Tuesday, December 6, 2011

Open Access versus ‘doing business on corpses’: Is PLoS ONE the choicest journal of the TB community?

It is heartening to see PLoS ONE emerge as a preferred destination for tuberculosis and lung diseases research and the journal has already published >1300 articles in this area (http://tinyurl.com/cvnvdnb), a volume equivalent to a 13 year output of the journal Tuberculosis (@ 100 articles per year) and of 6 years output of the International Journal of Tuberculosis and Lung Disease (IJTLD) (@ 240 articles per year).
Given this, I must congratulate all those authors who have by publishing in ONE in a way dumped the might of the journals that block Open Access to TB research - something like 'doing business on the corpses'. They have for years blocked access to TB works - the situation worsened in high burden countries such as India (where 320000 people died of TB in 2010 alone). Very surprising and painful is the reality that one of these journals, the IJTLD is published by the International Union Against TB and Lung Disease or the Union (www.theunion.org), one of the major champions of the cause of TB. While the Union is doing very laudable efforts in the area of TB control and prevention, I would urge them to consider widening unconditional Open Access to the IJTLD contents by the Indian TB communities (rather than linking access to membership/subscription). Why would someone become a member of the Union just to read an article in need? Currently, the Union makes available the journal through Ingenta Connect who charge about USD 40.00 per view, per article when accessed directly. The cost per view charged thereby is equivalent of the cost of food/ration for one month for a mid size, lower middle class family in India. The same is true with Tuberculosis articles, each accessible at the cost of USD 35.00 levied by Elsevier. The Union receives huge funding and donations from various sources and they should seriously think on converting their journal in to an Open Access, online only journal to better serve the down trodden.
World over, the research on TB is mainly funded by tax payers' money and in no way the TB community should allow these journals to carve business out of this dreaded epidemic. PLoS ONE on the other hand generously waives off cost of article processing for all the authors who request for the same. Each article is available free of cost for unlimited download and distribution with no strings attached. That's why PLoS ONE stands today as one of the choicest journal of the TB researchers.

Thursday, November 10, 2011

German cows get clean chit for the outbreak of Shiga toxin-producing E. coli O104:H4

No evidence of the Shiga toxin-producing E. coli O104:H4 outbreak strain or enteroaggregative E. coli (EAEC) found in cattle faeces in northern Germany, the hotspot of the 2011 HUS outbreak area

Lothar H Wieler, Torsten Semmler, Inga Eichhorn, Esther M Antao, Bianca Kinnemann, Lutz Geue, Helge Karch, Sebastian Guenther and Astrid Bethe  Gut Pathogens 2011, 3:17 doi:10.1186/1757-4749-3-17   Published: 3 November 2011

Ruminants, in particular bovines, are the primary reservoir of Shiga toxin-producing E. coli (STEC), but whole genome analyses of the current German ESBL-producing O104:H4 outbreak strain of sequence type (ST) 678 showed this strain to be highly similar to enteroaggregative E. coli (EAEC). Strains of the EAEC pathotype are basically adapted to the human host. To clarify whether in contrast to this paradigm, the O104:H4 out-break strain and/or EAEC may also be able to colonize ruminants, we screened a total of 2.000 colonies from faecal samples of 100 cattle from 34 different farms - all located in the HUS outbreak region of Northern Germany - for genes associated with the O104:H4 HUS outbreak strain (stx2, terD, rfbO104, fliCH4), STEC (stx1, stx2, escV), EAEC (pAA, aggR, astA), and ESBL-production (blaCTX-M, blaTEM, blaSHV). Results: The faecal samples contained neither the HUS outbreak strain nor any EAEC. As the current outbreak strain belongs to ST678 and displays an enteroaggregative and ESBL-producing phenotype, we additionally screened selected strains for ST678 as well as the aggregative adhesion pattern in HEp-2 cells. However, we were unable to find any strains belonging to ST678 or showing an aggregative adhesion pattern. A high percentage of animals (28%) shed STEC, corroborating previous knowledge and thereby proving the validity of our study. One of the STEC also harboured the LEE pathogenicity island. In addition, eleven animals shed ESBL-producing E. coli. Conclusions: While we are aware of the limitations of our survey, our data support the theory, that, in contrast to other Shiga-toxin producing E. coli, cattle are not the reservoir for the O104:H4 outbreak strain or other EAEC, but that the outbreak strain seems to be adapted to humans or might have yet another reservoir, raising new questions about the epidemiology of STEC O104:H4.  Access full article free of cost

Wednesday, October 26, 2011

Feast of the Open Access Week: PLoS Won

By Michael Eisen | it is NOT junk)

When Pat Brown, Harold Varmus and I started the Public Library of Science (PLoS) 10 years ago with the goal of making the scientific and medical literature a universally freely available resource, most people in the science publishing industry dismissed us as naive idealists who didn't understand that publishing is a business that has to make money, or derided us as dangerous radicals hellbent on destroying them.

