PLOS’ New Data Policy: Part Two

The past couple of weeks have led to an extraordinary outpouring of discussions on open data and its place in scientific publishing. We are grateful to everyone who took the trouble to tweet, blog or email about this and are heartened that so many people care as passionately as we do about open science. However, much of the discussion has centered on a misunderstanding in a previous blog post and we want to correct that now.

We apologize for causing confusion

In the previous post, and also on our site for PLOS ONE Academic Editors, an attempt to simplify our policy did not represent the policy correctly and we sincerely apologize for that and for the confusion it has caused. We are today correcting that post and hoping it provides the clarity many have been seeking. If it doesn’t we’d ask you once again to let us know – here on the blog, by email at data@plos.org, and via all the usual channels.

Two key things to summarize about the policy are:

  1. The policy does not aim to say anything new about what data types, forms and amounts should be shared.
  2. The policy does aim to make transparent where the data can be found, and says that it shouldn’t be just on the authors’ own hard drive.

Correction

We have struck out the paragraph in the original PLOS ONE blog post headed “What do we mean by data”, as we think it led to much of the confusion. Instead we offer this guidance to authors planning to submit to a PLOS journal.

What data do I need to make available?

We ask you to make available the data underlying the findings in the paper, which would be needed by someone wishing to understand, validate or replicate the work. Our policy has not changed in this regard. What has changed is that we now ask you to say where the data can be found.

As the PLOS data policy applies to all fields in which we publish, we recognize that we’ll need to work closely with authors in some subject areas to ensure adherence to the new policy. Some fields have very well established standards and practices around data, while others are still evolving, and we would like to work with any field that is developing data standards. We are aiming to ensure transparency about data availability.

An example

We are happy to answer questions about specific fields in detail. A generalized example of the type of question we have received recently, and our answer, is as follows.

Question sent to data@plos.org:

When I do an experiment taking a number of different measurements from cells, I usually report them in bar graphs as means from different experiments with their corresponding standard deviations, and the details of statistical analysis are provided in the methods section. Under this new policy is this information enough? Or does the new policy require that I upload the excel files with all the data underlying the graphs? And do I need to include every reading from the cells in raw form or can I provide just the summary in the excel files?

 
Answer:

There is no specific requirement with the new policy concerning the type of data that you make available – our focus at this stage is on making transparent where the data can be found. It has always been the case that different fields have different types of data that need to be provided – and indeed such requirements change over time, too. In the case of sensational claims, editors and reviewers frequently ask for more data than in other cases – as ‘extraordinary claims need extraordinary evidence’.

 

So, as was always the case, if you are providing graphs, it would indeed be helpful to provide the spreadsheet from which you generated the graph. If you think some other form of the data would be useful to other researchers who might want to understand, replicate or build on your work, please do include it. Conversely, if it is usual in publications in this field to provide only the summary information, then that remains sufficient now. As ever, reviewers and editors will tell you if they feel more data is needed to support your findings, as this is one of the key functions of peer review.

 
Where to go for more information

Data sharing policy: http://www.plosone.org/static/policies#sharing

FAQs: http://www.plosone.org/static/policies#faqs

Contact: data@plos.org

Image Credit: jonathangray.com

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The Science of Snakeskin: Black Velvety Viper Scales May be Self-Cleaning

West African Gaboon Viper

West African Gaboon viper

Whether you love them or hate them, snakes have long captivated our interest and imagination. They’ve spurred countless stories and fears, some of which may have even affected the course of human evolutionary history. We must admit, there is something a little other-worldly about their legless bodies, willingness to swallow and digest animals much bigger than them, and fangs and potentially fatal (or therapeutic?) venomous bites.

Not least of all, their scaly skin is quite mesmerizing and often laden with intricate and beautifully geometric patterns just perfect for camouflaging, regardless of whether they live high up in a tree, deep in murky waters, or on the forest floor. Snakeskin was the focus of recent research by the authors of this PLOS ONE study who sought to determine whether it has any special properties less obvious to the naked eye.

