CiteULike | Further Information

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Mendeley | Further Information

{"title"=>"Iridovirus and microsporidian linked to honey bee colony decline", "type"=>"journal", "authors"=>[{"first_name"=>"Jerry J.", "last_name"=>"Bromenshenk", "scopus_author_id"=>"16309148600"}, {"first_name"=>"Colin B.", "last_name"=>"Henderson", "scopus_author_id"=>"36948338900"}, {"first_name"=>"Charles H.", "last_name"=>"Wick", "scopus_author_id"=>"7006296586"}, {"first_name"=>"Michael F.", "last_name"=>"Stanford", "scopus_author_id"=>"16643631400"}, {"first_name"=>"Alan W.", "last_name"=>"Zulich", "scopus_author_id"=>"36138401700"}, {"first_name"=>"Rabih E.", "last_name"=>"Jabbour", "scopus_author_id"=>"11540864000"}, {"first_name"=>"Samir V.", "last_name"=>"Deshpande", "scopus_author_id"=>"8059026000"}, {"first_name"=>"Patrick E.", "last_name"=>"McCubbin", "scopus_author_id"=>"6602935136"}, {"first_name"=>"Robert A.", "last_name"=>"Seccomb", "scopus_author_id"=>"16310781400"}, {"first_name"=>"Phillip M.", "last_name"=>"Welch", "scopus_author_id"=>"36783673800"}, {"first_name"=>"Trevor", "last_name"=>"Williams", "scopus_author_id"=>"35450910800"}, {"first_name"=>"David R.", "last_name"=>"Firth", "scopus_author_id"=>"36784040800"}, {"first_name"=>"Evan", "last_name"=>"Skowronski", "scopus_author_id"=>"6602887265"}, {"first_name"=>"Margaret M.", "last_name"=>"Lehmann", "scopus_author_id"=>"23009618400"}, {"first_name"=>"Shan L.", "last_name"=>"Bilimoria", "scopus_author_id"=>"6603782293"}, {"first_name"=>"Joanna", "last_name"=>"Gress", "scopus_author_id"=>"36782124900"}, {"first_name"=>"Kevin W.", "last_name"=>"Wanner", "scopus_author_id"=>"7004086356"}, {"first_name"=>"Robert A.", "last_name"=>"Cramer", "scopus_author_id"=>"7102501409"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"78049248014", "doi"=>"10.1371/journal.pone.0013181", "pui"=>"359856620", "pmid"=>"20949138", "scopus"=>"2-s2.0-78049248014", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"764e3a3b-8587-3d3a-8dba-8d26e8685e5b", "abstract"=>"BACKGROUND: In 2010 Colony Collapse Disorder (CCD), again devastated honey bee colonies in the USA, indicating that the problem is neither diminishing nor has it been resolved. Many CCD investigations, using sensitive genome-based methods, have found small RNA bee viruses and the microsporidia, Nosema apis and N. ceranae in healthy and collapsing colonies alike with no single pathogen firmly linked to honey bee losses.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We used Mass spectrometry-based proteomics (MSP) to identify and quantify thousands of proteins from healthy and collapsing bee colonies. MSP revealed two unreported RNA viruses in North American honey bees, Varroa destructor-1 virus and Kakugo virus, and identified an invertebrate iridescent virus (IIV) (Iridoviridae) associated with CCD colonies. Prevalence of IIV significantly discriminated among strong, failing, and collapsed colonies. In addition, bees in failing colonies contained not only IIV, but also Nosema. Co-occurrence of these microbes consistently marked CCD in (1) bees from commercial apiaries sampled across the U.S. in 2006-2007, (2) bees sequentially sampled as the disorder progressed in an observation hive colony in 2008, and (3) bees from a recurrence of CCD in Florida in 2009. The pathogen pairing was not observed in samples from colonies with no history of CCD, namely bees from Australia and a large, non-migratory beekeeping business in Montana. Laboratory cage trials with a strain of IIV type 6 and Nosema ceranae confirmed that co-infection with these two pathogens was more lethal to bees than either pathogen alone.\\n\\nCONCLUSIONS/SIGNIFICANCE: These findings implicate co-infection by IIV and Nosema with honey bee colony decline, giving credence to older research pointing to IIV, interacting with Nosema and mites, as probable cause of bee losses in the USA, Europe, and Asia. We next need to characterize the IIV and Nosema that we detected and develop management practices to reduce honey bee losses.", "link"=>"http://www.mendeley.com/research/iridovirus-microsporidian-linked-honey-bee-colony-decline", "reader_count"=>346, "reader_count_by_academic_status"=>{"Unspecified"=>9, "Professor > Associate Professor"=>17, "Librarian"=>4, "Student > Doctoral Student"=>22, "Researcher"=>87, "Student > Ph. D. Student"=>71, "Student > Postgraduate"=>9, "Student > Master"=>39, "Other"=>18, "Student > Bachelor"=>44, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>3, "Professor"=>17}, "reader_count_by_user_role"=>{"Unspecified"=>9, "Professor > Associate Professor"=>17, "Librarian"=>4, "Student > Doctoral Student"=>22, "Researcher"=>87, "Student > Ph. D. 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• {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fplosone%2Farticle%3Fid%3D10.1371%252Fjournal.pone.0013181", "share_count"=>3, "like_count"=>3, "comment_count"=>17, "click_count"=>0, "total_count"=>23}

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• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/2f342c55-75be-4226-b14e-ee67b62600a2", "title"=>"Accessing 'Technical Report'", "body"=>"Can anyone tell me how to access Ref #20 of this article, the Army 'Technical Report' where all the details of the mass spec are supposedly reported?", "isRemoved"=>false, "created"=>"2010-10-07T02:32:40Z", "lastModified"=>"2010-10-07T02:32:40Z", "creator"=>{"userId"=>"81511"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Also work on honey bee proteomics"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>6, "mostRecentActivity"=>"2011-05-04T18:48:56Z", "replies"=>[{"type"=>"REPLY", "parentID"=>4207, "annotationUri"=>"info:doi/10.1371/reply/476f6f2f-c80b-446c-a4cd-ae5d9f08abb4", "title"=>"RE: Accessing 'Technical Report'", "body"=>"Sorry, just realized my real name doesn't show up. I am very interested in seeing this Technical Report so if someone can share it with the community that would be fantastic.\n\nThanks\n\nLeonard Foster\nUBC", "isRemoved"=>false, "created"=>"2010-10-07T21:52:53Z", "lastModified"=>"2010-10-07T21:52:53Z", "creator"=>{"userId"=>"81511"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2010-10-07T22:28:08Z", "replies"=>[{"type"=>"REPLY", "parentID"=>34587, "annotationUri"=>"info:doi/10.1371/reply/03d77a45-9ff0-425a-a485-c6367d7ee5a2", "title"=>"RE: RE: Accessing 'Technical Report'", "body"=>"I didn't look it up but you might try the National Technical Information Service\n NTIS.gov", "isRemoved"=>false, "created"=>"2010-10-07T22:28:08Z", "lastModified"=>"2010-10-07T22:28:08Z", "creator"=>{"userId"=>"167793"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-07T22:28:08Z", "replies"=>[]}]}, {"type"=>"REPLY", "parentID"=>4207, "annotationUri"=>"info:doi/10.1371/reply/73af9d4e-c695-4caa-8481-4ccdd639176f", "title"=>"RE: Accessing 'Technical Report'", "body"=>"Hi Leonard,\r\nThe proper avenue for requesting such reports is to email CBRN@conus.army.mil and request the public bulletin (in this case ECBC publication TR-814). However, as below, this critical bulletin is not actually available and the liaison said to 'try again in about two months''.\r\n Please folks, we truly want to believe that IIV's are widespread, or at least vet the actual data, and time is wasting. It is impossible to do so without any of the baseline data; MS/MS peptides for the proposed matches to IIV for starts, and the same for the suggested matches to 900(!) additional microbes. Incredible claims require at least credible evidence, and you should proudly display the data behind your extraordinary claims.