So it has given me considerable pleasure to watch, over the past year or so, as one traditional publisher after another has responded to the smashing success of PLoS One by launching direct ripoffs that seek to capitalize on the business model we have established.

For those of you who don't know, PLoS One, launched in 2006, does things a bit differently than most scientific journals. Every paper submitted to the journal is peer reviewed, but the reviewers and editors consider only the technical merits of the paper in deciding whether or not it should be published – they do not attempt (as virtually all other journals do) to gauge the potential significance or sexiness of the paper. The result is a simple and objective peer review process that gets papers published quickly and, because it is an open access journal, in a place where it is accessible for anyone to find and read. To cover the costs of running the journal and handling the paper, authors of accepted papers pay a fee (currently $1,350 – he money comes from their research grants or institutions, not from their own pockets, and any authors who say they can not pay are granted waivers).

And apparently authors love PLoS One, because they are sending us lots of paper. The journal published 6,700 articles in 2010 and will publish around 12,000 in 2011. This has clearly caught the attention of lots of established publishers, as the past year has seen the launch of a series of PLoS One clones, including:

joining already existing offerings from open access publishers BioMed Central, Hindawi and others.

This is, in many ways, exactly what we hoped would happen. In 2001 most publishers lacked both the foresight to see how publishing could better serve the research community, and the incentive to bother figuring it out. Now, PLoS One's volume, and the threat it poses to their existing journals, provides the motivation, and PLoS One's financial success (it is profitable) serves as an inspiration. Our goal was always to see that papers were published in open access journals. If they were PLoS journals – great. But if they were from other publishers – that's great too.

And here, there is a bit of a rub. PLoS and BMC established the standard for open access publishing by adopting the Creative Commons Attribution License (CC-BY), which allows for unrestricted reuse and redistribution subject only to the constraint that the original authors and source be cited. Several of the new journals follow our lead and use CC-BY, including G3, Open Biology and SAGE Open. I fully endorse what these publishers are doing, and have already published one paper in G3.

The others have not been so enlightened, using exclusively (or in one case optionally) licenses that restrict commercial reuse or the generation of derivitive works.

CC-BY-NC – BMJ Open

CC-NC-SA – mBio, Biology Open

CC-BY-NC-ND – Scientific Reports

CC-BY or CC-BY-NC-ND – Cell Reports

This is a very misguided decision on the part of these publishers. The rules governing reuse of content matter a lot if we are ever going to start making more effective use of the published scientific literature. The non-commercial licenses employed by BMJ, Nature, ASM, Company of Biologists, Cell Press and Nature all – rather absurdly – prevent PLoS from reusing their content in tools we are developing to help researchers organize literature in their fields and make the contents of papers they care about more useful. I hope this is a short-lived mistake and that, following Netflix, they realize the error of their ways and switch to a CC-BY license (in the meantime, I urge people who care about open access to continue supporting only those journals that use the CC-BY license).

There is, obviously, still a long way to go before we achieve our original goal of making every paper immediately freely available. Buit it's hard not to see events of the last year as anything but a major victory for PLoS and open access.

Happy Open Access Week!

[UPDATE: I want to clarify that Cell Reports does not view itself as a PLoS One clone, as it will be rejecting papers on the basis of impact/importance. I also want to commend them for offering the CC-BY license to authors, although I think that many will naively choose the NC version].

Friday, September 30, 2011

PLoSONE: Global Conservation Priorities for Marine Turtles

Wallace BP, DiMatteo AD, Bolten AB, Chaloupka MY, Hutchinson BJ, et al. (2011) Global Conservation Priorities for Marine Turtles. PLoS ONE 6(9): e24510 - Read full article here for free

Where conservation resources are limited and conservation targets are diverse, robust yet flexible priority-setting frameworks are vital. Priority-setting is especially important for geographically widespread species with distinct populations subject to multiple threats that operate on different spatial and temporal scales. Marine turtles are widely distributed and exhibit intra-specific variations in population sizes and trends, as well as reproduction and morphology. However, current global extinction risk assessment frameworks do not assess conservation status of spatially and biologically distinct marine turtle Regional Management Units (RMUs), and thus do not capture variations in population trends, impacts of threats, or necessary conservation actions across individual populations. To address this issue, we developed a new assessment framework that allowed us to evaluate, compare and organize marine turtle RMUs according to status and threats criteria. Because conservation priorities can vary widely (i.e. from avoiding imminent extinction to maintaining long-term monitoring efforts) we developed a "conservation priorities portfolio" system using categories of paired risk and threats scores for all RMUs (n = 58). We performed these assessments and rankings globally, by species, by ocean basin, and by recognized geopolitical bodies to identify patterns in risk, threats, and data gaps at different scales. This process resulted in characterization of risk and threats to all marine turtle RMUs, including identification of the world's 11 most endangered marine turtle RMUs based on highest risk and threats scores. This system also highlighted important gaps in available information that is crucial for accurate conservation assessments. Overall, this priority-setting framework can provide guidance for research and conservation priorities at multiple relevant scales, and should serve as a model for conservation status assessments and priority-setting for widespread, long-lived taxa. Image coutesy: WWF. Read full article here for free

Saturday, September 17, 2011

Aligarh sherwani is shining in Montreal!