Please meet the West African Gaboon viper, Bitis gabonica rhinoceros (pictured above). Native to the rainforests and woodlands of West Africa, these large, white-brown-and-black snakes can be identified by large nasal horns and a single black triangle beneath each eye—nevermind that, because they also lay claim to titles for the longest fangs and most venom volume produced per bite. The pattern of their skin is intricate and excellent for camouflage, and the black sections have a particularly velvety appearance. These eye-catching characteristics intrigued zoology and biomechanics researchers from Germany, who decided to take a closer look.

In a previously published paper, the authors analyzed the Gaboon viper’s skin surface texture by using scanning electron microscopy (SEM), as well as its optical abilities by shining light on the snakeskin in different ways to see how it’s reflected, scattered, or transmitted. They found that only the black sections contained leaf-like microstructures streaked with what they call “nanoridges” on the snake scales, a pattern that has not been observed before on snakeskin. What’s more, the black skin reflects less than 11% of light shone on it—a lot less than other snakes—regardless of the angle of light applied. The authors concluded from the previous study that both of these factors may contribute to the viper’s velvet-like, ultra-black skin appearance.

Scanning electron microscopy (SEM) of viper scales

Scanning electron microscopy (SEM) of viper scales

In their most recent PLOS ONE paper titled “Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros),” the authors conducted wettability and contamination tests in hopes of further characterizing the viper skin’s properties, particularly when comparing the pale and black regions.

To test the wettability of the viper scales, the authors sprayed droplets of water, an iodide-containing compound (diiodomethane), and ethylene glycol on the different scale types shown above, on both a live and dead snake, and then measured the contact angle—the angle at which a liquid droplet meets a solid surface. This angle lets us know how water-friendly a surface is; in other words, the higher the contact angle, the less water-friendly the surface.

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

Contact angle (A) and snake skin with water droplet on light and dark areas (B)

As you can see in the graph above, the contact angle was different depending on the liquid applied and the type of scale; in particular, the contact angle on the black scales was significantly higher than the others, in a category that the authors refer to as “outstanding superhydrophobicity,” or really, really, really water-repelling. This type of water-repelling has been seen in geckos, but not snakes.

Water droplet appearance on live snake skin

Water droplet appearance on live snake skin

The authors then took some of the snake carcass and dusted it with a sticky powder in a contamination chamber, after which they generated a fog for 30 minutes and took pictures.

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

Skin before dusting (A), skin under black light after dusting (B), skin under black light after fogging (C), section of SEM, showing light and dark skin (D)

After 30 minutes of fogging, the black areas were mostly free of the dusting powder, while the pale areas were still completely covered with dust. The powder itself was also water-repelling, and so the authors showed that despite this, the powder rolled off with the water rather than sticking to the black areas of snake skin. Therefore, as suggested by the authors, this could be a rather remarkable self-cleaning ability. The authors suspect that the “nanoridges,” or ridges arranged in parallel in the black regions, may allow liquid runoff better than on the paler areas of the snake.

How does this texture variation help the snake, you ask? The authors posit that all these properties basically contribute to a better form of camouflage. If the snake were completely covered in one color, it may stand out against a background of mixed colors (or “disruptive coloration”), like that of a forest floor. If the black regions have fairly different properties from the paler regions, mud, water, or other substances would rub off in these areas and continue to provide the light-dark color contrast and variation in light reflectivity that helps the snake do what it does best: slither around and blend in unnoticed.

Citations

Spinner M, Kovalev A, Gorb SN, Westhoff G (2013) Snake velvet black: Hierarchical micro- and nanostructure enhances dark colouration in Bitis rhinoceros. Scientific Reports 3: 1846. doi:10.1038/srep01846

Spinner M, Gorb SN, Balmert A, Bleckmann H, Westhoff G (2014) Non-Contaminating Camouflage: Multifunctional Skin Microornamentation in the West African Gaboon Viper (Bitis rhinoceros). PLoS ONE 9(3): e91087. doi:10.1371/journal.pone.0091087

Images

First image, public domain with credit to TimVickers

Remaining images from the PLOS ONE paper

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Infectious Earworms: Dealing with Musical Maladies

earworm - record playing This menace may leap out at you in the subway or find you when you’re tucked away, safe in your bed; it might follow you when you’re driving down the street or running at the gym. Hand sanitizer can’t protect you, and once you’re afflicted, the road to recovery can be a long one. However, this isn’t the Bubonic plague or the common cold—instead, the dreaded earworms!

