text:
Category Archives: scholarly publishing
Did Finishing the Drosophila Genome Legitimize Open Access Publishing?
I'm currently reading Glyn Moody's (2003) "Digital Code of Life: How Bioinformatics is Revolutionizing Science, Medicine, and Business" and greatly enjoying the writing as well as the whirlwind summary of the history of Bioinformatics and the (Human) Genome Project(s). Most of what Moody says that I am familiar with is quite accurate, and his scholarship is thorough, so I find his telling of the story compelling. One claim I find new and curious in this book is in his discussion of the sequencing of the Drosphila melanogaster genome, more precisely the "finishing" of this genome, and its impact on the legitimacy of Open Access publishing.
The sequencing of D. melanogaster was done as a collaboration with between the Berkeley Drosophila Genome Project and Celera, as a test case to prove that whole-genome shotgun sequencing could be applied to large animal genomes. I won't go into the details here, but it is a widely regarded fact that the Adams et al. (2000) and Myers et al. (2000) papers in Science demonstrated the feasibility of whole-genome shotgun sequencing, but it was a lesser-known paper by Celniker et al. (2002) in Genome Biology which reported the "finished" D. melanogaster genome that proved the accuracy of whole-genome shotgun sequencing assembly. No controversy here.
More debatable is what Moody goes on to write about the Celniker et al. (2002) paper:
This was an important paper, then, and one that had a significance that went beyond its undoubted scientific value. For it appeared neither in Science, as the previous Drosophila papers had done, nor in Nature, the obvious alternative. Instead, it was published in Genome Biology. This describes itself as "a journal, delivered over the web." That is, the Web is the primary medium, with the printed version offering a kind of summary of the online content in a convenient portable form. The originality of Genome Biology does not end there: all of its main research articles are available free online.
A description then follows of the history and virtues of PubMed Central and the earliest Open Access biomedical publishers BioMed Central and PLoS. Moody (emphasis mine) then returns to the issue of:
…whether a journal operating on [Open Access] principles could attract top-ranked scientists. This question was answered definitively in the affirmative with the announcement and analysis of the finished Drosophila sequence in January 2003. This key opening paper's list of authors included not only [Craig] Venter, [Gene] Myers, and [Mark] Adams, but equally stellar representatives of the academic world of Science, such as Gerald Rubin, the boss of the fruit fly genome project, and Richard Gibbs, head of sequencing at Baylor College. Alongside this paper there were no less than nine other weighty contributions, including one on Apollo, a new tool for viewing and editing sequence annotation. For its own Drosophila extravaganza of March 2000, Science had marshalled seven paper in total. Clearly, Genome Biology had arrived, and with it a new commercial publishing model based on the latest way of showing the data.
This passage resonated with me since I was working at the BDGP at the time this special issue on the finishing of the Drosophila genome in Genome Biology was published, and was personally introduced to Open Access publishing through this event. I recall Rubin walking the hallways of building 64 on his periodic visits promoting this idea, motivating us all to work hard to get our papers together by the end of 2002 for this unique opportunity. I also remember lugging around stacks of the printed issue at the Fly meeting in Chicago in 2003, plying unsuspecting punters with a copy of a journal that most people had never heard of, and having some of my first conversations with people on Open Access as a consequence.
What Moody doesn't capture in this telling is the fact the Rubin's decision to publish in Genome Biology almost surely owes itself to the influence that Mike Eisen had on Rubin and others in the genomics community in Berkeley at the time. Eisen and Rubin had recently collaborated on a paper, Eisen had made inroads in Berkeley on the Open Access issue by actively recruiting signatories for the PLoS open letter the year before, and Eisen himself published his first Open Access paper in Oct 2002 in Genome Biology. So clearly the idea of publishing in Open Access journals, and in particular Genome Biology, was in the air at the time. So it may not have been as bold of a step for Rubin to take as Moody implies.
Nevertheless, it is a point that may have some truth, and I think it is interesting to consider if indeed the long-standing open data philosophy of the Drosophila genetics community that led to the Genome Biology special issue was a key turning point in the widespread success of Open Access publishing over the next decade. Surely the movement would have taken off anyways at some point. But in late 2002, when the BioMed Central journals were the only place to publish gold Open Access articles, few people had tested the waters since the launch of BMC journals in 2000. While we cannot replay the tape, Moody's claim is plausible in my view and it is interesting to ask whether widespread buy-in to Open Access publishing in biology might have been delyaed if Rubin had not insisted that the efforts of the Berkeley Drosophila Genome Project be published under and Open Access model?
UPDATE 25 March 2012
After tweeting this post, here is what Eisen and Moody have to say:
@caseybergman @glynmoody @GenomeBiology it was a major milestone, gave GB a big bump, and established principle that genome papers be #OA
— Michael Eisen (@mbeisen) March 24, 2012
.@mbeisen – surprising to think this set of papers could have made a real difference – thanks for the insight into this chapter. #openaccess
— Casey Bergman (@caseybergman) March 24, 2012
@glynmoody @caseybergman @GenomeBiology no prob- #OA was in air- gerry was hearing from pat brown too – and he was already inclined to #OA
UPDATE 19 May 2012
It appears that the publication of another part of the Drosophila (meta)genome, its Wolbachia endosymbiont, played and important role in the conversion of Jonathan Eisen to supporting Open Access. Read more here.
Posted on March 24, 2012 by caseybergman.	Posted in genomics, history, open access, scholarly publishing	| 1 Comment
The Roberts/Ashburner Response
A previous post on this blog shared a helpful boilerplate response to editors for politely declining to review for non-Open Access journals, which I received originally from Michael Ashburner. During a quick phone chat today, Ashburner told me that he in fact inherited a version of this response originally from Nobel laureate Richard Roberts, co-discoverer of introns, lead author on the Open Letter to Science calling for a "Genbank" of the scientific literature, and long-time editor of Nucleic Acids Research, one of the first classical journals to move to a fully Open Access model. So to give credit where it is due, I've updated the title of the "Just Say No" post to make the attribution of this letter more clear. We owe both Roberts and Ashburner many thanks for paving the way to a better model of scientific communication and leading by example.
Posted on March 9, 2012 by caseybergman.	Posted in history, open access, peer review, scholarly publishing	| 1 Comment
Why the Research Works Act Doesn't Affect Text-mining Research
As the the central digital repository for life science publications, PubMed Central (PMC) is one of the most significant resources for making the Open Access movement a tangible reality for researchers and citizens around the world. Articles in PMC are deposited through two routes: either automatically by journals that participate in the PMC system, or directly by authors for journals that do not. Author deposition of peer-reviewed manuscripts in PMC is mandated by funders in order to make the results of publicly- or charity-funded research maximally accessible, and has led to over 180,000 articles being made free (gratis) to download that would otherwise be locked behind closed-access paywalls. Justifiably, there has been outrage over recent legislation (the Research Works Act) that would repeal the NIH madate in the USA and thereby prevent important research from being freely available.
However, from a text-miner's perspective author-deposited manuscripts in PMC are closed access since, while they can be downloaded and read individually, virtually none (<200) are available from the PMC's Open Access subset that includes all articles that are free (libre) to download in bulk and text/data mine. This includes ~99% of the author deposited manuscripts from the journal Nature, despite a clear statement from 2009 entitled "Nature Publishing Group allows data- and text-mining on self-archived manuscripts". In short, funder mandates only make manuscripts public but not open, and thus whether the RWA is passed or not is actually moot from a text/data-mining perspective.
Why is this important? The simple reason is that there are currently only ~400,000 articles in the PMC Open Access subset, and therefore author-deposited manuscripts are only two-fold less abundant than all articles currently available for text/data-mining. Thus what could be a potentially rich source of data for large-scale information extraction remains locked away from programmatic analysis. This is especially tragic considering the fact that at the point of manuscript acceptance, publishers have invested little-to-nothing into the publication process and their claim to copyright is most tenuous.
So instead of discussing whether we should support the status quo of weak funder mandates by working to block the RWA or expand NIH-like mandates (e.g. as under the Federal Research Public Access Act, FRPAA), the real discussion that needs to be had is how to make funder mandates stronger to insist (at a minimum) that author-deposited manuscripts be available for text/data-mining research. More-of-the same, not matter how much, only takes us half the distance towards the ultimate goals of the Open Access movement, and doesn't permit the crucial text/data mining research that is needed to make sense of the deluge of information in the scientific literature.
Credits: Max Haussler for making me aware of the lack of author manuscripts in PMC a few years back, and Heather Piwowar for recently jump-starting the key conversation on how to push for improved text/data mining rights in future funder mandates.
Be openly accessible or be obscure – A taxonomy of articles in PubMed Central
Posted on February 11, 2012 by caseybergman.	Posted in data mining, open access, scholarly publishing, text mining	| 8 Comments
A Open Archive of My F1000 Reviews
Following on from a recent conversation with David Stephens on Twitter about my decision to resign from Faculty of 1000, F1000 has clarified their terms for the submission of evaluations and confirmed that it is permissible to "reproduce personal evaluations on institutional & personal blogs if you clearly reference F1000".
@David_S_Bristol @caseybergman You're free to reproduce personal evaluations on institutional&personal blogs if you clearly reference F1000.
— F1000Prime (@F1000) January 6, 2012
As such, I am delighted to be able to repost here an Open Archive of my F1000 contributions. Additionally, this post acts in a second capacity as my first contribution to the Research Blogging Network. Hopefully these commentraies will be of interest to some, and should add support to the Altmetrics profiles for these papers through systems like Total Impact.
Nelson CE, Hersh BM, & Carroll SB (2004). The regulatory content of intergenic DNA shapes genome architecture. Genome biology, 5 (4) PMID: 15059258
My review: This article reports that genes with complex expression have longer intergenic regions in both D. melanogaster and C. elegans, and introduces several innovative and complementary approaches to quantify the complexity of gene expression in these organisms. Additionally, the structure of intergenic DNA in genes with high complexity (e.g. receptors, specific transcription factors) is shown to be longer and more evenly distributed over 5′ and 3′ regions in D. melanogaster than in C. elegans, whereas genes with low complexity (e.g. metabolic genes, general transcription factors) are shown to have similar intergenic lengths in both species and exhibit no strong differences in length between 5′ and 3′ regions. This work suggests that the organization of noncoding DNA may reflect constraints on transcriptional regulation and that gene structure may yield insight into the functional complexity of uncharacterized genes in compact animal genomes. (@F1000: http://f1000.com/1032936)
Li R, Ye J, Li S, Wang J, Han Y, Ye C, Wang J, Yang H, Yu J, Wong GK, & Wang J (2005). ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS computational biology, 1 (4) PMID: 16184192
My review: This paper presents a novel method for automating the laborious task of constructing libraries of transposable element (TE) consensus sequences. Since repetitive TE sequences confound whole-genome shotgun (WGS) assembly algorithms, sequence reads from TEs are initially screened from WGS assemblies based on overrepresented k-mer frequencies. Here, the authors invert the same principle, directly identifying TE consensus sequences from those same reads containing high frequency k-mers. The method was shown to identify all high copy number TEs and increase the effectiveness of repeat masking in the rice genome. By circumventing the inherent difficulties of TE consensus reconstruction from erroneously assembled genome sequences, and by providing a method to identify TEs prior to WGS assembly, this method provides a new strategy to increase the accuracy of WGS assemblies as well as our understanding of the TEs in genome sequences. (@F1000: http://f1000.com/1031746)
Rifkin SA, Houle D, Kim J, & White KP (2005). A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression. Nature, 438 (7065), 220-3 PMID: 16281035
My review: This paper reports empirical estimates of the mutational input to gene expression variation in Drosophila, knowledge of which is critical for understanding the mechanisms governing regulatory evolution. These direct estimates of mutational variance are compared to gene expression differences across species, revealing that the majority of genes have lower expression divergence than is expected if evolving solely by mutation and genetic drift. Mutational variances on a gene-by-gene basis range over several orders of magnitude and are shown to vary with gene function and developmental context. Similar results in C. elegans [1] provide strong support for stabilizing selection as the dominant mode of gene expression evolution. (@F1000: http://f1000.com/1040157)
References: 1. Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, & Thomas WK (2005). The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature genetics, 37 (5), 544-8 PMID: 15852004
Caspi A, & Pachter L (2006). Identification of transposable elements using multiple alignments of related genomes. Genome research, 16 (2), 260-70 PMID: 16354754
My review: This paper reports an innovative strategy for the de novo detection of transposable elements (TEs) in genome sequences based on comparative genomic data. By capitalizing on the fact that bursts of TE transposition create large insertions in multiple genomic locations, the authors show that detection of repeat insertion regions (RIRs) in alignments of multiple Drosophila genomes has high sensitivity to identify both individual instances and families of known TEs. This approach opens a new direction in the field of repeat detection and provides added value to TE annotations by placing insertion events in a phylogenetic context. (@F1000 http://f1000.com/1049265)
Simons C, Pheasant M, Makunin IV, & Mattick JS (2006). Transposon-free regions in mammalian genomes. Genome research, 16 (2), 164-72 PMID: 16365385
My review: This paper presents an intriguing analysis of transposon-free regions (TFRs) in the human and mouse genomes, under the hypothesis that TFRs indicate genomic regions where transposon insertion is deleterious and removed by purifying selection. The authors test and reject a model of random transposon distribution and investigate the properties of TFRs, which appear to be conserved in location across species and enriched for genes (especially transcription factors and micro-RNAs). An alternative mutational hypothesis not considered by the authors is the possibility for clustered transposon integration (i.e. preferential insertion into regions of the genome already containing transposons), which may provide a non-selective explanation for the apparent excess of TFRs in the human and mouse genomes. (@F1000: http://f1000.com/1010399)
Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, & Boeke JD (2006). Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America, 103 (47), 17632-7 PMID: 17101968
My review: This paper demonstrates the utility of whole-genome microarrays for the high-throughput mapping of eukaryotic transposable element (TE) insertions on a genome-wide basis. With an experimental design guided by first computationally digesting the genome into suitable fragments, followed by linker-PCR to amplify TE flanking regions and subsequent hybridization to tiling arrays, this method was shown to recover all detectable TE insertions with essentially no false positives in yeast. Although limited to species with available genome sequences, this approach circumvents inefficiencies and biases associated with the alternative of whole-genome shotgun resequencing to detect polymorphic TEs on a genome-wide scale. Application of this or related technologies (e.g. [1]) to more complex genomes should fill gaps in our understanding of the contribution of TE insertions to natural genetic variation. (@F1000: http://f1000.com/1088573)
References: 1. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, & Dunham MJ (2006). Global mapping of transposon location. PLoS genetics, 2 (12) PMID: 17173485
Haag-Liautard C, Dorris M, Maside X, Macaskill S, Halligan DL, Houle D, Charlesworth B, & Keightley PD (2007). Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature, 445 (7123), 82-5 PMID: 17203060
My review: This paper presents the first direct estimates of nucleotide mutation rates across the Drosophila genome derived from mutation accumulation experiments. By using DHPLC to scan over 20 megabases of genomic DNA, the authors obtain several fundamental results concerning mutation at the molecular level in Drosophila: SNPs are more frequent than indels; deletions are more frequent than insertions; mutation rates are similar across coding, intronic and intergenic regions; and mutation rates may vary across genetic backgrounds. Results in D. melanogaster contrast with those obtained from mutation accumulation experiments in C. elegans (see [1], where indels are more frequent than SNPs, and insertions are more frequent than deletions), indicating that basic mutation processes may vary across metazoan taxa. (@F1000: http://f1000.com/1070688)
References: 1. Denver DR, Morris K, Lynch M, & Thomas WK (2004). High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 430 (7000), 679-82 PMID: 15295601
Katzourakis A, Pereira V, & Tristem M (2007). Effects of recombination rate on human endogenous retrovirus fixation and persistence. Journal of virology, 81 (19), 10712-7 PMID: 17634225
My review: This study shows that the persistence, but not the integration, of long-terminal repeat (LTR) containing human endogenous retroviruses (HERVs) is associated with local recombination rate, and suggests a link between intra-strand homologous recombination and meiotic exchange. This inference about the mechanisms controlling the transposable element (TE) abundance is obtained by demonstrating that total HERV density (full-length elements plus solo LTRs) is not correlated with recombination rate, whereas the ratio of full-length HERVs relative to solo LTRs is. This work relies critically on advanced computational methods to join TE fragments, demonstrating the need for such algorithms to make accurate inferences about the evolution of mobile DNA and to reveal new insights into genome biology. (@F1000: http://f1000.com/1091037)
Giordano J, Ge Y, Gelfand Y, Abrusán G, Benson G, & Warburton PE (2007). Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS computational biology, 3 (7) PMID: 17630829
My review: This article reports the first comprehensive stratigraphic record of transposable element (TE) activity in mammalian genomes based on several innovative computational methods that use information encoded in patterns of TE nesting. The authors first develop an efficient algorithm for detecting nests of TEs by intelligently joining TE fragments identified by RepeatMasker, which (in addition to providing an improved genome annotation) outputs a global "interruption matrix" that can be used by a second novel algorithm which generates a chronological ordering of TE activity by minimizing the nesting of young TEs into old TEs. Interruption matrix analysis yields results that support previous phylogenetic analyses of TE activity in humans but are not dependent on the assumption of a molecular clock. Comparison of the chronological orders of TE activity in six mammalian genomes provides unique insights into the ancestral and lineage-specific record of global TE activity in mammals. (@F1000: http://f1000.com/1089045)
Schuemie MJ, & Kors JA (2008). Jane: suggesting journals, finding experts. Bioinformatics (Oxford, England), 24 (5), 727-8 PMID: 18227119
My review: This paper introduces a fast method for finding related articles and relevant journals/experts based on user input text and should help improve the referencing, review and publication of biomedical manuscripts. The JANE (Journal/Author Name Estimator) method uses a standard word frequency approach to find similar documents, then adds the scores in the top 50 records to produce a ranked list of journals or authors. Using either the abstract or full-text, JANE suggested quite sensible journals and authors in seconds for a manuscript we have in press, while the related eTBLAST method [1] failed to complete while I wrote this review. JANE should prove to be a very useful text mining tool for authors and editors alike. (@F1000: http://f1000.com/1101037)
References: 1. Errami M, Wren JD, Hicks JM, & Garner HR (2007). eTBLAST: a web server to identify expert reviewers, appropriate journals and similar publications. Nucleic acids research, 35 (Web Server issue) PMID: 17452348
Pask AJ, Behringer RR, & Renfree MB (2008). Resurrection of DNA function in vivo from an extinct genome. PloS one, 3 (5) PMID: 18493600
My review: This paper reports the first transgenic analysis of a cis-regulatory element cloned from an extinct species. Although no differences were seen in the expression pattern of the collagen (Col2A1) enhancer from the extinct Tasmanian tiger and extant mouse, this work is an important proof of principle for using ancient DNA in the evolutionary analysis of gene regulation. (@F1000: http://f1000.com/1108816)
Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, & Brilliant L (2009). Detecting influenza epidemics using search engine query data. Nature, 457 (7232), 1012-4 PMID: 19020500
My review: A landmark paper in health bioinformatics demonstrating that Google searches can predict influenza trends in the United States. Predicting infectious disease outbreaks currently relies on patient reports gathered through clinical settings and submitted to government agencies such as the CDC. The possible use of patient "self-reporting" through internet search queries offers unprecedented real-time access to temporal and regional trends in infectious diseases. Here, the authors use a linear modeling strategy to learn which Google search terms best correlate with regional trends in influenza-related illness. This model explains flu trends over a 5 year period with startling accuracy, and was able to predict flu trends during 2007-2008 with a 1-2 week lead time ahead of CDC reports. The phenomenal use of crowd-based predictive health informatics revolutionizes the role of the internet in biomedical research and will likely set an important precedent in many areas of natural sciences. (@F1000: http://f1000.com/1127181)