'Zara nam ho toh yeh mittee badee zarkhez hai saaqui'

My congratulations to Dr Hammad Shadab of AMU for his best presentation award at Alternatives Congress.

Tuesday, September 6, 2011

Hot in PLoS ONE: Do Facial Expressions Develop before Birth?

Citation: Reissland N, Francis B, Mason J, Lincoln K (2011) Do Facial Expressions Develop before Birth? PLoS ONE 6(8): e24081. doi:10.1371/journal.pone.0024081

Background

Fetal facial development is essential not only for postnatal bonding between parents and child, but also theoretically for the study of the origins of affect. However, how such movements become coordinated is poorly understood. 4-D ultrasound visualisation allows an objective coding of fetal facial movements.

Methodology/Findings

Based on research using facial muscle movements to code recognisable facial expressions in adults and adapted for infants, we defined two distinct fetal facial movements, namely "cry-face-gestalt" and "laughter- gestalt," both made up of up to 7 distinct facial movements. In this conceptual study, two healthy fetuses were then scanned at different gestational ages in the second and third trimester. We observed that the number and complexity of simultaneous movements increased with gestational age. Thus, between 24 and 35 weeks the mean number of co-occurrences of 3 or more facial movements increased from 7% to 69%. Recognisable facial expressions were also observed to develop. Between 24 and 35 weeks the number of co-occurrences of 3 or more movements making up a "cry-face gestalt" facial movement increased from 0% to 42%. Similarly the number of co-occurrences of 3 or more facial movements combining to a "laughter-face gestalt" increased from 0% to 35%. These changes over age were all highly significant.

Significance

This research provides the first evidence of developmental progression from individual unrelated facial movements toward fetal facial gestalts. We propose that there is considerable potential of this method for assessing fetal development: Subsequent discrimination of normal and abnormal fetal facial development might identify health problems in utero.

Wednesday, August 10, 2011

From PLoS Blogs: Ramadan: Holy month and field experiment

By Emily Anthes

During Ramadan, Muslims eat and get more active just when their bodies are used to winding down, creating sleep disruptions, hormonal changes, and sometimes mood impacts.

"Their biological clocks are no longer in harmony with their watches," said Yvan Touitou, a chronobiologist at Pierre and Marie Curie University in Paris. "Ramadan is capable of desynchronizing people."

Touitou's research has illustrated that Ramadan can alter the usual circadian patterns of cortisol, a stress hormone, and testosterone, with sharper decreases of these hormones in the morning and later rises at night – though the impact of these rhythm disruptions is unclear.

The holiday also changes the schedule of the release of leptin, a hormone that regulates appetite and weight, and decreases the peak levels of melatonin, a hormone released at night to induce sleep. Interestingly, despite the disruption in leptin and in daily eating patterns, Ramadan rarely causes significant changes in body weight. Investigating why this is the case could yield useful insights into human energy metabolism, said Tom Reilly, a sports scientist at Liverpool John Moores University in England who has studied circadian rhythms and Ramadan.

"Normally, your body clock is affected by the alternation of light and darkness – light is the signal to become alert. With Ramadan, fasting is obligatory at exactly the time the body is gearing up for activity," Reilly said. "It's an exact reversal of the usual pattern."

Florian Chapotot, a neuroscientist at the University of Chicago, found that subjects showed an overall decrease in the amount of sleep they got during the holiday – not surprising given that typically, Ramadan adherents often fit in two or three meals between sunset and sunrise.

What was most interesting, Chapotot said, was the finding that subjects also spent a smaller proportion of their sleep time in slow-wave and REM sleep, both of which "are important because they have restorative functions."

It's still not clear, however, whether sleep disruptions are a result of changes in melatonin secretion, other physiological rhythms or behavioral patterns during the holiday.

The effects of all these physiological changes are unknown. Research has shown that motor skills, such as reaction times, muscle, and learning performance decrease significantly during the holiday and that sleepiness and traffic accidents increase. But scientists are investigating whether these changes are direct results of circadian rhythm disruption.

And despite its usefulness, Ramadan is difficult to study, partly because of the sheer number of variables. The month, part of the lunar Islamic calendar, moves forward by about 11 days every year, and the length of daily fasting can range from 12 hours upward, depending on location and time of year.

Additionally, those who observe the holiday have wildly different ways of coping with the altered hours – some take naps during the day and stay up most of the night, while others only slightly alter their usual sleeping patterns.

"The use of Ramadan as a chronobiological model is a little bit messy. We cannot get control of all of the variables," Reilly said. But, "it's a beautiful field experimental condition."