\r\nthanks,\r\nJay Evans (acting as an individual concerned scientist)\r\n\r\n--------------------------------------------------------------------------------\r\nFrom: Henderkott, Patricia A Ms CIV USA [mailto:patricia.henderkott@us.army.mil]\r\nSent: Mon 9/27/2010 8:14 AM\r\nTo: Evans, Jay\r\nCc: Rasmussen, Emily A CIV USA; Lingard, Twyla J Mrs CIV USA AMC\r\nSubject: RE: CBRN-IRC Inquiry Ticket #10963 FW: ECBC publication? (UNCLASSIFIED)\r\n\r\n\r\nDr. Evans,\r\n\r\nPer Mr. D'Eramo's below request, this publication is not available at this time. Please resubmit your request at a later time (possibly 2 months) and I will see if review and approval for release has been completed.\r\n\r\n\r\nThank you for using the CBRN-Information Resource Center\r\n\r\nPatricia Henderkott\r\nIRC Officer\r\nInformation Technology Solutions Team\r\nDSN: 793-5680 Comm: 309-782-5680\r\nemail: patricia.henderkott@us.army.mil\r\nAll CBRN related questions contact the CBRN-IRC 24/7 at JACKS: https://jacks.jpeocbd.army.mil/\r\nComm: 309-782-7349 (DSN 793) U.S.A. (toll free) 1-800-831-4408 Germany (toll free) 0130810280 Korea (toll free) 0078-14-800-0335 FAX (DSN) 793-3226 (Commercial) 309-782-3226\r\nmailto:cbrn@conus.army.mil \r\n\r\n", "isRemoved"=>false, "created"=>"2010-10-08T03:35:10Z", "lastModified"=>"2010-10-08T03:35:10Z", "creator"=>{"userId"=>"94509"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"researcher in same field who shares a belief in pathogenic causes for bee declines"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-08T03:35:10Z", "replies"=>[]}, {"type"=>"REPLY", "parentID"=>4207, "annotationUri"=>"info:doi/10.1371/reply/2d84cfba-dbde-4b8a-a96b-31d1682c044e", "title"=>"RE: Accessing 'Technical Report'", "body"=>"I have just written a point-by-point technical response to this work that can be found at Mol. Cell. Proteomics: http://www.mcponline.org/content/early/2011/01/04/mcp.O110.006387.full.pdf+html\n\nLeonard Foster", "isRemoved"=>false, "created"=>"2011-01-09T05:22:58Z", "lastModified"=>"2011-01-09T05:22:58Z", "creator"=>{"userId"=>"81511"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-01-09T05:22:58Z", "replies"=>[]}, {"type"=>"REPLY", "parentID"=>4207, "annotationUri"=>"info:doi/10.1371/reply/8332d515-d40c-4558-9dd9-cbf637b8483a", "title"=>"RE: Accessing 'Technical Report'", "body"=>"This paper does not provide sufficient information to judge the validity of proteomics-based findings presented herein (MSP technology). However, the manuscript suggests that all necessary information is available in the US Army Technical Report (TR-814) which is referenced as a foundation for this work [ref. 20]. \r\n\r\nRecently I’ve read this report (http://www.dtic.mil/cgi-bin/GetTRDoc?AD=ADA534767&Location=U2&doc=GetTRDoc.pdf) and found serious errors in the proteomics work performed by the Army laboratory.\r\n\r\nFor example, the Authors reported search results of mass spectra against small database for tests #5 through #100 in Appendix B. However, they do not provide any information which samples they represent. Nevertheless, these summaries shed light on the interpretation of SEQUEST results used by the Authors. \r\n\r\n(a)\tIn each table shown in Appendix B one can find six columns with SEQUEST output parameters designated as: (a) (M + H); (b) ^M, (c) ^Cn, (d) Xcorr; (e) Sp; and (f) RSp. However, it is troubling that descriptions of these parameters, provided by the Authors in an introductory table, are incorrect for five of them!!!. For example, (ii) ^M (in fact it is ΔM or deltaM) is described as ”(M + H) – M“, instead as a mass difference between measured and theoretical values, (iii) ^Cn (in fact ΔCn or deltaCn) is described as “Error”, while it is the difference in cross-correlation score between the top-ranked peptide sequences (normalized to the highest Xcorr value); consequently, the higher value of this parameter is better (just the opposite to what the term error suggests!); (v) “Sp” is described as the “Highest peak in a given spectrum” and (vi) RSp as “Repeat of Sp”, while, in fact, “Sp” stands for the preliminary score of the top candidate peptide used to rank matching sequences, and the actual rank of a given sequence based on Sp values is called “RSp”. \r\n(b)\tThe most troubling is the description of the Xcorr (cross-correlation) score which the Authors named as “fitness match”. Although the term “fitness match” reflects the meaning of this score, the Authors added an explanation that “numbers > 1.5 are significant” and actually use this value for sorting all the matches and as a cut-off criterion for reporting assignments in all Appendix–B tables. \r\n\r\nThis is a serious flaw! Although SEQUEST assignments with Xcorr >1.5 are frequently considered as correct matches; this criterion is valid ONLY for +1 ions that usually represent less than 1% of reported assignments. For example, the analysis of results for Tests #6 and #100 (the first and the last test reported in Appendix-B) indicate that 66.1% of analyzed peptide ions were doubly charged (+2 ions), 33.1 % triply charged (+3 ions), while the +1 ions represented only 0.85% (there is only one +1 ion in test#6 and none in test#100). \r\n\r\nNOTE: Washburn-Yates (inventors of SEQUEST) criteria require Xcorr values to be ≥ 1.9, 2.2, and 3.75 for parent ion state charges +1, +2 and +3, respectively [Washburn et al., Nat. Biotechnol. 2001, 19, 242–247]. Nevertheless, nobody recommended lower cut-off criteria than Xcorr values of 1.5, 2.2 and 3.3 for charge states +1, +2 and +3, respectively [Durr et al., Nat. Biotechnol. 2004, 22, 985–992]. (In addition , these Xcorr cut-off criteria should be associated with deltaCn values ≥ 0.1).\r\n\r\nWhat happens when you will accept +2 ions with Xcorr >1.5? In short, you will select a set of matches with false positives reaching 90% (for example see Kall et al., J. Proteome Research 2008, 7, 29–34). \r\n", "isRemoved"=>false, "created"=>"2011-05-02T01:56:04Z", "lastModified"=>"2011-05-02T01:56:04Z", "creator"=>{"userId"=>"150341"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-05-02T01:56:04Z", "replies"=>[]}, {"type"=>"REPLY", "parentID"=>4207, "annotationUri"=>"info:doi/10.1371/reply/67d7e398-ac65-43dd-a6f1-6535d3f5b625", "title"=>"RE: Accessing 'Technical Report'", "body"=>"Analysis of the US Army Technical Report (TR-814) strongly suggests that serious errors were made in the proteomics work performed by the Army laboratory. As I described a few days ago, the Authors misinterpreted SEQUEST parameters and accepted all spectrum-sequence matches characterized by cross-correlation scores higher than 1.5. Next, they sorted them by Xcorr values and presented in Appendix B of the report. \r\nSEQUEST identified spectrum-sequence matches are associated with arbitrary scores that reflect the quality of such assignments but not a statistically meaningful significance measure. To validate their matches the Authors used a PeptideProphet algorithm that assigns probabilities to search results by computing their likelihood of being correct. The results obtained with PeptideProphet algorithm are reported in columns marked PP and indicate that correctness of all reported matches is better than 95%. However, it is puzzling to see that both +2 and +3 peptide ions with Xcorr values as low as 1.5 and deltaM > 1.0 are associated with 99% probabilities that they are correct [even for matches to sequences with missing amino acids, indicated by “*”]. It is surprising because any experienced user of SEQUEST would suggest that such assignments are simply incorrect (for example see Kall et al., J. Proteome Research 2008, 7, 29–34). How to explain these discrepancies? \r\nPeptide Prophet employs the EM algorithm to find distributions of matches and computes probabilities that matches are correct. It does so by partitioning the observed distributions into inferred correct and incorrect assignments which then contribute to the computed probability that any result is correct.