Derived from the German word ohrwurm, which translates literally to “ear-worm,” an earworm commonly refers to a song, or a snippet of a song, that gets stuck in your head. Earworms can occur spontaneously and play in our heads in a seemingly infinite loop. Think of relentlessly catchy tunes, such as “Who Let the Dogs Out?,” “It’s a Small World,” or any Top 40 staple. An estimated 90% of people fall prey to an earworm at least once a week and most are not bothersome, but some can cause distress or anxiety. And yet, despite the earworm’s ubiquity, very little is known about how we react to this phenomenon. With the assistance of BBC 6 Music, the authors of a recent PLOS ONE study set out to connect the dots between how we feel about and deal with these musical maladies.

Researchers drew upon the results of two existing surveys, each focusing on different aspects of our feelings about earworms. In the first, participants were asked to reflect on whether they felt positively or negatively toward earworms, and whether these feelings affected how they responded to them. The second survey focused on how effective participants felt they were in dealing with songs stuck in their heads. Responses to both surveys were given free form.

To make sense of the variety of data each survey provided, the authors coded participant responses and identified key patterns, or themes. Two researchers developed their own codes and themes, compared notes and developed a list, as represented below.

earworm - Finnish study

Survey responses. Participants either chose to “cope” with their earworms or “let it be.”

The figure above represents responses from the first survey, in which participants assigned a negative or positive value to their earworm experiences and described how they engaged with the tune. The majority didn’t enjoy earworms and assigned a negative value to the experience. These responses were clustered by a common theme, which the researchers labelled “Cope,” and were associated with various attempts to get rid of the internal music. A significant number of participants reported using other music to combat their earworms.

Participants in the second survey, which focused on the efficacy of treating earworms, responded in a number of different ways. Those whose way of dealing was effective often fell into one of two themes: “Engage” or “Distract.” Those that engaged with their earworms did so by, for example, replaying the song; those that wanted distraction often utilized other songs. Most opted to engage.

Ultimately, the researchers concluded that our relationships with these musical maladies can be rather complex. Yet, whether you embrace these catchy tunes or try to tune them out, the way we feel about earworms is often connected to how we deal with them.

Want to put in your two cents? You can tell the authors how you deal with earworms at their website, Earwormery. For more on this musical phenomenon, listen to personal anecdotes on Radiolab, read about earworm anatomy at The New Yorker, or dig deeper in the study.

 

Citation: Williamson VJ, Liikkanen LA, Jakubowski K, Stewart L (2014) Sticky Tunes: How Do People React to Involuntary Musical Imagery? PLoS ONE 9(1): e86170. doi:10.1371/journal.pone.0086170

 

Images: Record playing by Kenny Louie

Figure 1 from the paper.

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Falcon Physics: The Science of Diving Peregrine Falcons

Peregrine falcons, the world’s fastest-moving animal, are found on six continents around the world. Once an endangered species in the United States, their population comeback has been attributed to the widespread ban of DDT and other pesticides in the 1970s, and is a great success story in conservation. It is easy to see why these remarkable birds are so charismatic. Peregrine falcons hunt unknowing prey by diving from above at speeds of up to 200 miles per hour, maintaining an astounding degree of maneuverability and precision.  However, conducting in-depth analysis of the aerodynamic properties of peregrine falcons is no easy task. Dives are infrequent in the wild, we usually only see them from a distance, and their blistering speeds make the birds difficult to film. Nevertheless, that is exactly what a team of researchers in Germany managed to do, and they recently published the results in PLOS ONE.