Taher L, & Ovcharenko I (2009). Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics (Oxford, England), 25 (5), 578-84 PMID: 19168912
My review: This paper raises the important observation that differences in the length of genes can bias their functional classification using the Gene Ontology, and provides a simple method to correct for this inherent feature of genome architecture. A basic observation of genome biology is that genes differ widely in their size and structure within and between species. Understanding the causes and consequences of this variation in gene structure is an open challenge in genome biology. Previously, Nelson and colleagues [1] have shown, in flies and worms, that the length of intergenic regions is correlated with the regulatory complexity of genes and that genes from different Gene Ontology (GO) categories have drastically different lengths. Here, Taher and Ovcharenko confirm this observation of functionally non-random gene length in the human genome, and discuss the implications of this feature of genome organization on analyses that employ the GO for functional inference. Specifically, these authors show that random selection of noncoding DNA sequences from the human genome leads to the false inference of over- and under-representation of specific GO categories that preferentially contain longer or shorter genes, respectively. This finding has important implications for the large number of studies that employ a combination of gene expression microarrays and GO enrichment analysis, since gene expression is largely controlled by noncoding DNA. The authors provide a simple method to correct for this bias in GO analyses, and show that previous reports of the enrichment of "ultraconserved" noncoding DNA sequences in vertebrate developmental genes [2] may be a statistical artifact. (@F1000: http://f1000.com/1157594)
References: 1. Nelson CE, Hersh BM, & Carroll SB (2004). The regulatory content of intergenic DNA shapes genome architecture. Genome biology, 5 (4) PMID: 15059258
2. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, & Haussler D (2004). Ultraconserved elements in the human genome. Science (New York, N.Y.), 304 (5675), 1321-5 PMID: 15131266
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, & Manolio TA (2009). Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America, 106 (23), 9362-7 PMID: 19474294
My review: This article introduces results from human genome-wide association studies (GWAS) into the realm of large-scale functional genomic data mining. These authors compile the first curated database of trait-associated single-nucleotide polymorphisms (SNPs) from GWAS studies (http://www.genome.gov/gwastudies/) that can be mined for general features of SNPs underlying phenotypes in humans. By analyzing 531 SNPs from 151 GWAS studies, the authors discover that trait-associated SNPs are predominantly in non-coding regions (43% intergenic, 45% intronic), but that non-synonymous and promoter trait-associated SNPs are enriched relative to expectations. The database is actively maintained and growing, and currently contains 3943 trait-associated SNPs from 796 publications. This important resource will facilitate data mining and integration with high-throughput functional genomics data (e.g. ChIP-seq), as well as meta-analyses, to address important questions in human genetics, such as the discovery of loci that affects multiple traits. While the interface to the GWAS catalog is rather limited, a related project (http://www.gwascentral.org/) [1] provides a much more powerful interface for searching and browsing data from the GWAS catalog. (@F1000: http://f1000.com/8408956)
References: 1. Thorisson GA, Lancaster O, Free RC, Hastings RK, Sarmah P, Dash D, Brahmachari SK, & Brookes AJ (2009). HGVbaseG2P: a central genetic association database. Nucleic acids research, 37 (Database issue) PMID: 18948288
Tamames J, & de Lorenzo V (2010). EnvMine: a text-mining system for the automatic extraction of contextual information. BMC bioinformatics, 11 PMID: 20515448
My review: This paper describes EnvMine, an innovative text-mining tool to obtain physico-chemical and geographical information about environmental genomics samples. This work represents a pioneering effort to apply text-mining technologies in the domain of ecology, providing novel methods to extract the units and variables of physico-chemical entities, as well as link the location of samples to worldwide geographic coordinates via Google Maps. Application of EnvMine to full-text articles in the environmental genomics database envDB {1} revealed very high system performance, suggesting that information extracted by EnvMine will be of use to researchers seeking meta-data about environmental samples across different domains of biology. (@F1000: http://f1000.com/3502956)
References: 1. Tamames J, Abellán JJ, Pignatelli M, Camacho A, & Moya A (2010). Environmental distribution of prokaryotic taxa. BMC microbiology, 10 PMID: 20307274
Posted on January 28, 2012 by caseybergman.	Posted in open access, research blogging, scholarly publishing	| Leave a comment
Goodbye F1000, Hello Faculty of a Million
In the children's story The Sneetches, Dr. Suess' presents a world where certain members of society are marked by an arbitrary badge of distinction, and a canny opportunist uses this false basis of prestige for his financial gain*. What does this morality tale have to do with the scientific article recommendation service Faculty of 1000? Read on…
Currently ~3000 papers are published each day in the biosciences**. Navigating this sea of information to find articles relevant to your work is no small matter. Researchers can either sink or swim with the aid of (i) machine-based technologies based on search or text-mining tools or (ii) human-based technologies like blogs or social networking services that highlight relevant work through expert recommendation.
One of the first expert recommendation services was Faculty of 1000, a service launched in 2002 with the aim of "identifying and evaluating the most significant articles from biomedical research publications" though a peer-nominated "Faculty" of experts in various subject domains. Since the launch of F1000, several other mechanisms for expert literature recommendation have also come to the foreground, including academic social bookmarking tools like citeulike or Mendeley, the rise of Research Blogging, and new F1000-like services such as annotatr, The Third Reviewer PaperCritic and TiNYARM.
Shortly after I started my group at the University of Manchester in 2005 I was invited to join the F1000 Faculty, which I gratefully accepted. At the time, I felt that it was a mark of distinction to be invited into this select club, since I felt that it would be a good platform to voice my opinions on what work I thought was notable. I was under no illusion that my induction was based only on merit, since this invitation came from my former post-doc mentor Michael Ashburner. I overlooked this issue at the time, since when you are invited to join the "in-club" as a junior faculty member, it is very tempting since you think things like this will play a positive role in your career progression. [Whether being in F1000 has helped my career I can't say, but certainly it can't have hurt, and I (sheepishly) admit to using it on grant and promotion applications in the past.]
Since then, I've tried to contribute to F1000 when I can [PAYWALL], but since it is not a core part of my job, I've only contributed ~15 reviews in 5 years. My philosophy has been only to contribute reviews on articles I think are of particular note and might be missed otherwise, not to review major papers in Nature/Science that everyone is already aware of. As time has progressed and it has become harder to commit time to non-essential tasks, I've contributed less and less, and the F1000 staff has pestered me frequently with reminders and phone calls to submit reviews. At times the pestering has been so severe that I have considered resigning just to get them off my back. And I've noticed that some colleagues I have a lot of respect for have also resigned from F1000, which made me wonder if they were likewise fed up with F1000's nagging.
This summer, while reading a post on the Tree of Life blog, Jonathan Eisen made a parenthetical remark about quitting F1000, which made me more aware of why their nagging was really getting to me:
I even posted a "dissent" regarding one of [Paul Hebert's] earlier papers on Faculty of 1000 (which I used to contribute to before they become non open access).
This comment made me realize that the F1000 recommendation service is just another closed-access venture for publishers to make money off a product generated for free by the goodwill and labor of academics. Like closed access journals, my University pays twice to get F1000 content — once for my labor and once for the subscription to the service. But unlike a normal closed-access journal, in the case of F1000 there is not even a primary scientific publication to justify the arrangement. So by contributing to F1000, essentially I take time away from my core research and teaching activities to allow a company to commercialize my IP and pay someone to nag me! What's even more strange about this situation is that there is no rational open-access equivalent of literature review services like F1000. By analogy with the OA publishing of the primary literature, for "secondary" services I would pay a company to post one of my reviews on someone else's article. (Does Research Blogging for free sound like a better option to anyone?)
Thus I've come to realize that is unjustified to contribute secondary commentary to F1000 on Open Access grounds, in the same way it is unjustified to submit primary papers to closed-access journals. If I really support Open Access publishing, then to contribute to F1000 I must either must either be a hypocrite or make an artificial distinction between the primary and secondary literature. But this gets to the crux of the matter: to the extent that recommendation services like F1000 are crucial for researchers to make sense of the onslaught of published data, then surely these critical reviews should be Open for all, just as the primary literature should be. On the other hand, if such services are not crucial, why am I giving away my IP for free to a company to capitalize on?
Well, this question has been on my mind for a while and I have looked into whether there might be evidence that F1000 evaluations have a real scientific worth in terms of highlighting good publications that might provide a reason to keep contributing to the system. On this point the evidence is scant and mixed. An analysis by the Wellcome Trust finds a very weak correlation between F1000 evaluations and the evaluations of an internal panel of experts (driven almost entirely by a few clearly outstanding papers), with the majority of highly cited papers being missed by F1000 reviewers. An analysis by the MRC shows a ~2-fold increase in the median number of citations (from 2 to 4) for F1000 reviewed articles relative to other MRC-funded research. Likewise, an analysis of the Ecology literature shows similar trends, with marginally higher citation rates for F1000 reviewed work, but with many high impact papers being missed. [Added 28 April 2012: Moreover, multifactorial analysis by Priem et al on a range of altmetric measures of impact for 24,331 PLoS articles clearly shows that the "F1000 indicator did not have shared variability with any of the derived factors" and that "Mendeley bookmark counts correlate more closely to Web of Science citations counts than expert ratings of F1000".] Therefore the available evidence indicates that F1000 reviews do not capture the majority of good work being published, and the work that is reviewed is only of marginally higher importance (in terms of citation) than unreviewed work.
So if (i) it goes against my OA principles, (ii) there is no evidence (on average) that my opinion matters quantitatively much more than anyone else's, and (iii) there are equivalent open access systems to use, why should I continue contributing to F1000? The only answer I can come up with is that by being a F1000 reviewer, I gain a certain prestige for being in the "in club," as well as by some prestige-by-association for aligning myself with publications or scientists I perceive to be important. When stripped down like this, being a member of F1000 seems pretty close to being a Sneetch with a star, and that the F1000 business model is not too different than that used by Sylvester McMonkey McBean. Realizing this has made me feel more than a bit ashamed for letting the allure of being in the old-boys club and my scientific ego trick me into something I cannot rationally justify.
So, needless to say I have recently decided to resign from F1000. I will instead continue to contribute my tagged articles to citeulike (as I have for several years) and contribute more substantial reviews to this blog via the Research Blogging portal and push the use of other Open literature recommendation systems like PaperCritic, who have recently made their user-supplied content available under a Creative Commons license. (Thanks for listening PaperCritic!).
By supporting these Open services rather than the closed F1000 system (and perhaps convincing others to do the same) I feel more at home among the ranks of the true crowd-sourced "Faculty of 1,000,000" that we need to help filter the onslaught of publications. And just as Sylvester McMonkey McBean's Star-On machine provided a disruptive technology for overturning perceptions of prestige by giving everyone a star in The Sneetches, I'm hopeful that these open-access web 2.0 systems will also do some good towards democratizing personal recommendation of the scientific literature.
* Note: This post should in no way be taken as an ad hominem against F1000 or its founder Vitek Tracz, who I respect very much as a pioneer of Open Access biomedical publishing
** This number is an estimate based on the real figure of ~2.5K papers/day in deposited in MEDLINE, extrapolated to the large number of non-biomedical journals that are not indexed by MEDLINE. If any has better data on this, please comment below.
Posted on December 16, 2011 by caseybergman.	Posted in old boys' club, open access, peer review, scholarly publishing, social media	| 22 Comments
Just Say No – The Roberts/Ashburner Response
UPDATE: see follow-up post "The Roberts/Ashburner Response" to get more of the story on the origin of this letter.
I had the pleasure of catching up with my post-doc mentor Michael Ashburner today, and among other things we discussed the ongoing development of UKPMC and the importance of open access publishing. Although I consider myself a strong open access advocate, I did not sign the PLoS open letter in 2001, since at the time I was a post-doc and not in a position fully to control where I published. Therefore I couldn't be sure that I could abide by the manifesto 100%, and didn't want to put my name to something I couldn't deliver on. As it turns out this is still the case to a certain degree and (because of collaborations) my freely-available-article-index remains at a respectable 85% (33/39), but alas will never reach the coveted 100% mark.
Nevertheless, I have steadily adopted most of the policies of the open letter, especially as my group has gotten more heavily involved in text-mining research over the years. This became especially true after an encounter with a publisher in 2008 who forced my campus IT to shut down my office IP because I was downloading articles from a journal for which our University has a site license. Perhaps unsurprisingly, this nasty experience radicalized me into more of an open access evangelist. After discussing this event at the time with Ashburner, he reminded me of the manifesto and one of its most powerful tools for changing the landscape of scholarly publishing – refusing to reviewing for journals/publishers who do not submit their content to PubMed Central (see the white-list of journals here).
I have dug this letter out countless times since then and used versions of it when asked to review for non-PMC journals, as it expresses the principles in plain and powerful language. I had another call to dig it out today and thought that I'd post the "Ashburner response" so others have a model to follow if they chose this path.
From: "Michael Ashburner" <michael.ashburner@xxx.xxx>
Date: 30 August 2008 13:48:03 GMT+01:00
To: "Casey Bergman" <casey.bergman@xxx.xxx>
Subject: Just say No
Thank you for your invitation to review for your journal. Because it is not open access and does not provide its back content to PubMed Central, or any similar resource, I regret that I am unwilling to do this.
I would urge you to seriously reconsider both policies and would ask that you send this letter to your co-editors and publisher. In the event that you do change your policy, even to the extent of providing your back content to PubMed Central, or a similar resource, then I will be happy to review for you.
The scientific literature is at present the most significant resource available to researchers. Without access to the literature we cannot do science in any scholarly manner. Your journal refuses to embrace the idea that the purpose of the scientific literature is to communicate knowledge, not to make a profit for publishers. Without the free input of manuscripts and referees' time your journal would not exist. By and large, the great majority of the work you publish is paid for by taxpayers. We now, either as individuals or as researchers whose grants are top-sliced, have to pay to read our own work and that of our colleagues, either personally or through our institutes' libraries. I find that, increasingly, literature that is not available by open access is simply being ignored. Moreover, I am very aware that, increasingly, discovering information from the literature relies on some sort of computational analysis. This can only be effective if the entire content of primary research papers is freely available. Finally, by not being an open access journal you are disenfranchising both scientists who cannot afford (or whose institutions cannot afford) to pay for access and the general public.
There are now several good models for open access publication, and I would urge your journal to adopt one of these. There is an extensive literature on open access publishing, and its economic implications. I would be pleased to send you references to this literature.
Michael Ashburner
Times Higher Education – Peers, review your actions.
Sauropod Vertebra Picture of the Week – Researchers! Stop doing free work for non-open journals!
From the Bottom of the Heap – I'm on peer review strike!
Bishop Blog – Time for academics to withdraw free labour
Gower's Weblog – Elsevier — my part in its downfall
Jabberwocky Blog – Why I will no longer review for your journal
Reciprocal Space – Why I chose to decline an invitation to review by Elsevier
Azimuth – Ban Elsevier
Depth-First – Five Things to Do Instead of Protesting the Research Works Act (HR 3699)
Impact of Social Sciences – Comfort is the death knell of academia: why I'm standing down as a journal referee
Posted on December 2, 2011 by caseybergman.	Posted in open access, peer review, scholarly publishing, text mining	| 15 Comments
Is Science really "Making Data Maximally Available"?
Earlier this year Hanson, Sugdon and Alberts [1] argued in a piece entitled "Making Data Maximally Available" that journals like Science play a crucial role in making scientific data "publicly and permanently available" and that efforts to improve the standard of supporting online materials will increase their utility and the impact of their associated publications. While I whole-heartedly agreed with their view that improving supplemental materials is a better solution to the current disorganized [2] and impermanent [3] state of affairs (as opposed to the unwise alternative of discarding them altogether [4]), there were a few things about this piece that really irked me, and I had intended to write a letter to the editor on this with a colleague that unfortunately didn't materialize, so I thought I'd post them here.
First, the authors make an artificial distinction between the supporting online materials associated with a paper and the contents of the paper itself. Clearly the most important data in a scientific report is in the full text of the article, and thus if making data in supporting online materials "maximally available" is a goal, surely so must be making data in full-text article itself. Second, in the context of the wider discussion on "big data" in which these points are made, it must be noted that maximal availability is only one step towards maximal utility, the other being maximal access. As the entire content of Science magazine is not available for unrestricted download and re-use from PubMed Central's Open Access repository, maximal utility of data in the full text or supplemental materials of articles published in Science is currently fettered because it is not available for bulk text mining or data mining. Amazingly, this is true even for Author-deposited manuscripts in PubMed Central, which are not currently included in the PubMed Central Open Access subset and therefore not available for bulk download and re-use.
Therefore it seems imperative that, in addition to making a clarion call for the improved availability of data, code and references in supplemental materials, the Editors of Science should issue a clear policy statement about the use of full-text articles and supplemental online materials that are published in Science for text and data mining research. At a minimum, Science should join with other high profile journals such as Nature [5] in clarifying the use of Author-deposited manuscripts in PubMed Central for text and data mining that are required to be deposited under funding body mandates for these very purposes. Additionally, Science should make a clear statement about the copyright and re-use policies for supporting online materials of all published articles, which are freely available for download without a Science subscription, and currently fall in the grey area between restricted and open access.
As we move firmly into the era of big data where issues of access and re-use of data becoming increasingly acute, Science, as the representative publication of the world's largest general scientific society, should take the lead in opening its content for text and data mining, to the mutual benefit of authors, researchers and the AAAS.
1. Hanson et al. (2011) Making Data Maximally Available. Science 331:649
2. Santos et al. (2005) Supplementary data need to be kept in public repositories. Nature 438:738
3. Anderson et al. (2006) On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics 7:260
4. Journal of Neuroscience policy on Supplemental Material
5. Nature Press release on data- and text-mining of self-archived manuscripts
Watts Up with That – An Open Letter to Bruce Alberts of Science Magazine
Stoat – Nah, don't believe it
Kitware Blog – AAAS: Your Paper MUST include Data, MUST include Code.
NIF Blog – Supplementary material: Can NIF bring order to the netherworld of publishing?
The Tree of Life – Calling on AAAS to Deposit all Archives of Science in Pubmed Central
NeuroDojo – Occupy Science (the journal)
Posted on June 6, 2011 by caseybergman.	Posted in data mining, open access, scholarly publishing, text mining	| Leave a comment