Thursday, July 28, 2011

E. coli genome crowd-sourcing consortium publishes their data: why choose a closed access magazine for an Open Source project?

The E. coli O104:H4 Genome Analysis Crowd-Sourcing Consortium today published their findings in the New England Journal of Medicine. The paper ignores previous authors' published efforts on the similar lines and the findings reported are not surprising and not newer than the data published by two German groups in Archives Microbiology and PLoS ONE; I handled peer review for the latter study. Having said this, what is disgusting is that the crowd-sourcing consortium have in a way strengthened the agenda of closed access publishing syndicates who run the 'glamour magazines' of science and medicine!  As a consequence, the entire purpose of the idea of an Open Source platform for the analysis of the E. coli epidemic stands defeated. The journal may not allow universal access to the article by holding copy right over the much acclaimed 'Open Source' data of this consortium - meaning that no unrestricted access and creative reuse will be possible as against the practice of most Open Access journals.

Thursday, July 21, 2011

Prevent leptospirosis: wear good quality shoes during Monsoon

These pics explain why we get lepto outbreaks each year in June-July. The leptospira penetrate wet skin by by their cork-screw like action. No vaccine is needed as long as you wear long shoes and do not expose to contaminated water spills.
 
 
 

Prospective genomics in epidemics – lessons from the German E. coli outbreak

By Jennifer Laloup (EveryONE)

Today we published an article by Mellmann et al. entitled, Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology. The following is an opinion piece by Dr. Niyaz Ahmed, a section editor for PLoS ONE and the academic editor of this paper.  He is an expert in the area of molecular epidemiology and genomics of bacterial pathogens at the University of Hyderabad, India.



When a monstrously virulent strain of never-before-seen E. coli suddenly appeared in Germany last month, the rush to decode became an immediate focus. Several groups became engaged simultaneously to crack the genome of the underlying bug and then followed a huge crowd-sourcing effort on the internet as soon as the genome sequences were made available. Given that reasonable data were made available by these authors within 60 hours of the outbreak, not much of the evolutionary history of the organism had been dissected and a great deal of the interpretation remained vague.

An informed, scientific treatise was needed to help health control authorities and policy makers launch a serious mitigation campaign; this work, in that sense, constitutes the first official report on the genomic footprint of the underlying E. coli strain. The authors report chronological (step-wise) recombination of the genome in the outbreak strains over a period of ten years. This reveals the extraordinary capability of certain pathogens to recombine so that a devastating phenotype finally emerges with a multi-dimensional fitness advantage. Further, the study of Mellmann et al. demonstrates the might of present-day sequencing technologies such as Ion Torrent in enabling genome-guided epidemiology, diagnostics, and interventions.

I have no hesitation to say that the study carried out by Mellmann et al. is truly a technical masterpiece, a first time proof-of-principle whereby next generation sequencing could be harnessed in real-time when certain 'gold standards' such as serotyping failed miserably. This report has an important bearing on the new proposed field of 'epidemic forecasting' in which the spread potentials of a pathogen could be predicted based on genomic fingerprints – in other words, predicting if the infection will assume pandemic proportions.  The finding that the E. coli strains analyzed were enteroaggregative (EAEC) could explain this. EAECs could persist in recovered or subclinical cases and that they could be carried by the latter on travel routes worldwide.

One of the possible shortcomings of the study could be that it is silent on the mechanistic details of 'adornment' of these bacteria with several layers of fitness – multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one 'naturally' chimeric strain in just 10 years is extremely dramatic!  The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori, an organism notorious for its speed of recombination, recasting its entire genome every forty years. We recently had an opportunity to sequence and look at H. pylori genomes hierarchically obtained across ten years. We did not find major insertion, deletion and substitution events.

Technology helped with the dissection of the E. coli epidemic in hours and days, but the editorial process also was seamless and prompt enough to enable rapid dissemination of results. Open and early access is very important for the dissemination of findings during epidemic times because much of the control and mitigation measures need planning in the light of latest research findings.

Sunday, July 10, 2011

Impact Factors of Biomed Central journals

The 2010 edition of Thomson Reuters' Journal Citation Reports, released on June 28th 2011, provides further evidence that open access journals are delivering not only high visibility but also high rates of citation and impact.

Altogether, 101 BioMed Central journals now have official impact factors. 21 journals recorded their first impact factors this year. Meanwhile, among the 80 journals which already had impact factors, 52 increased while only 28 declined. The average change in impact factor was an increase of 0.19 points.