\r\n\r\nUnfortunately, in cases of questionable data quality, i.e. a low number of high-scoring peptides relative to low scoring ones (e.g., due to lack of correct matches in the database), PeptideProphet models are improperly fitting the negative/positive distributions, with the effect of giving too many high peptide probabilities to dubious matches. Therefore, according to developers of this software: “It is important to view distributions of search score and peptide properties learned by the program among correct and incorrect results of each parent charge. This model information …. should be used to be sure the program did an adequate job and as a diagnostic.” [Keller and Shteynberg, Methods Mol. Biol. Vol. 694, 169-189 (2011)]. Unfortunately, Bromenshenk et al. ignored this important step; therefore, the SEQUEST generated peptide-sequence assignments used in this work are not validated! \r\n\r\nPaul Sommer, PhD\r\nBrooklyn, NY\r\n\r\n", "isRemoved"=>false, "created"=>"2011-05-04T18:48:56Z", "lastModified"=>"2011-05-04T18:48:56Z", "creator"=>{"userId"=>"150341"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-05-04T18:48:56Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ab9c478d-5e77-47cd-a003-5a8acf39e2ee", "title"=>"Why bees fly away ", "body"=>"I saw the write up on this study in 10/7 NYT, and it occurred to me that infected and dying bees might fly away from their colonies to die, not because they're insane, but rather because they somehow recognize that they're ill, and don't want to further infect or damage the rest of the colony. This idea might fit with some of the bees' communication and societal coordination capabilities, and might suggest some new areas for further research.", "isRemoved"=>false, "created"=>"2010-10-07T19:18:40Z", "lastModified"=>"2010-10-07T19:18:40Z", "creator"=>{"userId"=>"143857"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2011-02-23T00:30:36Z", "replies"=>[{"type"=>"REPLY", "parentID"=>15357, "annotationUri"=>"info:doi/10.1371/reply/21954199-bf04-477c-80e6-b495aa98a00c", "title"=>"RE: Why bees fly away ", "body"=>"I agree, this was a misquote by NYT. I don't remember ever saying bees go insane. Some investigators speculate that bees forget how to find their way home. A simpler explanation might be that sick bees fly out, are too weakened to return, die in the field.", "isRemoved"=>false, "created"=>"2011-02-23T00:30:36Z", "lastModified"=>"2011-02-23T00:30:36Z", "creator"=>{"userId"=>"156545"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Corresponding Author"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-02-23T00:30:36Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/e7d05223-dfff-454d-ad00-c6cc154ebe1f", "title"=>"Human connection?", "body"=>"Any chance a combination such as this could be causing a rise in human autoimmune disease or autism?", "isRemoved"=>false, "created"=>"2010-10-07T19:56:37Z", "lastModified"=>"2010-10-07T19:56:37Z", "creator"=>{"userId"=>"155095"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-07T19:56:37Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/16a06fb8-5ea9-443a-bb0e-e6b52857b517", "title"=>"Honey Bee Colony Decline", "body"=>"The data in the study are very impressive. In addition to the IIV and Nosema link, could this be superimposed on a stress factor affecting the bees immune system?. One factor that comes to mind is the current commercial practices of colony seasonal migration. This might be an additional explanation for the the authors' finding of Montana's non-migratory colonies being less affected.", "isRemoved"=>false, "created"=>"2010-10-07T22:42:51Z", "lastModified"=>"2010-10-07T22:42:51Z", "creator"=>{"userId"=>"107221"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>3, "mostRecentActivity"=>"2010-10-17T01:43:31Z", "replies"=>[{"type"=>"REPLY", "parentID"=>1961, "annotationUri"=>"info:doi/10.1371/reply/c5df735e-042a-4bc6-a441-b812850c9dfb", "title"=>"RE: Honey Bee Colony Decline", "body"=>"Great question! Could the immune system be declining because the queen is no longer allowed to mate with the strongest drone who can fly to her heights for mating? Might the rectangular beehive, convenient for bee keepers, be an issue? Maybe Round-up and other pesticides weaken?", "isRemoved"=>false, "created"=>"2010-10-08T14:08:11Z", "lastModified"=>"2010-10-08T14:08:11Z", "creator"=>{"userId"=>"28715"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2010-10-17T01:43:31Z", "replies"=>[{"type"=>"REPLY", "parentID"=>34597, "annotationUri"=>"info:doi/10.1371/reply/a5d29642-9656-43d5-bdf7-44e66cf55dda", "title"=>"RE: RE: Honey Bee Colony Decline", "body"=>"Please consider my posting as I am totally ignorant of \"Bee\" science:Any Correlation to Genetic Mod Seed Virial RNAIntro Techniques?\r\n", "isRemoved"=>false, "created"=>"2010-10-17T01:43:31Z", "lastModified"=>"2010-10-17T01:43:31Z", "creator"=>{"userId"=>"111391"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-17T01:43:31Z", "replies"=>[]}]}, {"type"=>"REPLY", "parentID"=>1961, "annotationUri"=>"info:doi/10.1371/reply/74c4a0d3-375f-4eee-a244-38073d5ed670", "title"=>"RE: Honey Bee Colony Decline", "body"=>"The primary motivation for moving colonies is to get them to better pasture. For example, in Upstate NY, conditions are hostile to bees for six months out of the year. By the time spring arrives, up to half the hives may be dead and many severely weakened. This is nothing new, the bee literature of 100 years ago is filled with sad stories and advice on over-wintering. \n\nThe solution, which was begun in earnest decades ago, is to haul the bees south to better conditions. Trucking bees per se is not harmful. The mixing of colonies from all over the US and elsewhere, however, is a recipe for rapid distribution of any sort of contagious elements, and also, the recombination of various strains of these pathogens.\n\nViewed from the outside, the spectacle of trucking up to a million bee hives around the USA, making multiple moves, etc. seems perilous, but actually the trips are made quickly and the benefits of better weather, fresh nectar and pollen, etc. usually outweigh the damage done by the interstate hauling.\n\nPeter Loring Borst\nIthaca, NY", "isRemoved"=>false, "created"=>"2010-10-10T23:38:25Z", "lastModified"=>"2010-10-10T23:38:25Z", "creator"=>{"userId"=>"171659"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-10T23:38:25Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/d1c96e06-87c3-488b-b0dd-3231f6b9de71", "title"=>"Error in the Introduction regarding reference [11] in the paper.", "body"=>"In the Introduction, an incorrect statement was made with regards to reference [11].\r\n\r\n\"Whether these RNA fragments were from the host or RNA bee viruses is unknown [11].\"\r\n\r\nThe polyA ribosomal RNA fragments were identified in reference [11] as 5.8s and 28s. That would be of Honeybee origin (nuclear).\r\n\r\n", "isRemoved"=>false, "created"=>"2010-10-10T19:37:20Z", "lastModified"=>"2010-10-10T19:37:20Z", "creator"=>{"userId"=>"85569"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Commencing ssRNA virus research."}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-10T19:37:20Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/d9cb08a6-635e-44f5-a384-7763412bbbae", "title"=>"Potentially misleading description of cited work [12]", "body"=>"The authors write, \"A survey of bee samples from across the USA revealed traces of pesticides in many bee samples, but none were shown to correlate with CCD [12].\" \n\nIn everyday English, this would be taken to suggest that the cited survey found only small quantities of pesticides; and that its authors had concluded these did not have any causative relationship to CCD.