Try out your hand at one of the Hunger Games Training Days with this fun board game. Give everyone a gold mockingjay to wear and have people try to stay …... Tributes are residents of the 12 districts of Panem who are forced/volunteered to participate in an annual Hunger Games. Except in special cases, such as for Quarter Quells, twenty-four children between the ages of 12 and 18 are chosen at random.
River Horse are going to be landing on Kickstarter October 1st 2018 with their Hunger Games: Mockingjay - The Board Game. The game will no doubt bring to life the struggle of the rebellion for control of Panem.
The Hunger Games Game By Patrick Cassels INT. TEENAGE GIRL'S BEDROOM -- CIRCA 1990 A vintage ad for a teen girl board game. Sparkly, Cindy Lauper-ish MUSIC plays.


Construction works for the new Aberdeen FC training facility at Kingsford are finally underway with the breaking ground ceremony taking place on phase one of the project today (Tuesday 3 July 2018).
Dons Manager, Derek McInnes, AFC Community Trust Chief Exec, Ally Procter and Lord Provest, Barney Crockett put the first spades in the ground at the site this morning.
McIntosh Plant Hire have now been given the greenlight to begin the initial earthworks and ground remediation in preparation for the building works, which are due to commence in October 2018 with the facility being completed in Summer 2019.
Derek McInnes commented on the club website: "This is a hugely significant milestone for the Club as we embark on building long-awaited, best-in-class training facilities.
"Since I took on the role of manager at AFC I have been campaigning for better facilities so there's a huge sense of relief and excitement today to see work beginning on-site.
Ally Procter also comment on the website: "These purpose-built facilities will help us support more individuals in communities and reach even more participants of all ages and from different walks of life.
"We currently don't have sufficient space at Pittodrie or any kind of sporting or classroom facilities to call our own, which can make delivering many projects extremely challenging.