Peregrine falcon in flight

Peregrine falcon in flight

Researchers first trained several peregrine falcons to dive from the top of a dam to the bottom, following a specific and predictable flight path. A trainer at the top of the dam released a falcon from the same spot each time, and a second trainer at the base used a lure to attract the bird’s attention. High-speed cameras facing the dam wall filmed falcon dives from different angles. The authors used the dam in the background of the video footage as a frame of reference to precisely and accurately recreate the peregrine’s diving trajectory, something that is nearly impossible to do filming peregrines in the wild against the sky.

Stages of a Peregrine Falcon's dive

Stages of a peregrine falcon’s dive

Back at the lab, the scientists positioned the wings and body of a stuffed peregrine falcon to resemble a falcon diving at maximum speed, and then used it to create a life-sized plastic version. The plastic falcon was analyzed in a wind tunnel using two different methods of analysis:  oil-painting-based flow visualization and particle image velocimetry.  A brief description of both techniques:

  • Surface flow visualization: By coating an object in a thin layer of paint or oil and putting it in a wind tunnel, we can examine the streaking patterns left in the paint or oil to reveal flow lines.
Peregrine falcon surface flow

Peregrine falcon model after  oil-painting-based flow visualization, showing the air flow across the body

  • Particle image velocimetry: By introducing tiny tracer particles into the wind tunnel, illuminating them with a laser, and photographing them rapidly, we can use computers to track the movement of individual particles through a sequence of photographs, calculate the particles’ trajectories and velocities, and then use this data to build an accurate model of the wind flow.

By combining their wind tunnel analysis with the data from the video footage, the researchers created the most comprehensive analysis of a peregrine falcon dive to date, including factors such as lift, drag, acceleration, and trajectory. In particular, the high-speed footage revealed that small feathers pop up during the dive in key locations on the peregrine falcon’s body. The authors say that the feather position and wind tunnel analysis support the explanation that these feathers help keep air flowing smoothly over the bird’s body to reduce drag, similar to flaps on an airplane wing.

As if you needed someone to tell you that this bird is aerodynamic!

Diving peregrine and model

Diving peregrine and 3D computer model

Related links:

Having trouble calibrating your own particle image velocity experiments? This video may help, but be careful: lasers are dangerous!

Love fluid dynamics and tunnels? Whisker Shape and Orientation Help Seals and Sea Lions Minimize Self-Noise

And, this is just plain fun: Peregrine falcon chases a mountain bike

Citation: Ponitz B, Schmitz A, Fischer D, Bleckmann H, Brücker C (2014) Diving-Flight Aerodynamics of a Peregrine Falcon (Falco peregrinus). PLoS ONE 9(2): e86506. doi:10.1371/journal.pone.0086506

Images: Picture of flying falcon from Mike Baird. 2nd, 3rd, and 4th pictures taken from Figures 7, 15, and 4 of the published paper, respectively.

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Impending Flood? Hold Onto Your Family!

antsWith the extreme weather we’ve witnessed all over the US this winter, some people may be planning new ways to stay safe in the event of a natural disaster. If we can’t learn to predict these extreme events (as some animals may be able to) we may take a moment to learn from some often overlooked creatures, in this case, Formica selysi ants.

A group of researchers in Switzerland studied this species of ants’ technique for surviving a flooding event. They found that these ants, which regularly inhabit flood plains in the Alps and the Pyrenees, are well-prepared and ready to act in the event of impending submersion. The ants quickly form a “collective structure” by physically grasping on to one another to create a floating platform and raft to safety when a flood comes. This technique keeps nest-mates together, protects the queen, and ensures the survival of the majority of the colony.

Predictably, the researchers observed  that the ants place their queen towards the center of the rafts, in the most protected position. However, instead of likewise protecting their young, the worker ants use the buoyant properties of the brood by placing them at the bottom of the raft where they act as floatation devices. The young suffer little or no mortality from this placement and serve as vital support for the rest of the colony when incorporated into the raft in this fashion. Check out the ants in action in the video below (and on our Youtube channel).