\n\nThe findings of the survey, 'High Levels of Miticides and Agrochemicals in North American Apiaries: Implications for Honey Bee Health', published previously in PLoS one, were the opposite of what Bromenshenk et al. appear to imply. The survey found that \"unprecedented levels\" of a range of pesticide residues were widespread. Rather than that there was no correlation with CCD, the survey's authors suggested many synergistic interactions could be factors leading to CCD: \"[T]he potential for multiple pesticide interactions affecting bee health seems likely.\"\n", "isRemoved"=>false, "created"=>"2010-10-17T00:27:14Z", "lastModified"=>"2010-10-17T00:27:14Z", "creator"=>{"userId"=>"150581"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2011-03-15T03:05:18Z", "replies"=>[{"type"=>"REPLY", "parentID"=>19353, "annotationUri"=>"info:doi/10.1371/reply/2ba6ccd9-b566-464b-b830-db6679a5a767", "title"=>"RE: Potentially misleading description of cited work [12]", "body"=>"I would recommend reading about \"Bee\" in WIKIPEDIA. You will find there the following paragraph with references 5 through 7. It seems to me that reference #6 from this Wikipedia article may provide some clarification why the work by Mullin et al. is misinterpreted by Bromenshenk et al.\r\n \r\n\"After several years of research and concern, a team of scientists headed by Jerry Bromenshenk published a paper in October 2010 saying that a new DNA-based virus, invertebrate iridescent virus or IIV6, and the fungus Nosema ceranae were found in every killed colony the group studied. In their study they found that neither agent alone seemed deadly, but a combination of the virus and Nosema ceraneae was always 100% fatal. Bromenshenk said it is not yet clear whether one condition weakens the bees enough to be finished off by the second, or whether they somehow compound the other’s destructive power. \"They're co-factors, that’s all we can say at the moment. They’re both present in all these collapsed colonies.\"[5][6][7].\"", "isRemoved"=>false, "created"=>"2011-03-15T03:05:18Z", "lastModified"=>"2011-03-15T03:05:18Z", "creator"=>{"userId"=>"150341"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-03-15T03:05:18Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/a194ebf3-c288-46bf-9315-ede733bdb4a0", "title"=>"Any Correlation to Genetic Mod Seed Virial RNAIntro Techniques?", "body"=>"If Agricultural DNA and gene splicing techniques utilize certain bacteria and viral strains to introduce cells to modified gene material, then are any of these \"strains\" related to current discovery and could they even be correlated to Bee activity and/or contamination.", "isRemoved"=>false, "created"=>"2010-10-17T01:37:08Z", "lastModified"=>"2010-10-17T01:37:08Z", "creator"=>{"userId"=>"111391"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-10-17T01:37:08Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/959cae5b-bb21-436e-b87e-a70f487b3173", "title"=>"Request Technical Report", "body"=>"The US Army technical report was written and assigned a publication number before our PLoS ONE article was accepted. The final edits and clearance for publication by the Army is taking longer than anticipated.\r\n\r\nWe have discussed this with the PLoS ONE Executive Editor and offered to post the raw data from our study on PLoS ONE. The journal is looking into how best to publish this 2,000 line Excel file. \r\n\r\nIn the meantime, we have been asked by the Executive Editor to inform readers that the easiest approach would be for us to simply send the Excel file to those who request it. \r\n\r\nWe ask that you cc requests to Dr. Walter Leal, the Academic Editor, so that he can establish a master list.\r\n\r\n\r\n\r\n\r\n\r\n", "isRemoved"=>false, "created"=>"2010-10-18T16:43:48Z", "lastModified"=>"2010-10-18T16:43:48Z", "creator"=>{"userId"=>"156545"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>2, "mostRecentActivity"=>"2010-11-19T02:50:28Z", "replies"=>[{"type"=>"REPLY", "parentID"=>13563, "annotationUri"=>"info:doi/10.1371/reply/176f7175-8ce8-42f8-95eb-acb086e09b66", "title"=>"RE: Request Technical Report", "body"=>"I checked the Comment posting and realize that my e-mail address was not readily apparent.\r\n\r\nPlease submit requests for the PLoS ONE Excel file to Dr. Colin Henderson at colin.henderson@mso.umt.edu.\r\n\r\nPlease cc to me, Jerry Bromenshenk, at beeresearch@aol.com AND to \r\nDr. Walter Leal at wsleal@ucdavis.edu ", "isRemoved"=>false, "created"=>"2010-10-18T16:50:07Z", "lastModified"=>"2010-10-18T16:50:07Z", "creator"=>{"userId"=>"156545"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2010-11-19T02:50:28Z", "replies"=>[{"type"=>"REPLY", "parentID"=>34639, "annotationUri"=>"info:doi/10.1371/reply/58c20054-437f-48b7-ac10-465167eff2ce", "title"=>"RE: RE: Request Technical Report", "body"=>"I don’t think the Excel spreadsheet is going to satisfy people’s concerns. What people want to be able to do is assess the reliability of the results. To do this, they need to know sufficient details about how the analysis was done and have access to the data to search themselves.\nThe PLOS manuscript does not contain sufficient information to assess the reliability of the mass spectrometry data. The proteomics community, with support from all journals who regularly publish this type of analysis, have developed journal publication guidelines that outline minimal amounts of information required to be able to assess mass spectrometry-based proteomic results. These have been in place for five years and the most up-to-date guidelines can be found here:\nhttp://mcponline.org/site/misc/PhialdelphiaGuidelinesFINALDRAFT.pdf\nThese guidelines require reporting all data search parameters and they also now require submitting of raw data to a public repository. It should be straightforward to submit the raw data (or at least the mass spectrometry peak lists that were used for analysis) and the excel results spreadsheet to e.g. Tranche, then PLOS can link to the raw data in Tranche through the hash created (see final guideline in the link above). This will allow anyone free access to the data.", "isRemoved"=>false, "created"=>"2010-11-19T02:50:28Z", "lastModified"=>"2010-11-19T02:50:28Z", "creator"=>{"userId"=>"124671"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2010-11-19T02:50:28Z", "replies"=>[]}]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/30b0940a-3645-430a-aaa2-fa9ea82a5c09", "title"=>"Results of this study challenged in Mol. Cell. Proteomics", "body"=>"I have just written a point-by-point technical response to this work that can be found at Mol. Cell. Proteomics: http://www.mcponline.org/\n\nLeonard Foster", "isRemoved"=>false, "created"=>"2011-01-19T00:08:51Z", "lastModified"=>"2011-01-19T00:08:51Z", "creator"=>{"userId"=>"81511"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Working in the same field"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>4, "mostRecentActivity"=>"2011-01-31T21:13:58Z", "replies"=>[{"type"=>"REPLY", "parentID"=>4341, "annotationUri"=>"info:doi/10.1371/reply/a916b06e-f7ce-44a3-9d64-9f704ec7b92d", "title"=>"RE: Results of this study challenged in Mol. Cell. Proteomics", "body"=>"Thanks for the clear analysis, Leonard. Knowing the authors, in my opinion this was an honest mistake caused by querying a much reduced database, and thereby falling into the well known trap of False Discovery.\r\n\r\nYour results are supported by the associated Army report (now available by email request to CBRN@conus.army.mil for ECBC publication TR-814). This longer document includes the Query database (as Appendix A). As you infer in your reanalysis, this database was composed of honey bee viral RNA's, and (mostly) IIV-6 peptides from the moth, along with a small set of Nosema protein-coding genes and some oddities (including one nematode protein and the vasa protein of a Brazilian stingless bee, which were subsequently 'found' in sampled U.S. bees). You make a good case that, had the peptidic spectra been used to query a database inclusive of honey bee proteins, the results would be quite different.