Hivanson Week 12 - Revision history

Hivanson: deleted everything because I didn't include references. You can see what I did in the last version

2024-04-18T02:26:52Z

deleted everything because I didn't include references. You can see what I did in the last version

Hivanson: /* Bibliographic Entry */ more bib

2024-04-18T01:56:14Z

‎Bibliographic Entry: more bib

Hivanson: /* Bibliographic Entry */ editorial board

2024-04-18T01:53:42Z

‎Bibliographic Entry: editorial board

Hivanson: /* Bibliographic Entry */ bottom half of bibliography

2024-04-18T01:52:05Z

‎Bibliographic Entry: bottom half of bibliography

Hivanson: /* Presentation Prep */ more bib progress

2024-04-18T01:42:10Z

‎Presentation Prep: more bib progress

Hivanson: /* Bibliographic Entry */ COI

2024-04-18T01:34:32Z

‎Bibliographic Entry: COI

Hivanson: /* Bibliographic Entry */ three ones from the bottom bib

2024-04-18T01:33:19Z

‎Bibliographic Entry: three ones from the bottom bib

Hivanson: /* Presentation Prep */ paste bibliographic entry

2024-04-18T01:28:04Z

‎Presentation Prep: paste bibliographic entry

Hivanson: /* Questions about your article */ fig 2

2024-04-18T01:26:33Z

‎Questions about your article: fig 2

Hivanson: /* Questions about your article */ fig 1

2024-04-18T01:12:16Z

‎Questions about your article: fig 1

@@ Line 1: / Line 1: @@
 ==Presentation==
 [[Media:Hailey_Charlotte_Katie_Journal_Club_Presentation.pdf|Ivanson, Kaplan, Miller on Sha et al., 2013]]
 {{Hivanson}}

@@ Line 85: / Line 85: @@
 *#** Is the publisher a scientific society (some scientific societies partner with a for-profit publisher, some act as their own non-profit publisher)
 *#** Does the publisher belong to the [http://oaspa.org/membership/members Open Access Publishers Association]?
-*#* What country is the journal published in?
+*#* '''What country is the journal published in?'''
-*# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
+*#**The United States
-*# Are the articles in this journal peer-reviewed?
+*# '''How long has the journal been in operation?'''
 *# '''Provide a link to the scientific advisory board/editorial board of the journal.'''
 *#*[https://journals.plos.org/plosone/static/editorial-board? editorial board]

@@ Line 88: / Line 88: @@
 *# How long has the journal been in operaion? (e.g., browse the archive for the earliest article published)
 *# Are the articles in this journal peer-reviewed?
-*# Provide a link to the scientific advisory board/editorial board of the journal.
+*# '''Provide a link to the scientific advisory board/editorial board of the journal.'''
 *# '''What is the journal impact factor?'''
 *#*3.7

@@ Line 89: / Line 89: @@
 *# Are the articles in this journal peer-reviewed?
 *# Provide a link to the scientific advisory board/editorial board of the journal.
-*# What is the journal impact factor? (Look to see if it is provided on the journal home page.  Alternately, it may be found through a Google Search.)
+*# '''What is the journal impact factor?'''
-*# On what date was the article submitted?
+*#*3.7
-*# On what date was the article accepted?
+*# '''On what date was the article submitted?'''
-*# Did the article undergo any revisions before acceptance?
+*#*May 10, 2013
-*# When was the article published?
+*# '''On what date was the article accepted?'''
-*# What is the approximate elapsed time between submission and publication?
+*#*August 7, 2013
-*# What are the institutions with which the authors are affiliated?
+*# '''Did the article undergo any revisions before acceptance?'''
 *#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
 *# '''Have the authors published other articles on this subject?'''

@@ Line 95: / Line 95: @@
 *# When was the article published?
 *# What is the approximate elapsed time between submission and publication?
 *# What are the institutions with which the authors are affiliated?
-*# Have the authors published other articles on this subject? (How will you find this out?) Hint:
+*#*"Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, United States of America ; Bioinformatics Research Division, University of North Carolina at Charlotte, Kannapolis, North Carolina, United States of America." [https://pubmed.ncbi.nlm.nih.gov/24073228/ via PubMed]
-*#* [http://scholar.google.com/ Google Scholar]
+*# '''Have the authors published other articles on this subject?'''
-*#* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link)]
+*#*Sha has other articles that [https://doi.org/10.1002/yea.1442 relate to yeast metabolism] and [https://doi.org/10.1016/j.freeradbiomed.2011.03.002 the effects of oxidative stress].
 *# '''Is there a conflict of interest for any of the authors?'''
 *#*None declared

@@ Line 100: / Line 100: @@
 *#* [http://www.ncbi.nlm.nih.gov/sites/entrez?holding=calmulib PubMed (LMU-specific link)]
 *#* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
-*# Is there a conflict of interest for any of the authors?
+*#**
 *# '''Are the data associated with this article available?  If so, provide a link to the dataset.'''
 *#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]

@@ Line 101: / Line 101: @@
 *#* [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science (LMU pays subscription fee for access)]
 *# Is there a conflict of interest for any of the authors?
-*# Are the data associated with this article available?  If so, provide a link to the dataset.
+*# '''Are the data associated with this article available?  If so, provide a link to the dataset.'''
-*# Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):
+*#* The data can be accessed through [https://sgd-prod-upload.s3.amazonaws.com/S000204389/Sha_2013_PMID_24073228.zip SGD] or [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26169 GEO]
-*#* How many articles does this article cite?
+*# '''Perform a prospective search on your article in the [http://electra.lmu.edu:2048/login?url=http://webofknowledge.com/WOS Web of Science] and answer the following (note that LMU pays a subscription for this service, so you may not be able to access it off campus):'''
-*#* How many articles cite this article?
+*#* '''How many articles does this article cite?'''
 ==Presentation==

@@ Line 64: / Line 64: @@
 # What future directions should the authors take?
 # Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed.  Are there any major flaws to the paper?
 ==Presentation==

@@ Line 45: / Line 45: @@
 #*Hybridizing RNA: Affymetrix protocol for S98 arrays was used for hybridization.
 # '''What mathematical/statistical method did they use to analyze the data?'''
-#*ANOVA
+#*Robust Multichip Average and ANOVA
 # '''Are the data publicly available for download?  From which web site?'''
 #*GEO Database and SGD.
@@ Line 51: / Line 51: @@
 #*''Figure 1''
 #**X represents Concentration in µM; Y represents Time in minutes
-#**Quentification by HPLC
+#**Quantification by HPLC
-#**Trends show depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
+#**Figure 1 shows depletion of CHP and "replacement" by COH over time, revealing that yeast could break down the CHP it was exposed to within about 20 minutes.
 #*''Figure 2''
-#**
+#**X represents Time in minutes; Y represents the "number of genes that have changed expression level compared with the control"
-#* What do the X and Y axes represent (if applicable)?
+#**Measurements were made by extracting RNA from yeast at each time point from the control and treatment groups and seeing how many genes were expressed at that point.
 #* How were the measurements made?
-#* What trends are shown by the plots and what conclusions can you draw from the data?
+#* What trends are shown by the plots and what conclusions can you draw from the data?-->
 # How does this work compare with previous studies?
 # What are the important implications of this work?