Although we may not be able to literally grab onto each other and float above the water when threatened with a flood, the principle is what might be important. Lesson learned: be prepared and gather your family and friends close to tackle whatever challenge is approaching together.

 

Citation: Purcell J, Avril A, Jaffuel G, Bates S, Chapuisat M (2014) Ant Brood Function as Life Preservers during Floods. PLoS ONE 9(2): e89211. doi:10.1371/journal.pone.0089211

Image: Figure 1 from doi:10.1371/journal.pone.0089211

 

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PLOS’ New Data Policy: Public Access to Data

UPDATE 7 MARCH: Please see new blog post

UPDATE 26 FEBRUARY : A flurry of interest has arisen around the revised PLOS data policy that we announced in December and which will come into effect for research papers submitted next month. We are gratified to see a huge swell of support for the ideas behind the policy, but we note some concerns about how it will be implemented and how it will affect those preparing articles for publication in PLOS journals. We’d therefore like to clarify a few points that have arisen and once again encourage those with concerns to check the details of the policy or our FAQs, and to contact us with concerns if we have not covered them.

Is the policy about what to share, or about how and where to share it?

There is nothing new in the policy about what types and forms of data should be shared. As we said in December, “PLOS journals have requested data be available since their inception, but we believe that providing more specific instructions for authors regarding appropriate data deposition options, and providing more information in the published article as to how to access data, is important for readers and users of the research we publish.” As we have further clarified, “the Data Policy states the ‘minimal dataset’ consists “of the dataset used to reach the conclusions drawn in the manuscript with related metadata and methods, and any additional data required to replicate the reported study findings in their entirety. This does not mean that authors must submit all data collected as part of the research, but that they must provide the data that are relevant to the specific analysis presented in the paper.” The ‘minimal dataset’ does not mean, for example, all data collected in the course of research, or all raw image files, or early iterations of a simulation or model before the final model was developed. We continue to request that the authors provide the “data underlying the findings described in their manuscript”. Precisely what form those data take will depend on the norms of the field and the requests of reviewers and editors, but the type and format of data being requested will continue to be the type and format PLOS has always required.

What is changing is that authors need to indicate where the data are housed, at the time of submission. We want reviewers, editors and readers to have that information transparently available when they read the article. We strongly encourage deposition in subject area repositories (such as GenBank for sequences, clinicaltrials.gov for clinical trials data, and PDB for structures) where those exist, and in unstructured repositories such as Dryad or FigShare where there is no appropriate subject-domain repository. Some institutions provide appropriate centralized repositories for their researchers’ data; We recognize that for those with small amounts of data, they may be wholly included within the article itself as they are now, and that for some other smaller data types it might be most appropriate to include Supplementary Files with the article – although we would also like to ensure these files are used optimally.

What if my dataset is too large for any of these solutions?

We appreciate that some people now work with datasets that are too large for any of these solutions, and would like to work with them to develop methods of sharing that work in these instances. Authors should submit their manuscripts, noting the details of their situation, and we will work with you to arrive at a solution.

What about human patient data?

Like some other types of data, it is often not ethical or legal to share patient data universally, so we provide guidance on the routes available to authors of such data, and we encourage anyone with concerns of this type to contact the journal they would like to submit to, or the data team at data@plos.org.

Concerns about someone else benefiting from the data

Some raise the concern that, having collected data, they want to be the ones to analyze it and benefit from it. In our view, this sentiment applies to the period before publication. But after publication (in particular, after publication in an Open Access journal) the data should be available for re-use by others. This is not just our view: many institutions and funding agencies (e.g. NIH) now make data sharing a requirement. We understand that some authors will not want to share data, just as some choose not to make their articles available Open Access, but trust that most authors publish their work precisely in order to allow others to benefit from it.