Some highlights:

  • BMC Medicine (IF 5.75) saw a huge jump in its impact factor and is now in the top 10% of journals in the General Medicine category
  • Retrovirology (IF 5.24), is now 4th of 32 in the Virology category, overtaking Journal of Virology
  • Malaria Journal (IF 3.49) recorded its third successive increase and remains the 2nd most highly ranked journal in the Tropical Medicine category
  • Journal of Cardiovascular Magnetic Resonance (IF 4.33), official journal of the Society for Cardiovascular Magnetic Resonance, almost doubled its previous impact factor of 2.28
  • BMC Plant Biology (IF 4.09) increased from 3.77 to confirm its ranking in the top 10% of the Plant Science category
  • BMC Veterinary Research (IF 2.37) makes an exceptionally strong start, ranking 8th of 145 in the Veterinary Sciences category
  • Frontiers of Zoology (IF 2.42) debuts in the JCR in the top 10% of the Zoology category
  • Particle and Fibre Toxicology (IF 4.91) ranks 4th of 83 in the Toxicology category
  • Cell Division (IF 4.09) and Epigenetics & Chromatin (IF 4.73) also both make strong starts

 Full list of 2010 impact factors for BioMed Central journals
(journals listed in bold have new or improved impact factors) 

Journal 2010 IF  
Acta Veterinaria Scandinavica 1.20  
Algorithms for Molecular Biology 2.80  
Arthritis Research & Therapy 4.36  
Behavioral Brain Functions 2.31  
Biology Direct 3.74  
Biological Procedures Online 0.74  
BioMedical Engineering OnLine 1.12  
Biotechnology for Biofuels 4.15  
BMC Bioinformatics 3.03  
BMC Biology 5.20  
BMC Biotechnology 2.86  
BMC Cancer 3.15  
BMC Cardiovascular Disorders 2.02 New
BMC Cell Biology 2.46  
BMC Complementary and Alternative Medicine 2.20 New
BMC Developmental Biology 2.78  
BMC Evolutionary Biology 3.70  
BMC Family Practice 1.47  
BMC Gastroenterology 2.47  
BMC Genetics 2.49  
BMC Genomics 4.21  
BMC Health Services Research 1.72  
BMC Immunology 3.00  
BMC Infectious Diseases 2.83  
BMC Medical Education 1.20 New
BMC Medical Genetics 2.44  
BMC Medical Genomics 3.77  
BMC Medical Informatics and Decision Making 2.23  
BMC Medical Research Methodology 2.15  
BMC Medicine 5.75  
BMC Microbiology 2.96  
BMC Molecular Biology 3.19  
BMC Musculoskeletal Disorders 1.94  
BMC Nephrology 2.14 New
BMC Neurology 2.80  
BMC Neuroscience 3.09  
BMC Pediatrics 1.90 New
BMC Plant Biology 4.09  
BMC Psychiatry 2.89  
BMC Public Health 2.36  
BMC Structural Biology 2.26  
BMC Systems Biology 3.57  
BMC Veterinary Research 2.37 New
Breast Cancer Research 5.79  
Cardiovascular Diabetology 2.72  
Cardiovascular Ultrasound 1.56 New
Cell Division 4.09 New
Chemistry Central Journal* 1.12  
Critical Care 4.60  
Diagnostic Pathology 1.39  
Environmental Health 2.45  
Epigenetics & Chromatin 4.73 New
Frontiers in Zoology 2.52 New
Genetics Selection Evolution 1.48  
Genome Biology 6.89  
Geochemical Transactions 1.92  
Harm Reduction Journal 1.46 New
Human Resources for Health 1.38 New
Health and Quality of Life Outcomes 1.86  
Hereditary Cancer in Clinical Practice 0.96  
Implementation Science 2.51  
International Journal for Equity in Health 1.30 New
International Journal of Behavioral Nutrition and Physical Activity 3.17  
International Journal of Health Geographics 2.34  
Irish Veterinary Journal 0.33  
Journal of Biomedical Science 1.96  
Journal of Cardiothoracic Surgery 0.91  
Journal of Cardiovascular Magnetic Resonance 4.33  
Journal of Experimental & Clinical Cancer Research 1.92  
Journal of Hematology & Oncology 2.93  
Journal of Inflammation 2.02 New
Journal of Neurodevelopmental Disorders 1.27 New
Journal of NeuroEngineering and Rehabilitation 2.64  
Journal of Neuroinflammation 5.79  
Journal of the International Society for Sports Nutrition 2.68 New
Journal of Translational Medicine 3.51  
Lipids in Health and Disease 2.24  
Malaria Journal 3.49  
Microbial Cell Factories 4.54  
Molecular Cancer 3.78  
Molecular Neurodegeneration 5.36  
Molecular Pain 4.15  
Neural Development 3.40  
Nutrition & Metabolism 2.35  
Nutrition Journal 2.56 New
Orphanet Journal of Rare Diseases 5.93  
Parasites and Vectors 2.13  
Particle and Fibre Toxicology 4.91 New
Plant Methods 3.28  
Proteome Science 2.49  
Radiation Oncology 2.41  
Reproductive Biology and Endocrinology 1.70  
Respiratory Research 2.86  
Retrovirology 5.24  
Scandinavian Journal of Trauma, Resuscitation and Emergency Medicine 2.18 New
Substance AbuseTreatment, Prevention, and Policy 1.58  
Theoretical Biology and Medical Modelling 1.60 New
Trials 2.08  
Veterinary Research 3.77  
Virology Journal 2.55  
World Journal of Surgical Oncology 1.12 New

 * Based on Web of Science data, the impact factor listed for Chemistry Central Journal appears to be erroneously low and has been queried with Thomson Reuters.