Last Fri, S&P500 logged its largest one day fall since 3 Jan 2019, due in part to the weak European PMI and the yield curve inversion between U.S. 3-month bill and 10-year note yields.
At the time of writing this, Dow closed 0.55% higher on Tues as U.S. 10 year bond yields stabilise. Is last Fri's fall the precursor to something more serious? Or it is a false alarm?
First things first, what are the reasons for the sharp rally since late Dec?
e) Equity market valuations have become more palatable after the sell-off in Dec 2018.
e) In the coming weeks, we shall know how U.S. corporates fare in 1QFY19F and their guidance for 2Q. Samsung Electronics just warned on Tuesday that 1QFY19 financial results will be lower than market estimates. This is unlikely to be an isolated case due to the slowdown in Europe, China, business cycle etc.
h) U.S. reached its debt ceiling on 2 Mar 2019. Through extraordinary measures by the Treasury Department, U.S. is prevented from breaching its debt ceiling until late Sep or early Oct. This issue will likely rear its ugly head in the next few months as we head towards Sep / Oct.
i) Corporate debt –> Much has been written on U.S. corporate debt especially when U.S. economy is slowing down amid the global economic slowdown. A most telling chart can be seen in Chart 1 below. U.S. corporate debt has reached levels near prior peaks which preceded market falls. This phenomenon is not only seen in the U.S. Based on a Bloomberg article dated 26 Mar 2019, Singapore's top law firm Rajah & Tann Singapore LLP mentioned that weaker companies may find it challenging to refinance their debt amid a slowing Chinese economy and heightened risk aversion among alternative capital providers. Based on Bloomberg compiled data, Southeast Asian companies have maturing debt obligations amounting to US$17.9b in 2019 and this will swell to US$23.2b in 2023.
k) "Speculative frenzy" in some parts of the market which may render them highly vulnerable to sudden market falls. For example, China markets have soared almost 22% from 3 Jan 2019 through 26 Mar 2019. Based on a Bloomberg article dated 22 Mar 2019, Shanghai-based Foresight Fund, managed by Chen Guangming secures US$10b in funding in 10 hours for his fund (This seems to be a case in point for speculative frenzy). Closer to home, some Singapore small mid cap stocks have rallied in the region of 30-60% post their results last month far above analysts' target prices.
Based on Chart 2 below, S&P500 has broken the the long-term uptrend line established since Feb 2016. However, it has breached the short-term downtrend line established since Oct 2018 on 15 Jan 2019. S&P500 has touched a 5 month high since Oct 2018 on 21 Mar 2019 and closed at 2,818 on 26 Mar 2019, up 20.1% since the low on 26 Dec 2018. ADX closed around 20.1 on 26 Mar 2019 amid positively placed DI. RSI closed at 57.5 on 26 Mar 2019. All indicators especially OBV, MACD and MFI showed clear bearish divergence on 25 Feb 2019 and 21 Mar 2019 (the two recent peaks). [RSI showed mild bearish divergence].
Although the exponential moving averages ("EMAs") are still rising (i.e. Trend is up), the bearish divergences showed by the multiple indicators may indicate that the recent up-move is not sustainable.
Based on Chart 3 below, STI has jumped 215 points, or 7.2% from the intra-day low of 2,993 on 4 Jan 2019 to trade 3,208 today. In fact, STI has touched an intra-day high 3,286 on 20 Feb 2019 before profit taking set in. ADX last trades 10.5 on 26 Mar 2019 amid negatively placed Dis. Short term EMAs such as 20D and 50D are falling with 200D EMA flat. RSI last trades 48.7 on 27 Mar 2019 after touching a recent high of 68.1 on 20 Feb 2019.
It is noteworthy that unlike Hang Seng and S&P500, STI did not touch a multi-month high this month. This may be because STI may have peaked earlier last month. There is a confluence of support 3,183 – 3,188, followed by a more critical support region 3,150 – 3,158. We will only know whether STI may have peaked in Feb if it stages a sustained break below 3,150 – 3,158 with volume expansion. A sustained break below 3,150 may open STI to more downside.
c) There are some market watchers who point out that although the economy is experiencing a slowdown, the economy is not that weak. In fact, some say that the economy may have already bottomed etc etc.
Notwithstanding the plethora of information and data points which we need to take note, in my opinion, I am paying special attention to the following two drivers, namely 1QFY19 corporate results & their upcoming guidance and price action on the indices.
Firstly, we should start to have a sense of U.S. 1QFY19 corporate results in the next few weeks. Furthermore, it is imperative to see how the U.S. corporates guide for their 2Q results so as to gauge the probability of an earnings recession. Recall in my 23 Dec 2018 write-up (click HERE), I mentioned most strategists believe that the bull market is likely to end when three conditions occur, namely inverted yield curve, earnings recession and economic recession.
Secondly, I will see how the indices' chart pan out in the next few weeks. i.e. Whether they breach recent highs, or they break important supports may provide important clues to formulate future action plans.
In view of the above, I am generally cautious on the equity market with a view that volatility may return in the next couple of months. I am only 5% invested but remain ready for trading opportunities, especially if markets overshoot either on the upside or downside.
I have generated a list of stocks sorted by total potential return using Bloomberg data as of 25 Mar 2019 for my clients and have sent the full compilation to them two days ago. For the benefit of my readers, I have summarised the Top 10 stocks by total potential return in Table 1 and the last 10 stocks by total potential return in Table 2. Amara, Yoma and OUE rank as top 3 stocks sorted by total potential return. UMS, Cosco and Hi-P rank the lowest in terms of total potential return. Please refer to the tables and the important notes below.
1. This compilation is just a first level stock screening, sorted purely by my simple criteria above. It does not necessary mean that Amara is definitely better than Genting Singapore or UOB bank in terms of stock selection.
Naturally, my market outlook and trading plan are subject to change as charts develop. My plan will likely not be suitable to most people as everybody is different. Do note that as I am a full time remisier, I can change my trading plan fast to capitalize on the markets' movements (I am not the buy and hold kind). Furthermore, I wish to emphasise that I do not know whether markets will definitely rebound or continue to drop. However, I am acting according to my plans. In other words, my market outlook; portfolio management; actual actions are in-line with one other. Notwithstanding this, everybody is different hence readers / clients should exercise their independent judgement and carefully consider their percentage invested, returns expectation, risk profile, current market developments, personal market outlook etc. and make their own independent decisions.
ADX, Amara, analyst, bear, bearish, ceiling, Chair, chart, China, corporate, Cosco, curve, data, day, debt, Democrat, divergence, dividend, dovish, down, earning, ECB, economic, economy, Electronic, Ernest, fall, Fed, GDP, Genting, Hi-P, indices, invert, Jerome, largest, Lim, low, Mueller, OUE, Performance, place, positive, Powell, price, recession, remisier, Republican, resistance, return, risk, RSI, Russia, S&P, S&P500, Samsung, share, Singapore, slow, stock, support, target, tension, trade, Trump, U.S, UMS, UOB, volatile, volatility, yield, Yoma permalink.