Liz Silva, PLOS ONE
Theo Bloom, PLOS Biology
Emma Ganley, PLOS Biology
Maggie Winker, PLOS Medicine


ORIGINAL POST: Access to research results, immediately and800px-Open_Data_stickers without restriction, has always been at the heart of PLOS’ mission and the wider Open Access movement. However, without similar access to the data underlying the findings, the article can be of limited use. For this reason, PLOS has always required that authors make their data available to other academic researchers who wish to replicate, reanalyze, or build upon the findings published in our journals.

In an effort to increase access to this data, we are now revising our data-sharing policy for all PLOS journals: authors must make all data publicly available, without restriction, immediately upon publication of the article. Beginning March 3rd, 2014, all authors who submit to a PLOS journal will be asked to provide a Data Availability Statement, describing where and how others can access each dataset that underlies the findings. This Data Availability Statement will be published on the first page of each article.

What do we mean by data?

“Data are any and all of the digital materials that are collected and analyzed in the pursuit of scientific advances.” Examples could include spreadsheets of original measurements (of cells, of fluorescent intensity, of respiratory volume), large datasets such as

next-generation sequence reads, verbatim responses from qualitative studies, software code, or even image files used to create figures. Data should be in the form in which it was originally collected, before summarizing, analyzing or reporting.

What do we mean by publicly available?

All data must be in one of three places:

  • the body of the manuscript; this may be appropriate for studies where the dataset is small enough to be presented in a table
  • in the supporting information; this may be appropriate for moderately-sized datasets that can be reported in large tables or as compressed files, which can then be downloaded
  • in a stable, public repository that provides an accession number or digital object identifier (DOI) for each dataset; there are many repositories that specialize in specific data types, and these are particularly suitable for very large datasets

Do we allow any exceptions?

Yes, but only in specific cases. We are aware that it is not ethical to make all datasets fully public, including private patient data, or specific information relating to endangered species. Some authors also obtain data from third parties and therefore do not have the right to make that dataset publicly available. In such cases, authors must state that “Data is available upon request”, and identify the person, group or committee to whom requests should be submitted. The authors themselves should not be the only point of contact for requesting data.

Where can I go for more information?

The revised data sharing policy, along with more information about the issues associated with public availability of data, can be reviewed in full at:

http://www.plos.org/data-access-for-the-open-access-literature-ploss-data-policy/

http://www.plos.org/update-on-plos-data-policy/

Image: Open Data stickers by Jonathan Gray

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It’s a Mad, Mad, Mad, Mad, but Predictable World: Scaling the Patterns of Ancient Urban Growth

cities from sapce

With more than 7.1 billion people living across the globe, cities house more than 50% of the world’s population. The United Nations Population Fund projects that by 2030 more than 5 billion people will live in cities across the world. The Global Heath Observatory, a program run by the World Health Organization, predicts that by 2050, 7 out of 10 people will live in cities, compared to 2 of 10 just 100 years ago.

Recently, researchers developed what is called “urban scaling theory” to mathematically explain how modern cities behave in predictable ways, despite their unprecedented growth. Recent work in urban scaling research considers cities “social reactors”. In other words, the bigger the city, the more people and more opportunity for social interaction.  Think for a moment about the social interactions that occur just on the block outside of your local coffee shop; now multiply those interactions by millions. Cities magnify the number of interactions, increasing both social and economic productivity and, ultimately, encouraging their own growth.

The authors of a recent PLOS ONE paper sought to determine whether ancient cities “behaved” in predictable patterns similar to their modern counterparts. To do so, they developed mathematical models and tested them on archaeological settlements across the Pre-Hispanic Basin of Mexico (BOM, approximated by the red square in the figure below). Based on their findings, they suggest that the principles of settlement organization, which dictate city growth, were very much the same then as they are now, and may be consistent over time.

To test their predictions, the researchers analyzed archaeological data from over 1,500 sites in the BOM, previously surveyed in the 60s and 70s by researchers from the University of Michigan and Penn State.