For further information on impact factors and journal tracking, see BioMed Central's impact factor FAQ.

Posted by Matt Cockerill

Wednesday, July 6, 2011

Words to avoid in presentations and in speech

Barry J Marshall (courtesy: http://barryjmarshall.blogspot.com/)


This month I have decided to go public with my list of "meaningless words" which should no longer be used in public, especially not in meetings or presentations and never on TV or radio. Here are the ones I recall today.

1. Basically
a. This word has become a favourite of scientific people especially when they are answering questions. I am also guilty. Example as follows - Question: If the DNA is copied until the primer just falls off, how is it that all the pieces of DNA end up exactly the same length? Answer: Well, basically, you are almost correct however, only the first copy gives a random length. After that, basically, the primer in the next cycle has to start 637 base pairs from the start point of the first copy. So, basically, all except the first copy are the same length, basically 637.
2. I mean
a. This seems to be used as a spacer between sentences, where the speaker continually likes to embellish details and add ideas. I mean, just as one would normally give the listener person a chance to talk by leaving a short gap in the conversation, by using "I mean" the gap is stolen back so that the normal person might not get a word in edgeways. I mean, let's say that it was you being the listener, and you are a nice polite person; I mean, like Marj in the Simpsons. Then you never have a chance to speak because ...
3. Sort of
a. A vague term implying that the speaker has not put any thought into the discussion and is sort of making stuff up as he goes along. This seams to be common in presentations from young artists.
4. Yeah
a. Australians have become adept at placing this word in the middle of sentences as some kind of emphasis. I think it is very common in interviews with surfers; yeah – .
5. Absolutely
a. Television personalities, especially on gardening shows, continually say absolutely. Then the show "Absolutely Fabulous" started up perhaps as a send up of this trend. Recently it has been used more and more by almost everyone. By adding this word, a very vague concept suddenly becomes absolutely correct and proven beyond all doubt. Also, other words can be added to it, especially "fabulous" to make something rather mundane and boring into something apparently exciting. Take the concept of picking up handfuls of animal poo. We don't have smellovision yet, and the warm temperature of a putrefying heap is hard to transmit to the gardening audience. But I can call it compost and say how this material is absolutely the best thing for your garden. How absolutely fabulous it is to feel the warmth as you thrust your hands into the pile in order to experience nature as the good bacteria convert biodegradeable organic material into absolutely perfect plant nutrients. Actually, it sounds rather attractive as I write this.
6. Umm
a. A non word, also used as a spacer to stop other people butting in. Luckily there is no need to use this on TV interviews because a smart editor will cut out all the wasted time anyway, so as to add more content, or another "non umming" person to the time allocated for the story.
7. Like
a. This word is more often used by teenagers – or even myself actually – as emphasis in a story. But it is used rather informally, among friends, with alcohol on board usually, and often as a preamble to an acted out part of the story telling. I am having trouble explaining it but here goes. Just say that I am telling you about a scene from the movie Avatar. So the main actor Sam Worthington is just a dumb marine so he's like, "I need to walk again so I will do anything to pay for an operation"; but Sigourney weaver, she's like some kind of genius professor so she's like "don't break the machinery you dumbass!" etc.
8. You know
a. Everyone uses this Phrase, again a spacer to show that you probably don't know all the facts but what you say is probably about right. Of course, as the brainy listener, you probably have more information or already have heard this story, but if you do know it you would not be so rude as to correct the speaker or embellish his own story. You know.

I think it might be fun to add a few more of these and give funny examples. It would be good practice for a screen writer in a sitcom. My son reminded me of a program we used to have which converted normal speech to "Jive" which was a kind of black American street gang speech which most Australians would hardly ever hear but probably rappers and people from Los Angeles might be familiar with. Time is up – I can't spend my life just doing a blog. Back to real life.

Sunday, July 3, 2011

SPARC Innovator Award for PLoS ONE


Because the concept of PLoS ONE was so simple, yet so revolutionary, its launch in December 2006 was met with equal parts excitement and skepticism. In the PLoS ONE model, editors and reviewers would not attempt to assess the potential importance of the work. Rather, as long as the research was determined to be solid, the author would pay a flat fee, and up it would go on the Web. Could something as simple as publishing articles just because they were "good science" really work?

"The idea was to decouple impact assessment and technical assessment," says Mark Patterson, director of publishing for the Public Library of Science, who was one of the staff involved with the journal from the beginning. "We were also trying to take the hassle out of publishing."