Ready to capture the beauty?
Photography is about marveling at the ordinary moments that make up our lives. From breakfast to bedtime, rumpled sheets to crinkled smiles, crumpled candy bar wrappers to footprints in fresh mud, you'll learn how to elevate the ordinary . . . into something extraordinary.
With Elevate the Ordinary, you'll be invited to explore your own unique creative voice & visual style . . . to witness the world like a child . . . and to find ways to capture & celebrate your everyday life, as it unfolds.
Just as with Superhero Photo, anyone with a camera (point and shoots are totally welcome) is invited to participate.
Join me for this 6-week adventure. Take your photography to the next level — as you sink deeper into your miraculously 'ordinary' life.
Finding your creative voice & visual style, witnessing the world like a child, embarking on a photo safari, and more.
Elevate the Ordinary is all about awakening your artistic intuition, but you'll also deepen your understanding of lighting, post-processing, workflow, and more.
Download a collection of creative photo prompts, to inspire a spontaneous photography adventure.
Inspiring chats with super-talented photographers, like Karen Walrond, Kim Indresano, Kim Klassen, Aran Goyoaga, and Meredith Winn.
A warm & encouraging community space on Flickr to share & admire our work.
Making magic out of our everyday life.
Lessons, activities, treasure hunts and interviews all delivered to your inbox four days a week. There will also be a classroom site and a private Flickr group where we can share our work and connect with each other.
Anyone with a camera! No photography experience required & no fancy equipment necessary. Point and shoots work just fine.
Mission accomplished! My simple goal for this class was to take better snapshots with my iPhone since I always have it on me. Instead, you have introduced me to the world of photography and seeing the world in a completely different way.
Four days a week (on a private web site) I will be offering lessons, exercises and photo prompts that will help you explore your world in a rich, deep and colorful way. You will be inspired and engaged in a playful process while learning to wield your camera like nobody's business.You will also receive each lesson in your inbox so you can go at your own pace and see your lessons with your mobile device. You can also kick it old school and print out the lessons, treasure hunts and other goodies and work them at your leisure.
Your level of involvement is completely up to you! The lessons are designed to be digested quickly and for maximum FUN. The real joy will be when you're out with your camera, so if a daily practice isn't in the cards, even once a week will be just right!
There will be a private Flickr group for the students in this course to connect, share and learn from each other. This will be a safe place for encouragement, not a place to critique.
You'll need access to the internet, a digital camera (both point-and-shoots and DSLR's are great) and an email address to send your payment via Paypal. You will also need a Flickr account if you want to share your work.
Gift certificates are now available at the cost of the course ($99USD). Just add it to your cart by clicking here and you'll get a colorful PDF certificate to give that allows the recipient to sign up for a future class that works for them.