\r\n\r\nEven if, as seems more likely, a new virus was not found in this study, the raw peptidic data are presumably sound and would likely be a treasure for those wishing to mine for bee proteins or other microbes. Also the bioassays involving moth IIV with and without Nosema are solid and give credence to interactive effects among viruses and fungi.\r\n\r\nJay Evans", "isRemoved"=>false, "created"=>"2011-01-20T17:45:34Z", "lastModified"=>"2011-01-20T17:45:34Z", "creator"=>{"userId"=>"94509"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Working in same field"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2011-01-24T21:01:45Z", "replies"=>[{"type"=>"REPLY", "parentID"=>34883, "annotationUri"=>"info:doi/10.1371/reply/910ea587-6a7e-4ab2-a945-e97fa03c0fdd", "title"=>"RE: RE: Results of this study challenged in Mol. Cell. Proteomics", "body"=>"Thank you much for the reply Dr. Bromenshenk,\r\n\r\nI agree there will be more discoveries in the raw data, hints of which were given by Dr. Wick at the recent National Beekeeping meeting (from human skin cells to gonnorhea and thermophiles along with the known bee microbes). As requested by several scientists at that meeting, releasing these data as RAW or DTA files seems like the best thing to do if you wish to give this study 'legs' whether the iridovirus story holds up or not. I'll repeat that such data would be a treasure when it is available to the public (and key if you address the challenges in Dr. Foster's peer-reviewed MCP article).\r\n\r\nUntil then, your high-profile PlosOne paper argues for discovery and quantitative results which now appear to be based upon peptidic searches against a quite small database (Appendix A in Army report TR-814). Could you please confirm that the results in this paper (specifically Tables 1-3 and Figs 1 and 2) reflect queries of Appendix A in TR-814, or were they against a more complete database?\r\n\r\nAll the best and thanks for the dialogue,\r\nJay", "isRemoved"=>false, "created"=>"2011-01-24T21:01:45Z", "lastModified"=>"2011-01-24T21:01:45Z", "creator"=>{"userId"=>"94509"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"worker in the same field"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-01-24T21:01:45Z", "replies"=>[]}]}, {"type"=>"REPLY", "parentID"=>4341, "annotationUri"=>"info:doi/10.1371/reply/6f674d0d-55b4-439a-aa70-4f4eaa1de8cd", "title"=>"RE: Results of this study challenged in Mol. Cell. Proteomics", "body"=>"The US Army proteomics team is preparing their point by point response to Drs Evans and Foster. We will ask the journal that posted Foster's comments to post the Army's response to his critique.\r\n\r\nWe note that an Excel spreadsheet of the results used in our paper was provided to the editors of PloS ONE and to Drs. Evans and Foster, as well as the Army's Technical Report which now has been approved for clearance and has been printed.\r\n\r\nThese documents include only the data used in the analysis for the PLoS ONE paper, not the entire data set. We did see bee proteins and peptides, hundreds of plant pathogens, and an assortment of other insect and mammalian pathogens, such as one might expect to find when mice invade a colony. We are working on additional papers related to these discoveries and that part of the data set.\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n\r\n", "isRemoved"=>false, "created"=>"2011-01-21T20:07:06Z", "lastModified"=>"2011-01-21T20:07:06Z", "creator"=>{"userId"=>"156545"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"Corresponding Author"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2011-01-31T21:13:58Z", "replies"=>[{"type"=>"REPLY", "parentID"=>34887, "annotationUri"=>"info:doi/10.1371/reply/568770a3-a588-401b-87ac-62d878f021a2", "title"=>"RE: RE: Results of this study challenged in Mol. Cell. Proteomics", "body"=>"Thank you much for the reply Dr. Bromenshenk,\r\n\r\nI agree there will be more discoveries in the raw data, hints of which were given by Dr. Wick at the recent National Beekeeping meeting (from human skin cells to gonnorhea and thermophiles along with the known bee microbes). As requested by several scientists at that meeting, releasing these data as RAW or DTA files seems like the best thing to do if you wish to give this study 'legs' whether the iridovirus story holds up or not. I'll repeat that such data would be a treasure when it is available to the public (and key if you address the challenges in Dr. Foster's peer-reviewed MCP article).\r\n\r\nUntil then, your high-profile PlosOne paper argues for discovery and quantitative results which now appear to be based upon peptidic searches against a quite small database (Appendix A in Army report TR-814). Could you please confirm that the results in this paper (specifically Tables 1-3 and Figs 1 and 2) reflect queries of Appendix A in TR-814, or were they against a more complete database?\r\n\r\nAll the best and thanks for the dialogue,\r\nJay\r\n", "isRemoved"=>false, "created"=>"2011-01-31T21:13:58Z", "lastModified"=>"2011-01-31T21:13:58Z", "creator"=>{"userId"=>"94509"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"worker in same field"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-01-31T21:13:58Z", "replies"=>[]}]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/1aff3028-a3e2-4c62-b2f4-8c43037026e0", "title"=>"“Identification” of Nosema species", "body"=>"The Authors of this paper inform a reader about the identification of Nosema species. However, the approach used allows only for peptide identification. In the next step, based on amino acid sequences of identified peptides, a source protein may be identified if, and only if, the protein sequence coverage is 100%. In other cases one can only infer the protein identity with a probability computed at the protein level, e.g. by using a popular ProteinProphet algorithm. Unfortunately, at this time, there is no scientific justification for the identification of source organisms based solely on proteomics analysis of complex environmental samples. Consequently, a researcher may only use proteotypical peptides as biomarkers confirming the presence or absence of specific proteins and their potential sources (strains, species, genera). However, the use of any biomarker should be validated before applying it to answer specific questions. Unfortunately, my evaluation of proteomic results presented in the Appendix B of the US Army Technical Report [ref. 20] indicate that all the peptides used as biomarkers of Nosema species are lacking the required specificity and their identities are uncertain. \r\n\r\nTo assign sequences to acquired product ion mass spectra the Authors constructed a database (Appendix A) by selecting proteins derived from: (a) nine RNA viruses (their total proteome, consists of 22,539 amino acids), (b) one DNA virus, i.e. invertebrate iridescent virus IIV-6 (63,745 amino acids), and (c) 12 Nosema species (appox. 