PLoS co-founders Pat Brown, Michael Eisen, and Harold Varmus were also the visionaries behind PLoS ONE, once again creating a new channel by viewing publishing through the lens of scientists. Their vision was to do away with the redundant process of submitting a paper to a journal, waiting for a rejection that was so often based on subjective qualities such as impact, and then resubmitting to a new title. Instead, research would be peer-reviewed against objective criteria and published after it was deemed worthy of joining the scientific literature—often with just one round of revisions. New technology would be leveraged so readers could add value to the content. Those comments would then help to indicate the importance of the work to the body of scientific knowledge.

When the concept was first introduced, it created a lot of chatter—especially in the blogosphere, says Patterson. And, as with any new journal, no one knew what the response would be. Even supporters of PLoS ONE wondered if the model would be seen as selective and prestigious in the scientific community. "I found it very exciting at the time," says Cameron Neylon, a biochemist at the Rutherford Appleton Laboratory in Didcot, England, and member of the PLoS ONE Academic Editor board. "But I was less than convinced it would take off."

It didn't take long before PLoS ONE began emphatically to answer the skeptics.

In 2007, the journal received about 2,500 submissions and published 1,200 articles. In 2010, PLoS ONE received nearly 13,560 articles and published 6,800—with about 60 being published daily. It is now the single largest journal being published today.

The PLoS ONE business model is scalable. Its publishing costs have always been fully covered by the publication fees and it became a financial success. In 2010, due in part to this meteoric rise, PLoS became self-sustaining. The innovative concept and its capacity for rapid growth have caught the attention of other publishers. In a clear nod to the success of PLoS ONE, "clones" are popping up —from SAGE Open, to BMJ Open to Scientific Reports by Nature.

For its groundbreaking model of open-access publishing success, SPARC (the Scholarly Publishing and Academic Resources Coalition), has named PLoS ONE as its July 2011 Innovator.

"PLoS ONE is a game-changer," said Heather Joseph, SPARC's Executive Director. "It breaks through the preconception that authors— and readers—require a journal to determine the significance of scientific research, and demonstrates that the community is ready and willing to take on that role."

PLoS ONE has made a powerful—and quick—change in scientific publishing, which is a conventional industry, says Peter Jerram, chief executive officer of PLoS. "It's a testament to the idea," he says. "If you only look at how rigorous the science is and whether the conclusions are supported by the data, then a lot of great science gets out there more quickly, including some that wouldn't otherwise see the light of day."

The model represents something completely new and has attracted staff from more traditional publishers, such as Peter Binfield. In early 2008, Binfield succeeded Chris Surridge as managing editor of PLoS ONE. Binfield had been a career publisher who had always worked with the traditional subscription model. While he was one of the initial PLoS ONE skeptics, he felt Open Access was a better way to accelerate advancement in science and he very quickly became a fan of the journal.

"It seemed self-evident to me that this was the future of academic publishing," says Binfield.

It was groundbreaking to establish a journal that would publish first and only then figure out impact. With PLoS ONE, the author didn't get kudos or a badge of honor for being accepted to the journal. Rather, in this model the reader would make the judgment call as to how important the research was, from their unique vantage point.

The PLoS ONE process is more efficient and transparent than the traditional, subjective journal peer review process. "Not asking the impact question makes it a cleaner and more objective review," says Binfield.

And, contrary to early concerns that anything could make its way onto PLoS ONE, significant filters were established. On average, two external reviewers read every paper, and most are sent back to the author for revision. The journal applies stringent policies dealing with items such as disclosure requirements, data deposition standards, and ethical concerns. In addition, every paper has to pass a detailed technical checklist of over 40 items before even entering the peer review process. About 65-70 percent of submissions end up being published, says Binfield. Online tools are then used to evaluate, sort, and filter content after publication, not before.

There are approximately 10,000 publishers today, producing 25,000 journals with about 1.5 million articles per year. In an industry that has been slow to change, PLoS ONE is proving that new business models that don't charge subscription fees can survive—and thrive, says Binfield. In four years, this one journal has become the largest peer-reviewed journal in existence. On its current trajectory, PLoS ONE could be responsible for publishing fully 3 percent of the biomedical literature in 2012.

Looking ahead, Binfield sees the potential that, rather than having thousands of smaller journals, the vast majority of the world's literature could eventually be in as few as 100 journals, all with a similar profile to PLoS ONE. "It's moving very rapidly. It feels like a tipping point in the industry," he says.

The draw

Surveys of PLoS ONE authors help shed light on the journal's phenomenal success. The number one reason scientists submit is because it is open-access. They want their work to be freely accessible and widely available. The second draw is speed. Rather than waiting months or years to get a paper accepted in a traditional journal, PLoS ONE gets researchers' work out quickly. Finally, the quality of the PLoS brand is an important factor and the objective peer review is also appreciated, says Binfield.

Gary Ward, professor of microbiology and molecular genetics at the University of Vermont, who became Chair of the PLoS board of directors in January, just had his first paper accepted to PLoS ONE.

He and other researchers welcome the relief that PLoS ONE provides from the "treadmill" of submitting and resubmitting to traditional journals, says Ward.