From Hydraulic & Wheel Excavators, to Wheel Loaders, Backhoe Loaders, Telehandlers, Skid Steer Loaders, Motor Graders, all the way to Soil Compactors. More than 20 machines will be on display.
Apart from PURE INNOVATION, our Open Days are sure to create a unique environment for visitors to come together to network and have some fun!
Mark your calendars now to ensure that you will soon experience and believe, that our machines are definitely your one and only choice of equipment investment in terms of: world–class operator comfort, ease of operation, optimum power & fuel efficiency, reliability, durability, maximum productivity, ground-level serviceability, and lowest owning & operating cost.
We look forward to seeing you in our two-day agenda below.


text:
Italy's Statute-of-Limitations Reforms: A Helpful But Incomplete Step Toward Ending Impunity
Posted on November 11, 2019 by Maura Cremin
In 2015, a Naples court found former Italian Prime Minister Silvio Berlusconi guilty of paying a senator €3 million to support Berlusconi's Forza Italia party and sentenced him to three years in prison for this crime. Berlusconi did not serve a day. Under Italian law, defendants are typically entitled to two appeals, which must be resolved before the defendants begin serving their sentences (with a handful of exceptions). Moreover, the statute of limitations clock keeps ticking while these appeals are in process. In Berlusconi's case, the statute of limitations ran out before his case made its way through Italy's glacial judicial system—where criminal trials can last an average of four to five years in the court of first instance alone, and the appeals can add an extra three years to the process. This was not the first time Berlusconi had benefitted from Italy's slow judicial proceedings (see here and here). Nor was he the first politician to do so. In 2004, former Prime Minister Giulio Andreotti famously escaped punishment for mafia association in part due to the statute of limitations.
Corrupt politicians and other white-collar criminals got off scot-free in these and other cases due to the combination of three factors noted above. The first is the extremely slow pace of Italian criminal proceedings. The second is the rule that defendants do not have to begin serving their prison terms until their appeals have been exhausted. And the third concerns the rule that the statute of limitations clock begins when a crime is committed and continues to run for the duration of a defendant's investigation, trial, and appeal, with no option of suspension. The rationale for this approach to the statute of limitations has traditionally been that the prosecution should not be able to hold a defendant in legal limbo while the case wormed its way slowly through the courts. In practice, however, this system often served to guarantee impunity for corrupt politicians and other wealthy defendants who could afford the high-priced lawyers that would drag out the legal proceedings just long enough to ensure their clients could never be imprisoned.
Furthermore, under the traditional Italian system of calculating the statute of limitations, the clock starts ticking at the moment the crime is first committed, rather than from when the crime is completed. (These are generally the same time for simple crimes like homicide or robbery, but for complex white-collar schemes, such as a bid-rigging conspiracy, there may be a long gap between the moment the crime starts and the time when it ends.) This rule makes prosecuting corruption and other complex financial crimes even more difficult, because such crimes are hard to detect and the investigations often take considerable time. So, what seem to be technical rules of criminal procedure—rules that, in the abstract, might be defended as protecting private citizens from prosecutorial overreach—in practice helped to perpetuate the system of impunity for Italian officials and businesspeople that fuels Italy's already extraordinarily high levels of perceived corruption.
But there are hopeful signs that Italy may finally be addressing these problems. In December 2018, the Italian Parliament adopted a new anticorruption law, popularly referred to as Spazzacorrotti ("Bribe Destroyer"). (For English-language analyses, see here and here.) That new law, which will be fully implemented in 2020, contains a number of important provisions, including increased penalties for corruption and incentives for voluntary self-disclosure and cooperation. Crucially, the new legislation also amends Italy's statute of limitations law:
Under the revised law, the statute of limitations for completed crimes begins to run once the crime is completed, rather than when it is first committed. For attempted crimes, the statute of limitations now begins to run upon the cessation of criminal activity, and for ongoing crimes, with the cessation of the ongoing activity. In addition, the statute of limitations will now be "tolled"—that is, the clock will stop ticking—after the court of first instance renders its judgment. By changing the time at which the statute of limitations begins to run, Spazzacorrotti makes it harder for corrupt actors to shield bad behavior and gives investigators time to conduct more thorough investigations into corruption-related conduct. And the fact that the statute of limitations clock stops running while the first verdict is being appealed reduces the incentives for defense attorneys to drag out appellate proceedings, and hence may reduce the ability of those defendants with well-paid lawyers to leverage the country's judicial inefficiency to secure their own perpetual impunity.
Unfortunately, as with most efforts to tackle corruption in Italy, optimism should be tempered with skepticism. For starters, there's a pending constitutional challenge to the application of Spazzacorrotti to defendants whose alleged misconduct took place before the adoption of the law. While the Italian Constitutional Court may strike down the law, it may also provide an interpretation that brings the law into conformity with the Constitution, or it may strike down only specific provisions of the legislation. The constitutional concern is not trivial, but even if the Constitutional Court rules that the law as it stands is unconstitutional, Parliament could amend the statute to address the constitutional concerns, at least going forward.
But even putting the constitutional question to one side, Spazzacorrotti is not a panacea; opportunities to game the system remain. Defendants can still benefit from the statute of limitations if they are able to keep their crimes concealed or conduct them quickly, and defense attorneys will still have incentives to drag out proceedings in the court of first instance, particularly if the initial trial occurs near the end of the time limit. Such risks are probably not entirely avoidable as long as a crime involves a statute of limitations. Yet Spazzacorrotti certainly goes a long way towards improving the balance between the rights of defendants and the public's need for prosecution of corruption. Nevertheless, Italy still needs substantial judicial reform that will streamline the system and reduce the amount of time it takes to process cases.
Corruption has been endemic to Italian politics for many years, and it will take much more than this law to eradicate it. Even so, it is important to recognize the potential for the reforms undertaken by Spazzacorrotti to make a real difference. In tackling the statute of limitations system, Spazzacorrotti reduces the ability of the wealthy and well-connected to distort the rules of criminal procedure to guarantee their own impunity from prosecution. As such, it has the potential to contribute to the fundamental fairness and equity of the Italian judicial system, and perhaps to allow Italians to have more faith that their institutions are functioning correctly. And if it means fewer nullified convictions for Berlusconi and other corrupt actors, so much the better.
This entry was posted in Commentary and tagged Italy, Silvio Berlusconi, Spazzacorrotti, statute of limitations by Maura Cremin. Bookmark the permalink.
8 thoughts on "Italy's Statute-of-Limitations Reforms: A Helpful But Incomplete Step Toward Ending Impunity"
Richard E Messick on November 12, 2019 at 10:09 am said:
Comment on your very fine post by an Italian friend —
The Law will enter into force on January 2020 but powerful lobbies (the Lawyers) and trembling political parties (ie the Democrats) are trying to block the reform. There will be a mass protest of the defence lawyers at the beginning of December: they will not attend the hearings for some days. They believe it inhuman that the limitation clock does not keep ticking during the appeals. It's crazy but this is Italy….
Maura Cremin on November 12, 2019 at 7:05 pm said:
Thank you (and your friend) for pointing this out. I did not discuss the broader politics of Spazzacorrotti in this post, but it has certainly been a contentious issue. I do take seriously defense lawyers' concern about protecting their clients' interests. And, of course, they have real interests in arguing against these measures. I would argue that this goes to a more fundamental issue in the Italian legal system that is not addressed in Spazzacorrotti, namely the length of trials. Significant work has to be done to streamline court proceedings in order to truly ensure justice for the accused. With that said, as things currently stand, Spazzacorrotti has the potential to address at least one source of injustice in the Italian legal system. Hopefully efforts to block it won't come to fruition, and ideally there will be steps taken to make other needed reforms.
Rodrigo Telles de Souza on November 14, 2019 at 2:03 pm said:
Amazing post. If the statute of limitations is an anticorruption problem in Italy, where convicted defendants must serve their sentences after two appeals (three jurisdiction instances), one can imagine to what extent it is a concerning question in Brazil, which has a more slow-moving criminal procedure system. By the way, Brazilian Supreme Court last week ruled that convicted defendants must serve their sentences only after the exhaustion of all kinds of appeals that the country's law provides (four jurisdiction instances, with dozens of appeals in each one). Through all this way, especially after the first instance conviction, the limitations period continues to be counted. Rich and powerful defendants represented by influential lawyers usually manage to get away with white collar crimes. So, there is not any efficiency in the anticorruption law enforcement. The result is impunity, with a very low level of deterrence effect regarding corruption in the country. Congratulations to your post and to Italy, which is properly facing the problem. Some day perhaps Brazil learns from the Italian example.
Maura Cremin on November 15, 2019 at 4:22 am said:
Thank you Rodrigo! It's interesting to know that there is something similar happening in Brazil. It sounds like the system there is even more complex! I'm (very cautiously) hopeful that this will have positive results in Italy and then perhaps this reform can serve as a model.
Haggai Porat on November 15, 2019 at 6:32 pm said:
Thanks for the interesting post! While we should probably be grateful for any improvement, it is truly striking that the clock stops ticking only at the end of the trial, rather than when it starts. The most common justifications for the statute of limitations in criminal law – deterioration of possible acquitting evidence and the living under the fear of criminal prosecution – are irrelevant once the procedure begins. The only remaining justification seems to be the incentivizing effect on the prosecution not to drag the procedure, but this should hardly be sufficient justification when taking into account the much stronger incentives that defendants have to drag the procedure in the alternative scenario as well as the role of the court that can keep the prosecution in check
Thanks for the comment, Haggai, this is a great point to raise. I certainly don't think that this law will erase every opportunity for manipulation, and we'll have to keep an eye on prosecutions to see how great a problem this becomes. Even so, eliminating the ability to use appeals to run down the statute of limitations is a very significant improvement, given how long appellate proceedings can take. With that said, it is entirely possible that further changes may be necessary in the future.
Megan Duffy on November 30, 2019 at 12:17 pm said:
Thank you for this interesting post, Maura. It was a great snapshot of Italy's attempt to concretely change the culture of impunity when it comes to powerful, wealthy and well-connected elite in the country. You mentioned in your text that further judicial reform is needed to amplify the effects of laws like Spazzacorrotti and I was curious about the needs in this particular sector. Are the biggest judiciary-related problems the cumbersome processes or length of trials, or are there deeper-seated issues? For example, are judges seen as fair themselves in the eyes of the Italian public? I also wanted to know a bit more about the current make-up of the Italian Parliament. While this law is not a panacea, it seems to me like it's a big step forward in meaningfully starting to tackle corruption more systematically. Are members of Parliament representing a sort of new political class or are they mostly status quo officials that finally felt enough pressure to make some kind of tactical move to address corruption?
Inayat Sabhikhi on December 7, 2019 at 11:56 pm said:
Thank you Maura for explaining a complex concept with such clarity.
You've alluded to the rationale of the original approach, to prevent the prosecution from holding "a defendant in legal limbo while the case wormed its way slowly through the courts." Would be curious to get your perspective on whether this could now again be the case with the Spazzacorrotti (even as it solves for other problems such as dis-incentivising lawyers from dragging out appeal process). Do you see a potential for misuse, and what could be done to prevent this?