BOM Location

Using low-altitude aerial photographs and primary survey reports from the original surveyors, the researchers organized the following data from approximately 4,000 sites: the settled area, the average density of potsherds—broken pieces of ceramic material—within it, the count and total surface area of domestic architectural mounds, the settlement type, the estimated population, and the time period.

The researchers were interested in examining areas of the BOM that enabled social interaction between residents, so they excluded site types that did not allow social interaction, for example, isolated ceremonial centers, quarries, and salt mounds. They then grouped the remaining 1,500 sites into both chronological groups and size groups. For chronological grouping, each site was assigned to one of four time periods: the Formative period (1150 B.C.E.–150 B.C.E.), the Classic period (150 B.C.E.–650 C.E.), the Toltec period (650–1200 C.E.), and the Aztec period (1200-1519 C.E.). By the Aztec period, the area had developed from amorphous rural settlements to booming metropolises comprising over 200,000 people.

BOM Population

For site grouping, settlements greater than 5,000 people were categorized differently than smaller settlements. In the figure above, panel B denotes settlements dating to the Formative period (1150 B.C.E.–150 B.C.E.), and panel C, settlements dating to the Aztec period (1200-1519 C.E.).

After separating the data into both chronological groups and size groups, the researchers applied their mathematical models and tested their predictions about urban growth in the settlements of the BOM. One aspect of city development assessed by the researchers was the evolution of defined networks of roads and canals in growing cities. Because roads act as conduits, directly influencing social interaction—much like the roads leading to the aforementioned coffee shop—growing cities develop increasingly defined networks to connect social hubs to one another.

Take, for example, the figure below, which displays both a city in an early stage (panel A) and later (panel B) of growth:

Settlements

Panel A shows the early, or Amorphous Settlement Model, displaying a small settlement easily accessible to the individual via walking, and thus negating the necessity for clearly defined networks of roads. Panel B, on the other hand, shows the Networked Settlement Model, an infrastructure-dense area where networks are clearly defined to accommodate the increased size of the city and density of the residents. Larger cities analyzed by the authors, like Teotihuacan of the Classic period and Tenochtitlán of the Aztec period, epitomize the Networked Settlement Model with its organized network of roads and canals. The findings from the BOM echo the earlier-stated notion that, like their modern counterparts, ancient cities may have acted as “social reactors”, in part by facilitating an increasingly defined network of roads, themselves directly influencing the ability of residents to socially interact.

Scientists use urban scaling theory to show that population and social phenomena follow distinct, mathematical patterns over time. By developing mathematical models to predict measurable changes in city growth, these researchers applied the same patterns to ancient cities and concluded that the development of settlements over time in the BOM seem analogous to those observed in modern cities. Researchers predict that the same mathematical models could be reformatted to estimate population size of ancient cities, as well as to develop measures for calculating socio-economic output like the production of art and public monuments based on the relationship between settlement size and division of labor. Although there is still much to be solved through the equations of urban scaling theory, the consistency of city growth over time has implications for both the past and the present.

Citation: Ortman SG, Cabaniss AHF, Sturm JO, Bettencourt LMA (2014) The Pre-History of Urban Scaling. PLoS ONE 9(2): e87902. doi:10.1371/journal.pone.0087902

Image 1: Auroras Over North America as Seen From Space by the NASA Goddard Space Flight Center

Image 2: doi:10.1371/journal.pone.0087902

Image 3: doi:10.1371/journal.pone.0087902

Image 4: doi:10.1371/journal.pone.0087902

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Ask EveryONE: Corrections

My paper was recently published in PLOS ONE, but I’ve noticed an error. Can it be corrected?

PLOS ONE corrects major errors found in published articles via the addition of a Formal Correction to the paper. Formal Corrections are reserved for errors that significantly affect the understanding or utility of the paper.  In addition to being published on the PLOS ONE website, corrections are also indexed in PubMed Central and PubMed.

When a paper has been corrected, a correction notice will appear in a gray box at the top of the article page.  A CrossMark logo now appears on every PLOS article page and in the downloadable PDF; clicking the logo on a corrected article’s page will bring up a status box showing that the paper has been corrected.

