
Activity 2
• Introduction • Methods • Results • Discussion
In teams choose which parts of this paper you would like to have.
Activity 2
1. Why is this study important? 2. How was it done? 3. What did they find? 4. What are the implications of the findings?
Why is this study important?
Rarely human communities coexist in harmony with large predators. We examine the mechanisms permitting the coexistence of Asiatic lions (Panthera leo persica) and pastoral communities (Maldharis) in the Gir forests, India. Understanding people-carnivore relationship, is crucial for the conservation of large carnivores. Although large carnivores sometimes kill humans [5], [6], the major form of conflict arises due to their habit of predating livestock and the resulting threat on economic security of the pastorals. The Maldharis are on such community that raises livestock in an open reserve with Lions. Although the Maldharis have can suffer loses to their livestock, they also benfit from the free access to the forests resources . We examined the notion that the tolerance of the Maldharis towards lions is not only because of their beliefs but also because it is economically more profitable to live with lions
Background
How was it done?
We monitored six Maldhari settlements between 2005 and 2007 to quantify seasonal livestock holding. in western India. We estimated lion population using closed-population mark-recapture [34]. We used cues, including tracks, roars and alert behavior of prey to locate lions. A total head count of livestock in each ness was carried out. The lions’ diet was determined by analysis of 165 lion scats [43], [44] and by monitoring of four radio-collared lions continuously for 5–12 day sessions (detailed below) within the study area. At each study a local Maldhari was employed to provide information to the authors in the event of a livestock death.
Methods
What did they find?
We obtained 36 sightings of 20 individual lions (3 adult males, 10 adult females and 7 sub-adults). Lion density was calculated as 15±0.1 SE/100 km2. Livestock density was 25–31/km2 with buffaloes being most abundant. Average livestock holding of Maldhari families was 33±3 SE. Most (97.6%) lion scat contained a single prey type, while 2.4% of the scats had two prey items. Wild ungulates accounted for 76.4% of all prey occurrences, while domestic livestock (buffalo 13.7% and cattle 7.8%) contributed the rest (Table 1).
Results
What did they find?
Lion density was higher in areas with Maldhari livestock in comparison to areas without livestock. We estimated livestock to contribute between 25 to 42% of lions’ biomass consumptions, of which only 16% was predated; the rest scavenged. The lions predated mostly on unproductive cattle. The current lifestyles and livestock holdings of Maldharis seem to be beneficial to both lions and local pastoralists. Lions get a considerable part of their food from Maldhari livestock and Maldharis profit substantially by free access to forest resources. The local pastoralists have free grazing rights and unproductive cattle were mostly targeted by lion predation.
Discussion
What are the implications?
We conclude that a combination of strict protection regime for lions, Maldharis’ traditional reverence towards lions and the livelihood economics permit the delicate balance of lion-Maldhari coexistence. This situation is mutually beneficial to both groups. Indefinite increase in human and livestock population within Gir might upset this equilibrium undermining the conservation objectives. We conclude that a combination of strict protection regime for lions, Maldharis’ traditional reverence towards lions and the livelihood economics permit the delicate balance of lion-Maldhari coexistence. This situation is mutually beneficial to both groups. Indefinite increase in human and livestock population within Gir might upset this equilibrium undermining the conservation objectives.
Discussion
Thank you!
Any questions?
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Andrew Jackson: [email protected]