20141030 Edanz Kyushu Session 2

transcript

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.

photosynthesis

Sunlight

Aims of this study

Unmanned aerial vehicles (UAV)

Photographs

Ground survey

Number of fallen trees

Methods

Unmanned aerial vehicle equipped with a camera

Map of survey area

Results

211 aerial photographs

Mosaic of photos

Effect of tree characteristics on identification

Ground-Surveryfallen trees

Visuallyidentifiedfallen trees

Maximum trunk width (m)

>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

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

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.

photosynthesis

Sunlight

Aims of this study

Unmanned aerial vehicles (UAV)

Photographs

Ground survey

Number of fallen trees

Methods

Unmanned aerial vehicle equipped with a camera

Map of survey area

Results

211 aerial photographs

Mosaic of photos

Ground-Surveryfallen trees

Visuallyidentifiedfallen trees

Maximum trunk width (m)

>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

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

• 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

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

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

Effects of transgene on plant height

GM plants had similar heights as controls in both glasshouse and field environments

Glasshouse Field

GM Control Control GM

Journal club

Effects of transgene on seed yield

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

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

Different levels of expression of Pm3b…why?

• Cell culture-mediated effects

• Position effect (where it inserted in the genome)

• Anything else?

Journal club

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

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

literature Where can I find it?

Online Databases

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

literature Navigating databases

literature How to choose an article

– Online databases

Review articles

– Review articles

literature Journal websites

Stay up to date

Most viewed

Most cited

literature Sign up for alerts

Email alerts

Follow on social network sites

literature Social networks

Facebook Twitter

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

literature

Background

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

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

literature

Bentall et al. Am J Transplant. 2013;13:76–85.

Methods

Conclusions

Background

Results

Finding information in abstracts

literature

Key words - objectives: aim, examined, explored, studied, investigated, but, however

Key words – results: showed, compared, identified, found, stronger, higher, lower

Key words – conclusions: conclusion, summary

Key words in abstracts

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!

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”

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

Paper management

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

Paper management

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

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

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

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?

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

Reading strategies Introduction

General introduction

Specific aims Aims

Current state of the field

Problem in the field

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

Reading strategies Discussion

Summary of findings

Relevance of findings

Implications for the field

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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20141030 Edanz Kyushu Session 2

Education