"I love the concept of eliminating this huge waste of time by simply removing subjective evaluations of importance from the review process," says Ward. "If the paper is well-written and the conclusions don't overreach, then let the community decide the impact."

Ward calls the PLoS ONE approach the ultimate in "crowd sourcing" that also contains rigorous review—just a different kind of peer review.

PLoS ONE features original research from all disciplines within science and medicine (although most submissions are in life and health sciences). By providing an interdisciplinary platform, the hope is to facilitate discovery of connections between papers and subject areas. "The fact that you can read around the edges of a field is a big deal," says Binfield. "PLoS ONE forms a home for any article; it no longer has to have a journal of its own."

Behind the success

The concept of publishing without having to battle the system was the big driver behind the explosive growth of PLoS ONE. The trust of the PLoS brand also helped, says Patterson. Of course, there is the human capital that has had to expand to keep up with the rapidly growing journal.

Handling 2,000 submissions a month and publishing 60 articles daily takes a substantial group of people. The paid staff on the journal, which handles the checks and balances of the system, has increased to handle the growing number of submissions. There are about 35 full-time equivalents, with some positions contracted out. Then there are 1,700 academic editors on the journal, individually handling each paper and finding peer reviewers so that every paper is appropriately reviewed.

"We have been up to the challenge; we've kept pace," says Patterson.

CEO Jerram says he is amazed at the dedication of the people who work for PLoS ONE and that has made a palpable difference in the journal's success. "There is a real passion and commitment there," he says.

Binfield says while the staff works hard and the work can be stressful, it is a mission-driven organization, and they are energized by what they are doing. "We feel like we are doing the right thing for the right reasons," he says.

The process has worked because the model scales with the volume of submissions: Every article adds more work, but also adds revenue. The publication fee for each published paper is $1,350, which is usually covered by grant money. Unlike a traditional journal, PLoS ONE allows researchers to publish papers of unlimited length, with full color throughout and containing any amount of supplemental material such as spreadsheets or videos. Occasionally authors take fee waivers, but about 90 percent of authors pay the full amount.

The goal of making PLoS self-sustaining was met last year. The organization was originally established with the help of foundations and outsider support, but as the suite of publications has grown to make PLoS self-sustaining, they have been able to develop additional innovations such as article-level metrics, PLoS Currents and PLoS Hubs.

The followers and the future

"The model is working beautifully. It's financially sustainable and there is increasing rapid growth. This is something science is really embracing," says Ward. "The competition is crazy not to go this way," says Ward. The mission of PLoS is to make as much of the literature open-access as possible, and to show how Open Access can transform the literature into a more powerful resource for education and research.

While PLoS ONE pioneered coverage of the whole of science, many who have adapted the model are using it for single subject areas, says Binfield. "We are encouraged and excited to see these clones launched," he says. "It validates that this model is here to stay … We can see the future path and the launch of these clones just cements it."

Will PLoS adopt the PLoS ONE model for its other journals?

Chairman of the Board Ward says that the history of PLoS, (which is based in San Francisco and Cambridge, England and is the world's largest not-for-profit open-access journal publisher) has always been one of an organization pushing the envelope. "We are constantly looking at the editorial structure, the business model," he says. However, once a journal is established, it is harder to make wholesales changes. Ward says PLoS will continue to consider what works best for all of its titles and the organization is committed to being innovative. "We want to keep PLoS on the cutting edge," says Ward.

A goal of PLoS is to help publishers move into Open Access and PLoS ONE is indeed a new model for publishing, says Jerram. In the future, he says there may be better ways to communicate science than through journals. The real power and promise of Open Access is to make scientific information and data not only able to be read, but also re-used. "Open Access is the enabler that makes other things possible," says Jerram.

Binfield envisions more and more journals following PLoS ONE's lead and he says that it is very exciting to see the transformations that are underway. "I come into work every day with the knowledge that I am helping to advance science by accelerating and improving the process of disseminating scientific results," he says. "It's an important thing to have the knowledge that what we are doing is making a big difference in the world."

by Caralee Adams

Thursday, June 30, 2011

Impact Factors of Indian Science Journals in 2011

Year

Impact Factor (IF)

Total Articles

Total Cites

2010

1.826

166

3169

2009

1.516

178

2812

2008

1.883

178

2458

 

                                                                                      Indian Journal of Medical Research

 

Year

Impact Factor (IF)

Total Articles

Total Cites

2010

1.494

77

414

2009

0.813

77

194

2008

0.358

77

58

 

                                                                                      Journal of Genetics

 

Year

Impact Factor (IF)

Total Articles

Total Cites

2010

1.888

60

1630

2009

1.956

82

1274

2008

1.703

82

1045

 

                                                                                      Journal of Biosciences

 

Year

Impact Factor (IF)

Total Articles

Total Cites

2010

0.824

58

696

2009

0.574

59

696

2008

0.579

59

603

 

                                                                                       Indian Journal of Biochemistry and Biophysics