redpajama_set_name: RedPajamaCommonCrawl


This story was originally published on January 29, 2016.
Kurt Fristrup is standing in the middle of a prairie and he's the loudest thing for miles. He and I are huddled near an empty cattle pen in Pawnee National Grassland in northern Colorado. Before he pulled out his tools, the silence here was palpable. The breeze carried no sound except the rustle of a million stalks of yellow grass. A family of pronghorn, kind of like furry antelope, padded over to us to investigate.
Fristrup is disrupting this serene soundscape for a reason: He wants to better understand it—by recording it. Cows chewed through a microphone he set up a few months ago. And now he's here to install a new one.
Fristrup is a senior scientist with the National Park Service in Fort Collins, Colorado. And he's tasked with protecting a natural resource. It's not water or minerals or endangered species. It's sound. Natural sound. His team is studying how man-made noise is drowning out the sounds of birds and insects and rain. And as more and more research links our well-being to what we hear, Fristrup and his colleagues are pointing to natural sound as something to be managed—and even protected.
Most of us can probably agree—our world is pretty noisy. But just how noisy is something Fristrup is trying to figure out. For a decade, he and a small team of engineers, physicists and biologists have hidden microphones in parks around the United States. Some are really remote—think grizzly bears and back-country skiing. But others are in urban areas, like Civil War memorials and the Statue of Liberty.
Each microphone recorded 24 hours a day for a month, capturing fantastic sounds—like the trumpeting of elk and goofy birds called ptarmigans. Not to mention the grunts of bears destroying the microphones, which Fristrup says was totally worth it.
But what Fristrup was after was loudness. Each device measured decibel levels 33 times per second. That mountain of data fed a model that created a sound map of the contiguous United States. It took the qualities of each site, like how close it is to roads or water, and calculated median sound levels for the entire rest of the country—even places outside parks.
That big picture may not be all that surprising. But the differences in noise levels are staggering.
Every rise of three decibels doubles the sound hitting our eardrums. Now consider this: The loudest places in the U.S. are around 40 decibels noisier than the quietest. So if you do the math, Manhattan can be around 8,000 times louder than Great Sand Dunes National Park—one of the darkest spots on the map.
Our biggest noise producer is transportation—cars, trucks, motorcycles. Even the hiss of tires against pavement. But even far away from roads, there are still airplanes. Fristrup estimates man-made noise really took off in the mid-20th century, when flying became commonplace. Now, most of us are so used to planes, we don't even notice them. After hiking with friends, Fristrup likes to ask how many they heard.
So if we're not even conscious of the man-made noises around us, then what's the big deal? Researchers at Penn State are trying to figure that out.
The first step was stress. I had to imagine I was applying for a big job and gave a five-minute speech in front of a one-way mirror. It was kind of intense. Then came the soundscape. Costigan whisked me into a dark room. I put on headphones and settled in to watch a video. On the screen was Half Dome, the majestic centerpiece of Yosemite Valley. The sun crept across the granite. Red and yellow leaves fluttered. But when I heard a garbage truck interrupt, and then a motorcycle, I cringed.
"We would like to know, when is sound helpful, when is noise harmful, under what circumstances and for what people?" says Joshua Smyth, a professor of biobehavioral health at Penn State who's coordinating the soundscape study.
His hypothesis is that natural sound will speed up stress recovery, even with people making noise in the background. But some test subjects watched that video with no man-made sound at all, and Smyth thinks they'll recover even faster.
For each test subject, he and Costigan tracked heart rate and also measured cortisol—a hormone in saliva. Cortisol is a kind of stress indicator, and chronically stressed people produce a lot of it. Studies have connected that highly stressed state with all sorts of health issues—heart problems, breathing problems, musculoskeletal problems and a higher susceptibility to viruses and infections.
"So we just generally see a decay in the capacity of the body [in] response to these sort of chronic conditions of stress," Smyth says.
So when we hear irritating sounds, even if we try not to let them bother us, Smyth suspects that our stress levels still spike, priming our bodies for other health problems. But could noise ever be so bad that it alone breaks down our immune defenses? Probably not.
So our cars, our airplanes—some of the very advances that make our lives easier and more productive—they might also be sabotaging us. So what's the solution? Stop driving? Renounce technology? A social scientist across campus offers a gentler perspective.
Newman is studying why people visit parks and what they do once they're there.
In the past, studies have shown we recover better from surgery when we can see nature. Newman says we also benefit from hearing it. Research shows natural sounds can improve cognition, mood and general well-being. And that's an idea a lot of people already buy into. It's easy to find recordings of relaxing nature sounds.
But Newman argues that we can preserve sound in the real world too. He points to a success story in Muir Woods, a national monument outside San Francisco. In an experiment in 2009, he and a few colleagues posted signs for quiet zones and showed visitors how to be less noisy.
"We actually were able to reduce the amount of noise there by about three decibels, which was the equivalent of doubling people's listening area," Newman says.
Conserving sound in parks may seem to be at odds with the Park Service mission of bringing people there. But back in Colorado, Kurt Fristrup sees these opposing values as a challenge. He knows the solution isn't to keep people away. Instead, he's helping develop new technology. Like quieter pavement and electric airplanes that could someday lead silent air tours. His team is also developing roadside noise gauges, kind of like the blinking signs that tell you how fast your car is moving, only it's how loud you are.
Throwing that switch won't be easy, but we all have an incentive to try. Because who wants a world in which recordings of nature are our only option? So next time you're outside, turn off your car, stop talking and listen. What you hear might just be good for you. And it's free. For everyone. Natural sound is a truly infinite resource. All we have to do is not drown it out.
Kerry Klein is a science reporter based in California. This story is a production of the STEM Story Project, which is distributed by PRX and made possible with funds from the Alfred P. Sloan Foundation.
Kerry Klein is a science reporter based in California.


Cuttingedge 3D realistic gameplay. Pick your favorite car and compete against real players across the world. Play & chat with over 100 thousand online players from around the world.
Team up with friends to form a crew, choose your favorite car, drive around, drift and chat with other players. Drift Online is allnew; download for free and start racing now!
Race against other players in real time.
Organize your own race competition.
Compete with other players and try to reach the highest drift score.
Show off your drifting skills.
Drift Online features loads of vehicles from the worlds most desirable car manufacturers.
Show off your gears to other players online.
Please review Drift and Race Online Game and submit your comments below. We will collect all comments in an effort to determine whether the Drift and Race Online app is reliable, perform as expected and deliver the promised features and functionalities.


text:
import urwid

from gertty import keymap
from gertty.view.diff import BaseDiffComment, BaseDiffCommentEdit, BaseDiffLine
from gertty.view.diff import BaseFileHeader, BaseFileReminder, BaseDiffView

LN_COL_WIDTH = 5

class SideDiffCommentEdit(BaseDiffCommentEdit):
    def __init__(self, app, context, old_key=None, new_key=None, old=u'', new=u''):
        super(SideDiffCommentEdit, self).__init__([])
        self.app = app
        self.context = context
        # If we save a comment, the resulting key will be stored here
        self.old_key = old_key
        self.new_key = new_key
        self.old = urwid.Edit(edit_text=old, multiline=True)
        self.new = urwid.Edit(edit_text=new, multiline=True)
        self.contents.append((urwid.Text(u''), ('given', LN_COL_WIDTH, False)))
        if context.old_file_key and (context.old_ln is not None or context.header):
            self.contents.append((urwid.AttrMap(self.old, 'draft-comment'), ('weight', 1, False)))
        else:
            self.contents.append((urwid.Text(u''), ('weight', 1, False)))
        self.contents.append((urwid.Text(u''), ('given', LN_COL_WIDTH, False)))
        if context.new_file_key and (context.new_ln is not None or context.header):
            self.contents.append((urwid.AttrMap(self.new, 'draft-comment'), ('weight', 1, False)))
            new_editable = True
        else:
            self.contents.append((urwid.Text(u''), ('weight', 1, False)))
            new_editable = False
        if new_editable:
            self.focus_position = 3
        else:
            self.focus_position = 1

    def keypress(self, size, key):
        r = super(SideDiffCommentEdit, self).keypress(size, key)
        commands = self.app.config.keymap.getCommands(r)
        if ((keymap.NEXT_SELECTABLE in commands) or
            (keymap.PREV_SELECTABLE in commands)):
            if ((self.context.old_ln is not None and
                 self.context.new_ln is not None) or
                self.context.header):
                if self.focus_position == 3:
                    self.focus_position = 1
                else:
                    self.focus_position = 3
            return None
        return r

class SideDiffComment(BaseDiffComment):
    def __init__(self, context, old, new):
        super(SideDiffComment, self).__init__([])
        self.context = context
        oldt = urwid.Text(old)
        newt = urwid.Text(new)
        if old:
            oldt = urwid.AttrMap(oldt, 'comment')
        if new:
            newt = urwid.AttrMap(newt, 'comment')
        self.contents.append((urwid.Text(u''), ('given', LN_COL_WIDTH, False)))
        self.contents.append((oldt, ('weight', 1, False)))
        self.contents.append((urwid.Text(u''), ('given', LN_COL_WIDTH, False)))
        self.contents.append((newt, ('weight', 1, False)))