41,807 amino acids). Next, they searched all spectra against this mini-database with SEQUEST. This way, only sequences from above preselected species were allowed to be assigned to any acquired mass spectrum. Sets of top spectrum-sequence matches from 89 experiments were sorted and are presented in Appendix B of the report. \r\nThese results show that matches are dominated by peptides from IIV-6 and Nosema and, on average, the Authors “identified” more peptides from the DNA virus. For example, by taking results from tests # 6, #11, #86, #98, and #100 I’ve found that spectra were assigned to IIV-6 and Nosema at the ratio of 1.64 ± 0.37. It is quite important because the mini-database constructed by the Authors is also dominated by IIV-6 and Nosema proteins (82.4%) at the ratio of 1.52 (IIV-6/Nosema, 63,745 aa/41,807 aa). Therefore, the observed assignments could be random and simply reflect protein composition of the database. \r\n\r\nMy analysis of these assignments (Appendix B) found 41 peptides matching “Nosema” species and satisfying quite “relaxed” criteria for accepting spectrum-sequence assignments as correct (Xcorr, 1.5, 2.2, 3.3 for +1 +2 and +3 ions, respectively; delta Cn> 0.1). [For further explanations, see my responses to the comment Accessing 'Technical Report']. Among them, 28 peptides were found once, while 4 other only twice. Therefore their occurrence seems random and I will ignore them. The most frequently observed matches (expressed as the number of occurrences in all 89 reported tests) for the remaining 9 peptides were as follows: 39; 27; 22; 11; 11; 7; 5; 3; and 3.\r\nBy performing a BLAST search against the NCBI nr-database with the most frequently, i.e., 39 times occurring peptide (SYELPDGQVIKIGSER) the origin of this sequence could be confirmed as a segment from Nosema locustae actin protein. However, it is highly probable that this assignment is incorrect because a similar peptide (SYELPDGQVITIGNER) could originate from human actin, a ubiquitous protein forming cytoskeleton in every human cell. First of all, nominal masses of these two peptides are the same and could not be resolved by a low resolution mass spectrometer used in this work [monoisotopic mass of T + N from human actin (215.091 u) is practically the same as mass of K + S from Nosema actin (215.127 u)]. Second, the suggested Nosema variant contains an internal trypsin specific cleavage site that somehow survived the overnight exposure to this enzyme without releasing the SYELPDGQVIK peptide. Third, we know that these bee samples were handled by humans! Of course, the inclusion of a human database during searches or the inspection of a mass spectrum for the presence of diagnostic fragment ions (b11 , b14 ,y3, and y6) could resolve this issue. However, this information is missing. \r\n\r\nThe purported peptide HKGVMVGMGQK could also originate from Nosema actin filaments and was “identified” as such during 22 tests. Nevertheless, I am doubtful that this identification is correct: (1) A honey bee protein (Apis mellifera, XP_003251465.1) variant of this peptide (HQGVMVGMGQK) has the same nominal mass as the one from Nosema, due to the substitution of the internal Lysine residue (K, 128.095 u) by Glutamine (Q, 128.059 u). (2) Monoisotopic mass difference between these two amino acids (0.036 u) is not distinguishable by a low resolution instrument. (3) The survival of a peptide with a missed cleavage site is not very probable. And finally, HQGVMVGMGQK should be expected in the analyzed sample because it originates from the organism they analyzed, while there is lack of a tryptic peptide (GVMVGMGQK) that would be the expected from Nosema. \r\n\r\nThe following “Nosema” peptides {sequence (frequency)}: VXDIIK (27); LAVNMVPFPR (11); IWHHTFYNELR (11); FPGQLNADLR (5); RIDIAGR (3) match also barley (Hordeum vulgarum) and many other species, while IKKELSTR (3) may originate from common fishes (e.g. Danio). In addition, VXDIIK has no diagnoistic value (can originate from countless number of species - from bacteria to humans), while the assignments for RIDIAGR and IKKELSTR are very questionable (note missed internal cleavages). Finally, IIAQVVSSITASLR (7) – is also of low diagnostic value because it can originate from many other species, e.g., from genera Oikopleura, Encephalitozoon, Edhazardia, Fasciola, Glugea, Trachipleistophora, and Endoreticulatus, in addition to Nosema. \r\n\r\nIn conclusion, flaws in experimental design and data analysis indicate that the Authors provided insufficient evidence for identification of IIV-6 (see L. Foster, Mol Cell Proteomics 2011 March; 10(3): M110.006387 ) and Nosema species in analyzed honey bee samples. \r\n\r\nPaul Sommer, PhD\r\nBrooklyn, NY\r\n", "isRemoved"=>false, "created"=>"2011-05-04T19:08:35Z", "lastModified"=>"2011-05-04T19:08:35Z", "creator"=>{"userId"=>"150341"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-05-04T19:08:35Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/ec0ff512-7e84-4d1e-aed3-afcbdc1d5567", "title"=>"Publication of re-analysis of a subset of the raw data ", "body"=>"We have just published an article in PLoS One that is a re-analysis of the raw mass spectrometry data from three of the fractions in this Bromenshenk et al study:\nhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0020873\nWe gained access to three of the raw data files (Xcalibur .raw files) from Dr Wick, one of the authors on the original study. By searching the data using standard search parameters against the whole NCBInr database, we found no evidence that peptides from Iridovirus and Nosema were present in these fractions, but were able to re-interpret a significant percentage of the spectra assigned to viral peptides as being peptides derived from bee proteins.\nWe have made the raw data from these fractions available on Tranche if other people wish to independently re-assess the data.", "isRemoved"=>false, "created"=>"2011-06-14T23:11:37Z", "lastModified"=>"2011-06-14T23:11:37Z", "creator"=>{"userId"=>"124671"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-06-14T23:11:37Z", "replies"=>[]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/5af27095-478e-4d49-91de-f8fcf392172f", "title"=>"Media Coverage of This Article", "body"=>"The following article represents some of the media coverage that has occurred for this paper:\n\nPublication: Angry by Choice \nTitle: “Groom of Fungus vs. Hymenoptera OR Told you so”\nhttp://angrybychoice.fieldofscience.com/2011/07/groom-of-fungus-vs-hymenoptera-or-told.html\n\nIf you see any additional coverage of this paper in the press or blogosphere, please reply to this thread and add the link to the article. \n", "isRemoved"=>false, "created"=>"2011-08-05T14:45:10Z", "lastModified"=>"2011-08-05T14:45:10Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"PLoS ONE Staff"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2013-08-02T17:46:41Z", "replies"=>[{"type"=>"REPLY", "parentID"=>8319, "annotationUri"=>"info:doi/10.1371/reply/3dd77fa9-3421-441b-be17-2fa5f73274ca", "title"=>" Media Coverage of This Article", "body"=>"The following article represents some of the media coverage that has occurred for this paper:\n\nPublication: Gizmodo Japan \nTitle: “Why do bees to mass death? Clarification at last mystery”\nhttp://www.gizmodo.jp/2010/10/post_7810.html\n\nIf you see any additional coverage of this paper in the press or blogosphere, please reply to this thread and add the link to the article. \n", "isRemoved"=>false, "created"=>"2013-08-02T17:46:41Z", "lastModified"=>"2013-08-02T17:46:41Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"PLOS ONE Staff"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2013-08-02T17:46:41Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/904045b8-4d6b-4ae4-828c-4c3eb140b404", "title"=>"Reanalysis of the full dataset indicates no IIV peptides", "body"=>"First of all, thank you to the authors for releasing what is apparently the full set of raw data for this study at Tranche. I have gone through the same exercise with the authors' own data as I had done previously with another dataset, as well as the re-analysis done by Chalkley and Knudsen. In short, if honey bee AND viral proteins are considered in the database search then there is no confidently-identified iridovirus proteins identified at all. Conversely, if one does not consider the honey bee proteins in the search then there are several very weak identifications of iridovirus proteins.