Practical 1: Paper Review

Question 1

What are impact factors?

Answer 1

Impact factors are used to measure the importance of a journal by calculating the number of times selected articles are cited within the last few years.

The higher the impact factor, the more highly ranked the journal

Question 2

Define impact factor

Answer 2

It is the average number of citations per paper published in that journal during the two preceding years

Question 3

How is impact factor calculated?

Answer 3

A = the number of times articles published in 2022 and 2023 were cited by indexed journals during 2024
B = the total number of “citable items” published by that journal in 2022 and 2023
=> 2024IF = A/B

Question 4

Explain in your own words how impact factor is calculated

Answer 4

The number of times articles ppublished in a specific journal have been cited in the past two years divided by the overall number of articles published in that journal in the past two years

Question 5

What is a review article

Answer 5

An attempt to sum up the current thinking on topic
They are usually written by an expert in the field
They contain information such as:
- main people working in the field
- recent advances and discoveries
- significant gaps in the field
- current debates
- ideas of where the research may go next

Question 6

What are the six steps to submitting a paper?

Answer 6

Drafted by a corresponding author

Approved by the other authors

Submitted electronically (including references, images, supplemental data etc)

Review by scientist in the field (peer reviewed)

Accepted/accepted with changes/rejected

Correct and resubmission

Question 7

What are the different organisational components of a paper?

Answer 7

IMRAD (introduction, materials, results and discussion)

Also; title, abstract, authors, acknowledgements, declarations, references

Tables, figures, legends, online supplemental material (usually gross data, genes etc)

Question 8

What is an introduction to a paper

Answer 8

A background to the work and the rationale for the study

Question 9

What is the materials/methods of a paper?

Answer 9

A description of the work undertook - should be in sufficient detail to repeat experiment

Question 10

What is the results of a paper?

Answer 10

Report of the data generated, graphs etc

Question 11

What is the discussion of a paper?

Answer 11

What are the significance of the results
What is their context with the wider literature

Question 12

What is a p-value?

Answer 12

A measure of how likely the result you obtained is by random chance

p=1 would be random chance
p=0.00001 would be very unlikely to be random chance

Question 13

What is usually our p-value cut off?

Answer 13

p<0.05 for p-value results

This means we can be 95% sure that the results are real

Question 14

What are three characteristics of a good paper?

Answer 14

They should progress logically

They should not be cluttered with acronyms and jargon

They should be clear about methods employed

Question 15

What are four characteristics of good study design?

Answer 15

High number of subjects or high numbers of replicated experiments

Correct controls (positive and negative)

Double-blind, placebo controlled drug tests

Correct randomisation

Question 16

What are five signs of a bad paper

Answer 16

Information delivery failure - incomprehensible, badly written, needlessly complicated

A lack of evidence for the hypothesis. Was the theory tested using only one kind of approach or was it repeated too few times?

Novelty - a paer must present something new and timely

Ease of replicatoin - sufficient detail presented such that others could reproduce the experiments

Outrageous hypotheses - making too much of these results

Question 17

What two drugs did our paper look at?

Answer 17

Basiliximab
Alemtuzumab

Question 18

What is Basiliximab, how does it work?

Answer 18

It is a monoclonal antibody which binds and blocks the interleukin-2 receptor located on the surface of activated T lymphocytes

It prevents binding of IL-2 to the IL-2-R of CD4 T cells (which normally supports the development and homeostasis of regulatory T cells)

Question 19

What is Alemtuzumab, how does it work?

Answer 19

Alemtuzumab is a depleting agent i.e. it kills cells

It binds to CD-52 on CD4 T-cells -> it kills T cells (lyses lymphocytes)

Binding to CD-52 on CD4 T cells brings about complement activation result in cell lysis - preventing rejection but has bad renal side effects

Question 20

How was rejection monitored in the patients in our paper?

Answer 20

Flow cytometric measurement of de novo HLA class I and II donor-specific antibodies at 4 months and 1 year post transplant

Serum creatinine levels, creatinine clearance from 24hour urine and kidney biopsies for C4d at 4months and 1 year post trasnplant

Question 21

How are DSAs measured using flow cytometry?

Answer 21

EDTA treated serum sample
Looking for IgG antibodies against HLA class I and II using LABScreen single antigen beads

Question 22

Explain how microbeads are used to measue anti-HLA antibodies using flow cytometry

Answer 22

Microbeads are coated with 100 purified HLA class I or II antigens and preoptimised reagents to detect HLA antibodies in human serum

A negative control serum is used to establish the background value for each bead in a test batch

Test serum is incubated with the coated LABScreen beads

If any HLA natibodies are present in the test serum they will bind to the antigens on the beads

The antibodies are then labelled with PE-conjugated goat anti-human igG (fluorescentl labelled AHG)

The LABScan flow analyser simultaneously detects the fluorescent emission of PE and a specific dye signature from each bead -> allows us to simultaneously identify what HLA antigen has bound (which bead) and if DSA is present (antibody binding)

Question 23

What are DSAa?

Answer 23

Donor specific antibodies

Anti HLA antibodies formed against MHC I or II

Question 24

How do we know if the anti-HLA antibodies present are against MHC I or II?

Answer 24

We can only find out by separatin the lymphocytes of a blood sample into T lymphs (MHCI) and B lymphs (MHCI and II)

If binding only occurs with B lymphs then we know its only anti-HLA antibodies agains MHC II

If binding occurs in T lymphs only we know its only anti-HLA antibodies against mHC I

If binding occurs in both we know there is definitely anti-HLA against MHC I but cannot confirm anti-MHC class II

Question 25

What do we use anti-C4d as an indicator of rejection in tissues?

Answer 25

C4d is a deposited product of complement

C4d is very stable and is therefore a good IHC target

Question 26

What is the prozone effect?

Answer 26

This is interference caused by very high levels of antibodies

So positive the sample is negative upon addition of AHG

• so much binding occurs that there is no room form cross binding for agglutination etc

Question 27

What is an induction therapy?

Answer 27

An immunosuprresive therapy administered at time of transplant to reduce rejection

Question 28

What were the concluions of the paper?

Answer 28

Basilizimab treated patients did not produce DSAs after 1 year of treatment, while 20% of Alemtuzumab patients did

There was no difference between kidney function results or C4d deposition

Question 29

What is PRA?

Answer 29

Pannel reactive antibody

It is expressed as a % of population against which the recipient has DSA against

e.g. 20% PRA means the recipient produces antibodies against 20% of the population

Question 30

What is KDPI

Answer 30

Kidney donor profile index

a numerical measure that combines ten donor factors, including clinical parameters and demographics, to summarize into a single number the quality of deceased donor kidneys relative to other recovered kidneys

A measure of how a kidney will function post transplant

Question 31

What does a KDPI of 20 mean?

Answer 31

It means the kidney will function better than 80% of transplanted kidneys

You want a lot KDPI

Question 32

What does a KDPI of 20 mean?

Answer 32

It means the kidney will function better than 80% of transplanted kidneys

You want a lot KDPI