To see the full correction, click the “View correction” link in the gray box.  This will direct you to a page with the full correction details, including any updated figures, tables, or supporting information, along with a PDF version of the correction notice available for download.  An example of a correction notice on the original article is shown below.

corrections image 1

Example of a Formal Correction notice (click to enlarge)

If you notice an error in your published paper, you should contact our corrections team at corrections@plos.org.  Please include the title and DOI of your paper; a description of the problem; and any corrected figures, tables, or supporting information files. PLOS staff will decide whether a Formal Correction is appropriate and will work with you to publish a correction as quickly as possible.

If there is an error in one of your figures, tables, or supporting information files, the corrected items will be included in the Formal Correction. An example of a Formal Correction is shown below.

corrections image2Example of a Formal Correction (click to enlarge)

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Ask EveryONE: Why does my corrected article show up twice in PubMed?

After my paper was published, I discovered an error and contacted PLOS ONE to have it fixed. Now my paper shows up twice in PubMed. Is this a mistake?

If your paper had a formal correction, this is not a mistake; your paper will be listed in PubMed twice.

If a published paper contains a significant error, we publish a Formal Correction to fix that error; the Formal Correction is its own publication and therefore has its own DOI.  The Formal Correction then receives its own, separate entry in PubMed in order to link to the original correction on the PLOS ONE website. The correction’s title will include the word “Correction” followed by the original paper’s title. PubMed mandates that the original and the correction both be entered in its database, as you can see here.

Please note that your corrected paper will show up only once in PMC (PubMed Central), because the correction will be embedded in the PMC entry for the original paper itself.

 

 

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Buzz Me Baby: Unusual Courtship Songs for Valentine’s Day

 We heart the Ostrinia nubilalis

When most people think of Valentine’s Day, images of love, candy, and flowers pop to mind.  However, this Valentine’s Day, we thought we’d share two animals with you that use scales, wings, and other things to create songs that attract that special someone.

Moth Melodies

Male moths use a combination of pheromones and ultrasound—sound with frequencies above the range of human hearing—to woo females. To better understand moth sounds during courtship, researchers in this PLOS ONE study recorded and examined the ultrasounds emitted by three types of grass moths. They found that two of the three moth species had sex-specific wing and thoracic scales that played a role in ultrasound production, and that using these scales increased mating success. This audio clip is the recorded ultrasound of Ostrinia nubilalis (pictured above), aka the European corn borer, slowed down 10 times so that human ears can hear it.

CotesiaWasp Chorus

Cotesia Wasp

Rapid wing fanning is the attraction tool of choice for male wasps when courting females. According to this PLOS ONE study, parasitic wasp wing fanning has been studied before, but the mechanism for how the sound is generated has not.  The researchers characterized the wasp songs and found that they contain a two-part signal with sequences of buzzes and boing sounds. While scientists could characterize  the male courtship songs, how they produce the sound remains a mystery. This audio clip starts with wing fanning, which produces a buzz sound, and is followed by a series of boing sounds.

 


Whether you choose to scale, buzz, or boing to impress your mate with beautiful music, we wish you a Happy Valentine’s Day from PLOS ONE!

 

Citations: 

Takanashi T, Nakano R, Surlykke A, Tatsuta H, Tabata J, et al. (2010) Variation in Courtship Ultrasounds of Three Ostrinia Moths with Different Sex Pheromones. PLoS ONE 5(10): e13144. doi:10.1371/journal.pone.0013144

Bredlau JP, Mohajer YJ, Cameron TM, Kester KM, Fine ML (2013) Characterization and Generation of Male Courtship Song in Cotesia congregata(Hymenoptera: Braconidae). PLoS ONE 8(4): e62051. doi:10.1371/journal.pone.0062051

Image Credits:

Photo a Ostrinia nubilalis by dhobern. Heart added by us.

Dorsal view of one pair of wings of a male Cotesia congregata. Figure 8. doi:10.1371/journal.pone.0062051.g008

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