\n\nThus, reanalysis of this data supports the authors' own findings that IIV DNA cannot be amplified in these samples. The reason, now clear, is that there simply never was any iridovirus in the samples to begin with.\n\nLeonard Foster", "isRemoved"=>false, "created"=>"2011-09-26T18:03:21Z", "lastModified"=>"2011-09-26T18:03:21Z", "creator"=>{"userId"=>"81511"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>false}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>1, "mostRecentActivity"=>"2011-10-03T23:18:02Z", "replies"=>[{"type"=>"REPLY", "parentID"=>13091, "annotationUri"=>"info:doi/10.1371/reply/71e6ef25-d874-4ea2-bc7c-3d1ac6df7c0a", "title"=>"RE: Reanalysis of the full dataset indicates no IIV peptides", "body"=>"They have now uploaded 68 raw data files from their study to Tranche. It can be accessed at the following page:\nhttps://proteomecommons.org/dataset.jsp?i=XvaxH3MQ5dMJYzD4l4%2FEPvwIn02tyV2%2BdvuoJZ1lFZD6sFkLmSy9F7Et0WiSV9IZpKcQPrf%2Frr4OQfh3UxDljvjqPWIAAAAAAAAfcQ%3D%3D\nWe have searched all of this data, and it appears that the three samples analyzed in our June PLoS One paper were representative of the rest of the data; i.e. there is no evidence for iridescent iridovirus in any of these samples. Indeed, there isn’t significant evidence of any viral protein in these samples. The main species identified in the samples were Apis Melifera (as expected), then Drosophila Melanogaster. Mosquito, wasp, bumble bee, moth and ant were all reported (along with human keratin), but we predict that some of these species identifications may not be exactly correct as we suspect the real species are probably not in the database, so these are the closest relations available. Hopefully, if the original authors are intending to further analyze this data, they will include at least these species in the database that they query.\nIn conclusion, our results independently agree with those reported by Leonard Foster that there is no evidence for iridoviral infection from these samples. \n", "isRemoved"=>false, "created"=>"2011-10-03T23:18:02Z", "lastModified"=>"2011-10-03T23:18:02Z", "creator"=>{"userId"=>"124671"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"I authored a manuscript indicating a lack of evidence for iridoviral infection after analyzing three of the samples described in this manuscript."}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-10-03T23:18:02Z", "replies"=>[]}]}
• {"type"=>"COMMENT", "annotationUri"=>"info:doi/10.1371/annotation/4127db96-a67e-4a62-9dc4-33c92b3af79f", "title"=>"Comment on behalf of the authors - Raw Mass Spectrometry Data of Honey Bee Samples ", "body"=>"*.RAW files were uploaded to Tranche on Aug 30 2011, at 05:22:15.236 PM.\n\nDescription: These *.RAW mass spectrometry files represent samples of honey bees that were used for analysis.\n\nData in these files served as the basis for a 2010 article in PLoS ONE - PLoS ONE 5(10) e13181.doi:10.1371/journal.pone. 0013181. Bromenshenk et al., Iridovirus and Microsporidian Linked to Honey Bee Colony Decline.\n\nThis data is provided to assist those analyzing honey bee samples for honey bee pathogens. We are preparing two new papers for publication based on other (non-honey bee) pathogens identified in these samples. We do not waive our rights to publish these additional results, and we will vigorously defend our rights against unauthorized use of any data that is not related to our prior publication.\n\nAs the lead author of the aforementioned paper, I should disclose that I am a research professor at The University of Montana, where some of the work was done. I am also the CEO of Bee Alert Technology, Inc.; a Montana University System Regent's Approved Technology Transfer Company that is affiliated with The University of Montana. The sampling was supported by contracts and donations to Bee Alert from beekeeping associations and non-profit research funding groups. There was no funding received from USDA or any private corporation.\n\nThe proteomics –based species identification was conducted by the U.S. Army, using their own, unique ABOID software system. Statistical analysis for the ABOID results was performed at The University of Montana. Nosema studies and verifications by microscopy and PCR were conducted at Montana State University.\n\nMore information about this upload:\n\nNetwork: ProteomeCommons.org Tranche Citation:\n\n--------------------------------------------------------------------------\nThe data associated with this manuscript may be downloaded from ProteomeCommons.org Tranche using the following hash: \n\nXvaxH3MQ5dMJYzD4l4/EPvwIn02tyV2+dvuoJZ1lFZD6sFkLmSy9F7Et0WiSV9IZpKcQPrf/rr4OQfh3UxDljvjqPWIAAAAAAAAfcQ==\n\nThe hash may be used to prove exactly what files were published as part of this manuscript's data set, and the hash may also be used to check that the data has not changed since publication.\n--------------------------------------------------------------------------\n\n", "isRemoved"=>false, "created"=>"2011-12-09T15:47:24Z", "lastModified"=>"2011-12-09T15:47:24Z", "creator"=>{"userId"=>"80539"}, "highlightedText"=>"", "competingInterestStatement"=>{"creatorWasPrompted"=>true, "hasCompetingInterests"=>true, "body"=>"PLoS ONE Staff"}, "parentArticle"=>{"doi"=>"info:doi/10.1371/journal.pone.0013181", "state"=>"published", "journals"=>{"PLoSONE"=>{"journalKey"=>"PLoSONE", "eIssn"=>"1932-6203", "title"=>"PLOS ONE"}}}, "replyTreeSize"=>0, "mostRecentActivity"=>"2011-12-09T15:47:24Z", "replies"=>[]}

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• {"id"=>"330569891541303296", "text"=>"http://t.co/ZahSbn3riw", "created_at"=>"2013-05-04T06:29:38Z", "user"=>"skyblue0420_xxx", "user_name"=>"わだbot", "user_profile_image"=>"http://a0.twimg.com/profile_images/3533869935/c304b0a7763045dd55e35bd760d64987_normal.jpeg"}
• {"id"=>"347870795843895296", "text"=>"これでしたね。ウイルスと細菌のコラボ「蜂群崩壊症候群（CCD：colony collapse disorder）」の原因判明 http://t.co/2C4HjnTLBt", "created_at"=>"2013-06-21T00:17:15Z", "user"=>"seishounagon", "user_name"=>"醤油猫（安藤猫奈津（", "user_profile_image"=>"http://a0.twimg.com/profile_images/2682244694/94f0ca699cc8c2c04f90512e4b700319_normal.png"}
• {"id"=>"407164949601857536", "text"=>"プリントなう\n#PLOSONE: Iridovirus and Microsporidian Linked to Honey Bee Colony Decline http://t.co/GJrxLMyrd0", "created_at"=>"2013-12-01T15:11:03Z", "user"=>"bumbum4513", "user_name"=>"Shota＠野いちご中毒", "user_profile_image"=>"http://pbs.twimg.com/profile_images/378800000629022307/daa0b62b1e56808feb377bc6f17cb0b5_normal.jpeg"}
• {"id"=>"602585371067711488", "text"=>"http://t.co/YuvSqAguE0\n\nSave the bees! Serious research on CCD (colony collapse disorder) #savethebees #bees #honeybees #bumblebees", "created_at"=>"2015-05-24T21:22:02Z", "user"=>"HuskAndHoneyLDN", "user_name"=>"Husk and Honey", "user_profile_image"=>"http://pbs.twimg.com/profile_images/498199051272065024/0MFqH2zz_normal.png"}

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• {"title"=>"List of diseases of the honey bee", "url"=>"http://en.wikipedia.org/wiki/List_of_diseases_of_the_honey_bee", "timestamp"=>"2019-02-21T19:48:32Z"}
• {"title"=>"Bee", "url"=>"http://en.wikipedia.org/wiki/Bee", "timestamp"=>"2019-02-21T19:29:55Z"}
• {"title"=>"Colony collapse disorder", "url"=>"http://en.wikipedia.org/wiki/Colony_collapse_disorder", "timestamp"=>"2019-03-14T19:59:11Z"}
• {"title"=>"Colony collapse disorder", "url"=>"http://nl.wikipedia.org/wiki/Colony_collapse_disorder", "timestamp"=>"2018-07-18T12:37:59Z"}
• {"title"=>"Nosema ceranae", "url"=>"http://fr.wikipedia.org/wiki/Nosema_ceranae", "timestamp"=>"2019-02-15T20:47:41Z"}
• {"title"=>"Apis (genre)", "url"=>"http://fr.wikipedia.org/wiki/Apis_(genre)", "timestamp"=>"2019-02-16T11:36:29Z"}
• {"title"=>"Apicultura", "url"=>"http://pt.wikipedia.org/wiki/Apicultura", "timestamp"=>"2019-03-10T22:45:50Z"}