class SideDiffLine(BaseDiffLine):
    def __init__(self, app, context, old, new, callback=None):
        super(SideDiffLine, self).__init__('', on_press=callback)
        self.context = context
        columns = []
        for (ln, action, line) in (old, new):
            if ln is None:
                ln = ''
            else:
                ln = '%*i' % (LN_COL_WIDTH-1, ln)
            ln_col = urwid.Text(('line-number', ln))
            ln_col.set_wrap_mode('clip')
            line_col = urwid.Text(line)
            if action == '':
                line_col = urwid.AttrMap(line_col, 'nonexistent')
            columns += [(LN_COL_WIDTH, ln_col), line_col]
        col = urwid.Columns(columns)
        map = {None: 'focused',
               'added-line': 'focused-added-line',
               'added-word': 'focused-added-word',
               'removed-line': 'focused-removed-line',
               'removed-word': 'focused-removed-word',
               'nonexistent': 'focused-nonexistent',
               'line-number': 'focused-line-number',
               }
        self._w = urwid.AttrMap(col, None, focus_map=map)

class SideFileHeader(BaseFileHeader):
    def __init__(self, app, context, old, new, callback=None):
        super(SideFileHeader, self).__init__('', on_press=callback)
        self.context = context
        col = urwid.Columns([
                urwid.Text(('filename', old)),
                urwid.Text(('filename', new))])
        map = {None: 'focused-filename',
               'filename': 'focused-filename'}
        self._w = urwid.AttrMap(col, None, focus_map=map)

class SideFileReminder(BaseFileReminder):
    def __init__(self):
        self.old_text = urwid.Text(('filename', ''))
        self.new_text = urwid.Text(('filename', ''))
        col = urwid.Columns([self.old_text, self.new_text])
        super(SideFileReminder, self).__init__(col)

    def set(self, old, new):
        self.old_text.set_text(('filename', old))
        self.new_text.set_text(('filename', new))

class SideDiffView(BaseDiffView):
    def makeLines(self, diff, lines_to_add, comment_lists):
        lines = []
        for old, new in lines_to_add:
            context = self.makeContext(diff, old[0], new[0])
            lines.append(SideDiffLine(self.app, context, old, new,
                                      callback=self.onSelect))
            # see if there are any comments for this line
            key = 'old-%s-%s' % (old[0], diff.oldname)
            old_list = comment_lists.pop(key, [])
            key = 'new-%s-%s' % (new[0], diff.newname)
            new_list = comment_lists.pop(key, [])
            while old_list or new_list:
                old_comment_key = new_comment_key = None
                old_comment = new_comment = u''
                if old_list:
                    (old_comment_key, old_comment) = old_list.pop(0)
                if new_list:
                    (new_comment_key, new_comment) = new_list.pop(0)
                lines.append(SideDiffComment(context, old_comment, new_comment))
            # see if there are any draft comments for this line
            key = 'olddraft-%s-%s' % (old[0], diff.oldname)
            old_list = comment_lists.pop(key, [])
            key = 'newdraft-%s-%s' % (new[0], diff.newname)
            new_list = comment_lists.pop(key, [])
            while old_list or new_list:
                old_comment_key = new_comment_key = None
                old_comment = new_comment = u''
                if old_list:
                    (old_comment_key, old_comment) = old_list.pop(0)
                if new_list:
                    (new_comment_key, new_comment) = new_list.pop(0)
                lines.append(SideDiffCommentEdit(self.app, context,
                                                 old_comment_key,
                                                 new_comment_key,
                                                 old_comment, new_comment))
        return lines

    def makeFileReminder(self):
        return SideFileReminder()

    def makeFileHeader(self, diff, comment_lists):
        context = self.makeContext(diff, None, None, header=True)
        lines = []
        lines.append(SideFileHeader(self.app, context, diff.oldname, diff.newname,
                                    callback=self.onSelect))

        # see if there are any comments for this file
        key = 'old-None-%s' % (diff.oldname,)
        old_list = comment_lists.pop(key, [])
        key = 'new-None-%s' % (diff.newname,)
        new_list = comment_lists.pop(key, [])
        while old_list or new_list:
            old_comment_key = new_comment_key = None
            old_comment = new_comment = u''
            if old_list:
                (old_comment_key, old_comment) = old_list.pop(0)
            if new_list:
                (new_comment_key, new_comment) = new_list.pop(0)
            lines.append(SideDiffComment(context, old_comment, new_comment))
        # see if there are any draft comments for this file
        key = 'olddraft-None-%s' % (diff.oldname,)
        old_list = comment_lists.pop(key, [])
        key = 'newdraft-None-%s' % (diff.newname,)
        new_list = comment_lists.pop(key, [])
        while old_list or new_list:
            old_comment_key = new_comment_key = None
            old_comment = new_comment = u''
            if old_list:
                (old_comment_key, old_comment) = old_list.pop(0)
            if new_list:
                (new_comment_key, new_comment) = new_list.pop(0)
            lines.append(SideDiffCommentEdit(self.app, context,
                                             old_comment_key,
                                             new_comment_key,
                                             old_comment, new_comment))
        return lines

    def makeCommentEdit(self, edit):
        return SideDiffCommentEdit(self.app, edit.context)

    def cleanupEdit(self, edit):
        if edit.old_key:
            self.deleteComment(edit.old_key)
            edit.old_key = None
        if edit.new_key:
            self.deleteComment(edit.new_key)
            edit.new_key = None
        old = edit.old.edit_text.strip()
        new = edit.new.edit_text.strip()
        if old or new:
            if old:
                edit.old_key = self.saveComment(
                    edit.context, old, new=False)
            if new:
                edit.new_key = self.saveComment(
                    edit.context, new, new=True)
        else:
            self.listbox.body.remove(edit)

redpajama_set_name: RedPajamaGithub


Five L-series lenses and a superzoom are set to pad out the firm's new mirrorless system before the year is up.
This article was posted in $699, $99, 2.5", 2014, 2018, 2019, 3D, 5, 5k, 5mm, 615, A9, abs, adblock, ADS, advert, AI, AIO, air, AIT, Amazon, American, Android, animation, API, app, Apple, ar, ara, architecture, art, Articles, at&t, ATIV, audio, Australia, av, AWS, b:, best laptops, bing, Black, blue, body, book, brands, Britain, bu, bug, build, c7, california, camera, Cameras, canonical, case, CD, CDN, CES, CIA, cloud, code, color, competitions, components, computing, Computing components, console, core, Cree, currency, custom, data, Deals, design, desktop, display, download, downloads, Dropbox, EA, EDGE, EFI, email, environment, EU, event, events, F1, FAA, Facebook, factory, fail, fan, fault, Feature, flash, future, Gadgets, galaxy, gallery, gaming, GBA, ge, global, Google, Google Drive, gui, guide, HBO, hd, head, holidays, how to, hp, Huawei, ID, IEC, image stabilization, inks, input, interaction, IP, iPad, iphone, IR, ISP, ISS, Java, keys, laptop, laptops, leak, leaks, LED, lens, lenses, LG, LiFi, light, list, location, logitech, logo, LTE, mapping, math, MCU, meta, MH, mini, Mir:ror, MIT, Mobile, Mod, models, module, motorola, MSI, nails, nand, NES, News, NSA, nui, NX, optical, OS, pal, pan, PC, performance, phone, phones, photography, pi, PIN, pixel, Playstation, PoP, ports, POS, power, price, privacy, prototype, PS3, PS4, PS5, Radar, RAM, rat, recommendation, recover, recovery, RED, release date, rendering, research, Reviews, rig, ring, RMA, ROM, rss, rumors, samsung, SAN, san francisco, screen, SDK, search, SEL, sensor, sensors, September, server, SGI, signals, Size, SOC, social, Sol, space, spam, static, STEM, storage, system, t-mobile, T1, T3, tablet, tablets, tails, Tech, Tegra, television, televisions, text, thumbs, TN, Tor, touch, touch IC, tracking, transparent, travel, Tron, TV, TVs, Twitter, UHD, UI, UK, un, Uncategorized, update, UPS, used, ux, value, video, vision, VPN, VR+, wd, wearable, wearables, web, webkit, whatsapp, will, wind, window, windows, x6, Xbox, YouTube and tagged $99, best laptops, console, hbo, leak, nails, ps3, tech, used. Bookmark the permalink. Follow comments with the RSS feed for this post.Both comments and trackbacks are closed.


text:
Field marshal (FM) is the five-star rank of the Sri Lanka Army and ranks immediately above general. the rank has been awarded only once, to Sarath Fonseka as an  honorary rank. It is equivalent to admiral of the fleet and marshal of the Sri Lanka Air Force.

Privileges
A field marshal remains a serving officer on the active list of the Sri Lankan Army for life. It is an honorary position with no command or administrative responsibilities, and the officer is not subject to the Army Act. Therefore, a field marshal is permitted to engage in political activities and take up political appointments. In the order of precedence, the rank holder is equivalent to a cabinet minister. He can participate in uniform to all ceremonial occasions. An officer of this rank is entitled to an office maintained by the Army along with an aide-de-camp and personal staff; as well as all privileges entitled to a serving General for life. This includes pay, an official residence, transport and a security detail. Furthermore, such an officer is entitled to receive a guard of honor composed of four officers and 150 other ranks and a military funeral on his death with a 21-gun salute. The widow of such an officer is entitled to the pay, allowances and residence given to her husband for life.

Insignia of rank
A field marshal's insignia consists of the National emblem over a crossed batons in a lotus blossom wreath. Field marshals are awarded a Gold-tipped baton (which they may carry on formal occasions), five stars insignia (vehicle star plate) and a personal flag.

The Sri Lanka Army Dress Regulations, lays out the field marshal's uniform. It is in line with the uniform of a general officer (with underling parent regimental traditions) with a few unique variations. These include the gorget patches of the field marshal pattern of gold/silver oak leaf chain of two oak leave, five gold/silver stars on scarlet background with a gold/silver button; worn on Dress No 2A, 4, 5, 5A, 6, 6A, 6B, 7 and 8; and special epaulettes for Dress No 2 and 2A.

List of field marshals
Sarath Fonseka was the first and, to date, only Sri Lankan Army officer to be promoted to the rank. He was promoted on 22 March 2015.

References

Military ranks of the Sri Lanka Army

Ceremonial officers in Sri Lanka
Five-star officers
Lists of Sri Lankan military personnel

redpajama_set_name: RedPajamaWikipedia