• {"title"=>"Список хвороб медоносних бджіл", "url"=>"http://uk.wikipedia.org/wiki/Список_хвороб_медоносних_бджіл", "timestamp"=>"2018-09-29T15:42:29Z"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/825733"], "description"=>"<p>Function 1 explains 81 percent of discriminating variance and contrasts higher incidence of iridovirus (IIV), <i>Nosema</i>, and to a lesser extent BQCV in failing colonies with higher incidence of DWV and some IAPV in the remaining groups. Vertical and horizontal lines mark the non-CCD out-group as a reference set.</p>", "links"=>[], "tags"=>["differences", "pathogen", "peptide", "counts", "collapsed"], "article_id"=>496052, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Discriminant_Function_Analysis_for_differences_in_pathogen_peptide_counts_among_strong_failing_and_collapsed_honey_bee_colonies_/496052", "title"=>"Discriminant Function Analysis for differences in pathogen peptide counts among strong, failing, and collapsed honey bee colonies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:00:08"}
• {"files"=>["https://ndownloader.figshare.com/files/825825"], "description"=>"<p>The peptides were detected in dead worker honey bee samples collected from a single collapsing observation hive at the University of Montana, Missoula. Forager flights are absolute counts per day, tabulated by an automated honey bee counter. Peptide counts are the summed counts by day of collection for all unique IIV <i>Nosema</i> peptides in each sample. We suspended sampling in mid-August, as the bee population was too weak to sample without affecting the colony. We collected the queen and last few bees for a final sample in early September. Sample size varied from about ten bees to more than 100 per sample interval, depending on how many dead bees were obtained from the entrance tube.</p>", "links"=>[], "tags"=>["forager", "flights", "conjunction", "counts", "iridovirus"], "article_id"=>496161, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Decline_in_forager_flights_in_conjunction_with_increasing_counts_of_iridovirus_IIV_and_Nosema_peptides_/496161", "title"=>"Decline in forager flights in conjunction with increasing counts of iridovirus (IIV) and <i>Nosema</i> peptides.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:00:43"}
• {"files"=>["https://ndownloader.figshare.com/files/825932"], "description"=>"<p>Newly emerged, 1–3 day old, bees were used in all experiments. Figure represents the combined survival results for 4 biological replications (N = 30 bees in each group for each biological replicate). Bees that perished within 24 hours of inoculation were not included in the survival curve analyses. Deaths in control group were confirmed not to be pathogen related via mass spectroscopy analyses. Inoculum sizes and doses described in materials and <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013181#s4\" target=\"_blank\">methods</a> section. Log Rank Tests Kaplan-Meier Curve Analyses: 1) Control VS. <i>N. ceranae</i> - P = 0.01, 2) Control VS. IIV alone – P<0.01 (0.008), 3) Control VS. <i>Nosema </i>+ IIV – P<0.01 (0.0001), 4) <i>Nosema</i> alone vs. IIV alone – P = 0.90, 5) <i>Nosema</i> alone VS. <i>Nosema </i>+ IIV – P = 0.04, 6) Virus alone VS. <i>Nosema </i>+ IIV – P = 0.04. These results strongly suggest that the combination of <i>N. ceranae</i> and IIV is associated with increased bee mortality.</p>", "links"=>[], "tags"=>["fourteen", "post-infection", "observed", "cage-trials", "iiv", "infected"], "article_id"=>496272, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Survival_over_a_fourteen_day_post_infection_period_observed_in_cage_trials_of_Nosema_ceranae_and_IIV_infected_honey_bees_/496272", "title"=>"Survival over a fourteen day post-infection period observed in cage-trials of <i>Nosema ceranae</i> and IIV infected honey bees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 23:01:17"}
• {"files"=>["https://ndownloader.figshare.com/files/826028"], "description"=>"a<p>Columns summarize thirty-one colonies from initial CCD study in 2006; eighteen subsamples taken from an observation colony monitored through its collapse from March through August 2007; and a third sample of nine colonies sampled during a CCD incident in Florida in 2008. A hyphen indicates that the value could not be calculated.</p>", "links"=>[], "tags"=>["occurrence", "peptide", "counts", "viral", "pathogens", "colonies", "sampled"], "article_id"=>496358, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Frequency_Frq_of_occurrence_and_mean_peptide_counts_of_viral_pathogens_and_Nosema_in_honey_bee_colonies_sampled_in_2006_2007_and_2008_a_/496358", "title"=>"Frequency (Frq) of occurrence and mean peptide counts of viral pathogens and <i>Nosema</i> in honey bee colonies sampled in 2006, 2007, and 2008^a.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 23:01:44"}
• {"files"=>["https://ndownloader.figshare.com/files/826085"], "description"=>"<p>Cumulative variance, significance, and coefficients for derived discriminant functions.</p>", "links"=>[], "tags"=>["coefficients", "derived", "discriminant"], "article_id"=>496433, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cumulative_variance_significance_and_coefficients_for_derived_discriminant_functions_/496433", "title"=>"Cumulative variance, significance, and coefficients for derived discriminant functions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 23:02:05"}
• {"files"=>["https://ndownloader.figshare.com/files/826150"], "description"=>"<p>Pooled within-groups correlations between discriminating variables and standardized canonical discriminant functions ordered by absolute size of correlation within function.</p>", "links"=>[], "tags"=>["within-groups", "correlations", "discriminating", "variables", "standardized", "canonical", "discriminant", "functions", "ordered"], "article_id"=>496489, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pooled_within_groups_correlations_between_discriminating_variables_and_standardized_canonical_discriminant_functions_ordered_by_absolute_size_of_correlation_within_function_/496489", "title"=>"Pooled within-groups correlations between discriminating variables and standardized canonical discriminant functions ordered by absolute size of correlation within function.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 23:02:23"}
• {"files"=>["https://ndownloader.figshare.com/files/826216"], "description"=>"a<p>Spearman's rank correlation (rho; n = 266).</p>b<p>Sorensen's index of similarity were calculated for each pairwise comparison. East-, West-CCD colonies sampled 2007–2008; Collapsing Observation Colony, 2008; Florida Collapse, 2009; Inoculation Trials, 2009–2010.</p>", "links"=>[], "tags"=>["occurrence", "iridescent", "peptides", "samples", "pathogens"], "article_id"=>496551, "categories"=>["Medicine", "Biochemistry", "Ecology", "Infectious Diseases"], "users"=>["Jerry J. Bromenshenk", "Colin B. Henderson", "Charles H. Wick", "Michael F. Stanford", "Alan W. Zulich", "Rabih E. Jabbour", "Samir V. Deshpande", "Patrick E. McCubbin", "Robert A. Seccomb", "Phillip M. Welch", "Trevor Williams", "David R. Firth", "Evan Skowronski", "Margaret M. Lehmann", "Shan L. Bilimoria", "Joanna Gress", "Kevin W. Wanner", "Robert A. Cramer Jr"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0013181.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_in_occurrence_of_specific_iridescent_virus_peptides_among_different_samples_analyzed_for_evidence_of_pathogens_associated_with_CCD_/496551", "title"=>"Similarity in occurrence of specific iridescent virus peptides among different samples analyzed for evidence of pathogens associated with CCD.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 23:02:46"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime