A TEXT POST

Invasion of Asian camel crickets in North American houses - Author Interview

Mary Jane Epps - postdoctoral researcher in the Dunn Lab – explores the ecology of insect communities associated with human homes. She is the lead author of “Too big to be noticed: Cryptic invasion of Asian camel crickets in North American houses”, which we published today. Her work shows that non-native camel cricket species have spread into homes across the eastern United States. “The good news is that camel crickets don’t bite or pose any kind of threat to humans”, she says.

We were interested in hearing more about these crickets, so we invited Mary Jane to comment on her research and her experience publishing with us.

PJ: Can you briefly explain the research you published in PeerJ?

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MJE: All of our data were generated with the help of citizen scientists, people who were just interested in learning more about the life around them. Scientists often go to far-off places to do their research, but at the same time we know very little about the life right under our noses. In the case of camel crickets, some of these insects have been long known to inhabit our homes, but we knew relatively little about their biology, especially in these habitats.

With help from the public we were able to sample the crickets living in a wide distribution of human residences. First, we sent out a series of surveys asking people across the country whether or not they had observed camel crickets in their homes, and if they had, to send us pictures or specimens that we could use to identify them. What was our surprise when the vast majority of camel crickets living in homes turned out to be an Asian species known as the greenhouse camel cricket (Diestrammena asynamora) that up to now was mainly known from commercial greenhouses, and not thought to be particularly common. Instead of the better-known native species, the greenhouse camel cricket appears to be far more common in homes, where it can become extremely abundant.

Contributions from participating citizen scientists showed that the greenhouse camel cricket has a broad distribution across at least the eastern half of the US, though it is still unclear whether the cricket has moved west of Colorado. We also conducted a supplemental trapping study in urban yards of volunteers in Raleigh, NC, showing that the greenhouse camel cricket is also present in yards outside, though there is some evidence it may be most abundant close to houses. Interestingly, we also received photographs of what is clearly a second non-native species of Diestrammena from a few residences in the northeastern US—a species living with us in our homes (for who knows how long!) that had never formally been reported in this country.

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Photo: Lauren Nichols, YourWildLife.org


PJ: What surprised you the most with these results?

MJE: I was amazed to find how common the greenhouse camel cricket is, a species that had always been thought of as fairly obscure and infrequent. Here was this little-known species hiding in plain sight all around us, sometimes in huge numbers, and scientists had no idea! I was also very excited to discover living in our homes a second species of camel cricket that was previously unknown from this country outside of a few anecdotal reports.

PJ: What kinds of lessons do you hope the public takes away from the research?

MJE: I would love for this study (the brunt of which was really done by the public) to inspire people about their ability to make real contributions to science. We still know so little about the world around us, even many of the things that are right under our noses! I think many non-scientists tend to assume that we already know a lot more than we really do about the natural world; but the wonderful, exciting fact is that that world is so vast we’ve really only scratched the surface!

PJ: Where do you hope to go from here?

MJE: I would love to learn more about the relative distributions and abundances of native versus nonnative camel crickets outside the home. Is the greenhouse camel cricket exclusively associated with human-rendered habitats, or can it also hold its own in wilder habitats? Also, we really don’t know the extent to which the nonnative camel crickets are competing with native species, either indoors or in outside habitats; despite its abundance we have no idea if the greenhouse camel cricket poses any conservation threat or if it is just a harmless hitchhiker in our homes.

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Photo: Lauren Nichols, YourWildLife.org

PJ: Why did you choose to reproduce the complete peer-review history of your article?

MJE: Because our study was based almost entirely on citizen-scientist contributions, my collaborators and I felt strongly that we wanted to make the process as transparent as possible to the public.

PJ: What persuaded you to submit to us?

MJE: Because the public made such an important contribution to this research, we felt it was important to publish our work in an open-access journal, and PeerJ seemed like a good fit.

PJ: How would you describe your experience of our submission/review process?

MJE: Fantastic. Submitting to PeerJ was a very smooth process, with helpful staff and a remarkably quick turnaround at all stages.

PJ: In conclusion, how would you describe PeerJ in three words?

MJE: Smooth, user-friendly, and efficient.

PJ: Many thanks for your time!

We encourage you to check out some of our other Entomology PeerJ publications. Join Mary Jane Epps and thousands of other satisfied PeerJ authors - send your next article to PeerJ!

A TEXT POST

Insect fossils in the Late Jurassic lagoon of France - Interview with an Author

During the course of two field expeditions in 2012 and 2013, French researchers working with the help of two active teams of amateur scientists (Société des Naturalistes et Archéologues de l’Ain and the Group ‘Sympetrum Recherche et Protection des Libellules’) discovered the first Upper Jurassic insects from the Orbagnoux outcrop, together with traces of activities of these organisms on leaves and in the sediment. The newly discovered insect was described today, in PeerJ.

We were interested in learning more about this work, so we invited the first author, André Nel, to comment on his research and his experience publishing with us.

imagePJ: Can you tell us a bit about yourself?

AN: I am a Professor at the Muséum national d’Histoire naturelle in Paris, France. I study fossil insects, and I’ve been working on this subject since 1980.

PJ: Can you briefly explain the research you published in PeerJ

AN: We worked on the marine limestone in the area around Orbagnoux (France) and recorded the first Upper Jurassic insects and the traces of their activities. Although such fossils are well known in Siberia, China, and Germany, none had been identified in our country until now.

PJ: Do you have any anecdotes about this research?

AN: This area of the French Alps was well known for their fish and plant fossils, but no one had ever looked for insects around there. A friend of mine (Claire Griot) lives there, but I never had the opportunity to go and visit the site. She contacted me three years ago and invited me to explore the site, just in case there would be something. So this is really thanks to her that this discovery happened! It’s also through the great help of the very active local naturalists and citizen scientists in the field that we found this new material.

PJ: What surprised you the most with these results?

AN: To be honest, I didn’t believe we would find something on site! Not a single insect fossil has been recorded in this area since the first paleontological investigations in the 19th century!

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Fossilized aquatic bug from the Orbagnoux outcrop of the Rhone valley: Gallomesovelia grioti (scale bar 1 mm) - Photo:André Nel


PJ: What kinds of lessons do you hope the public takes away from the research?

AN: A collaboration between scientific researchers and citizen scientists is an asset, and it helps towards finding extraordinary new data for science.

PJ: Where do you hope to go from here?

AN: We want to look for new material! Earlier this year, we went back to Orbagnoux and we found a new type of insect activity on plant fossils (and maybe new insects that we are currently studying).

PJ: If you had unlimited resources, what study would you run?

AN: There are many outcrops that are not well studied due to the lack of resources. I would hire a highly motivated research assistant, and I would encourage the search for fossil insects in France. Palaeoentomology is not an expensive science, and it can give quite important new data on the evolution of continents and life, as insects constitute about 60-70% of the world biodiversity.

PJ: Why did you choose to reproduce the complete peer-review history of your article?

AN: I am convinced that this manuscript is the result of an active interaction between citizen scientists, scientific researchers, and reviewers. We wanted to make the review process as transparent as possible, so everybody could have access to it.

PJ: How did you first hear about PeerJ, and what persuaded you to submit to us?

AN: A colleague in our lab, Philippe Grandcolas, is an Academic Editor for PeerJ and highly recommended us to submit our manuscript to PeerJ.

PJ: How would you describe your experience of our submission/review process?

AN: The process was quick and friendly.

PJ: In conclusion, how would you describe PeerJ in three words?

AN: Active promising journal

PJ: Many thanks for your time!

If you also like bigger fossils, check out some of our Paleontology publications in PeerJ. We have thousands of highly satisfied authors. If you would like to experience the PeerJ process for yourself, then submit your next article to us!

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Author Interview with Alex Clark

Two weeks ago, we published “Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation”. In this study, Alex Clark and his colleagues describe a hybrid machine learning / interactive method for marking up bioassay data. Alex shared his “very positive experience” of submitting to us on his blog so we got in touch with him, as we wanted to hear more about his work.

PJ: Can you tell us a bit about yourself?

imageAC: I grew up in New Zealand, and migrated abroad as scientists tend to do, living in the United States initially before settling in Canada. As a kid, I became fascinated with computer programming, but quickly realized that I did not want to make that my only profession, and so went to university and eventually ended up with a doctorate in chemistry in 1999. Pursuing a career that involves equal parts science and software engineering has been quite the balancing act, and in 2010 entrepreneur was added to my list of day jobs when I founded Molecular Materials Informatics, Inc., which is dedicated to helping bring chemical informatics into the modern software era. The most visible products to date are a variety of chemistry themed mobile apps for Apple iOS and Google Android devices, though there are a number of advanced original algorithms keeping things moving under the hood.

While many of the projects that I work on are exclusive to my own company, about half of them are collaborative in nature, involving joint efforts with individuals and companies, such as Collaborative Drug Discovery, Inc.

PJ: Can you briefly explain the research you published in PeerJ?

AC: The research addresses the fact that when scientists setup a new screening experiment for testing small molecules for bioactivity, they document the details using plain scientific English text. This is a problem for informaticians, who would like to create software capable of analyzing activity measurements, which is rate limited by the inability of a computer to determine whether two screening configurations are measuring the same thing. The solution is to express the experiments using semantic markup, where the important properties such as disease target, cell line, protein, measurement type, reference controls, etc., are annotated using a consistent scheme.

Past efforts to solve this problem have mainly focused on either fully automated parsing of text, or completely manual user-operated markup. Unfortunately the former tends to have an unacceptable error rate, while the latter consumes far too much of a scientist’s time. We built a proof of concept software tool that splits the difference between the two extremes: taking the best of automated text-to-markup machine learning in order to get the right answer most of the time, while keeping the user in the loop to confirm when the automated assignments are correct, and step in and intervene when they are not. In this way scientists can make their experiment descriptions useful to informatics software with just a few minutes of their time per experiment - a burden which decreases as more annotations are collected, which improves the quality of the training sets.

PJ: Do you have any anecdotes about this research?

AC: Once we built the initial prototype and had it working well in our hands, we demonstrated it to a number of colleagues in the industry. One of the many things we learned is that recognition of the problem is widespread: it seems like every organization that has collected a significant number of textual assay descriptions is well aware of the limitations, and many have already looked into trying to find a solution. I’m accustomed to having to provide a reasonably thorough introduction to why a problem is important and why current solutions are not as good as they could be, but in this case that part was pretty much taken as given.

PJ: What surprised you the most with these results?

AC: First of all that the first approach I tried worked well (black box natural language processing followed by Bayesian analysis). And secondly as I mentioned before, that explaining the need for this research was relatively easy due to high awareness of the importance of the problem and that it remains largely unsolved.

PJ: What kinds of lessons do you hope the public takes away from the research?

AC: That writing up an experiment in human readable text is only the first half of the exercise. To be fully useful, documentation has to be processed into a form that computers can use for precise searching, categorization and large-scale decision support informatics. If your data remains as words and arbitrary diagrams, it will remain just an isolated data point that will only ever be read by a handful of other humans. If it is machine readable, it will be able to influence every relevant scientific decision that follows. The research seeks to demonstrate that by balancing the best of natural language processing and the best of user interface design, it is possible to reduce the amount of time a scientist needs to invest in this process to a nominal commitment that is quickly paid back in terms of new capabilities.

PJ: Where do you hope to go from here?

AC: We intend to upgrade the prototype into a modular web interface that can be plugged into a number of data entry systems, starting with CDD Vault. As users annotate more bioassay descriptions with semantic terminology, the training set will continue to improve. As domain coverage increases, the likelihood that an assay can be marked up very quickly increases, i.e. the user just approves all the predicted annotations, rather than having to hunt through and dig them out. As the data grows, the capabilities that we can built on top of it grow too: being able to search for assay properties, or compare assays for similarity, are immediate examples, but there are larger scale options too: once the marked up data becomes prevalent, analysis software can observe trends over the entire domain of drug discovery, revealing trends that might have otherwise been very difficult to spot.

PJ: If you had unlimited resources, what study would you run?

AC: First of all, I would hire enough expert professionals to painstakingly annotate every biological assay ever written down, and thus create an exhaustive training set. Then I would commission every creator of data entry software for biological content to make use of the annotation interface, so that all lab notebook software would provide scientists with the opportunity to conveniently describe their bioassays in a machine-friendly format.

PJ: Why did you choose to reproduce the complete peer-review history of your article?

AC: The reviews were thoughtful and constructive, and I saw no reason to keep them private. And since the first reviewer had taken the first step and made her identity known to us, it only seemed fair.

PJ: How did you first hear about PeerJ, and what persuaded you to submit to us?

AC: I heard about it before it went live, on a blog or a tweet, I forget which. The PeerJ decision was a combination of moral and financial reasons: I am personally a gigantic fan of open access scientific literature, since the peer review process is essentially an exercise in crowd sourcing, and the whole point of science is to be open. Unfortunately the current breed of scientific publishers has carried over its legacy cost structure from the dead-tree era, which means that scientists have a choice between reader-pays and author-pays, and the fees involved can be prohibitive to many. That system works fine if everyone who is involved in creating or consuming science is rolling around in excess grant money, but that certainly does not describe all of us. PeerJ could be summed up as bringing the lean startup technology movement to scientific publishing. In my opinion it’s not a moment too soon, and I welcome the opportunity to play a small part.
 
PJ: Do you have any anecdotes about your overall experience with us? Anything surprising?

AC: In context it is not surprising, but the responsiveness of the staff took some getting used to: having an email conversation with an identifiable person on the other end is unusual for scientific publishing. I tend to expect to receive automated messages from noreply@bigpublisher.com whenever I have an inquiry. The manuscript submission process gave me the overall impression that the journal was a partner with an interest in making this happen smoothly, rather than a system that is rather indifferent about my contribution.

PJ: How would you describe your experience of our submission/review process?

AC: The website for receiving submissions is very well designed. Given that it is quite detailed, it is no surprise that there are one or two ambiguities, but as long as the staff keep paying attention and iterating, I am optimistic that the design will reduce a significant amount of manual labour for both the authors and publishers. Also, the peer review was done very promptly, and no less thoroughly for its quick turnaround.

PJ: Did you get any comments from your colleagues about your publication with PeerJ?

AC: Just the usual congratulatory encouragement, but it’s early days yet.

PJ: Would you submit again, and would you recommend that your colleagues submit?

AC: I would ideally like to make PeerJ my go-to journal, but there are no categories for chemistry or cheminformatics, which means I can only use it when I occasionally venture out into bioinformatics. I look forward to the day when PeerJ branches out in the direction of chemistry, and/or when other publishing startups recognize that the PeerJ business model is successful and rush to fill all of the other vacant niches.

PJ: Anything else you would like to talk about?

AC: I wish the company every success. In terms of the bigger picture, it’s really important that PeerJ can successfully demonstrate that its lean business model works, because the contemporary journal fee structures are keeping authors and readers out of science. This is indefensible in the information age, but somebody has to step up and show that there is a better way.

PJ: In conclusion, how would you describe PeerJ in three words?

AC: Disrupting scientific publishing.

PJ: Many thanks for your time!

AC: My pleasure.

We encourage you to check out some of our Computational Science publications in PeerJ. Join Alex Clark and thousands of other satisfied authors, and submit your next article to PeerJ.

A TEXT POST

'I study how crabs sniff' - Author Interview

Yesterday we published the work of Lindsay Waldrop and her colleagues in which they modeled how the performance of the hermit crab’s antennae might change as they both grow and transition from water to air. We invited Lindsay to comment on her research and her experience publishing with us.

PJ: Can you tell us a bit about yourself?

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LW: I am a postdoctoral research associate with Prof. Laura Miller at the University of North Carolina at Chapel Hill in the Departments of Biology and Mathematics.  I did my graduate work at the University of California, Berkeley with Prof. Mimi Koehl in the Department of Integrative Biology.

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PJ: Can you explain the research you published in PeerJ?

LW: This work is an extension of my dissertation research on how crabs capture odors from their fluid environments. I studied both marine crabs and terrestrial hermit crabs and found that they use different ways of capturing odors. Marine crabs use a very dense tuft of chemosensory hairs on their first antennae to capture and hold a discrete sample of water close to these hairs; it’s important for them to hold this sample because it gives time for odor molecules to diffuse to the surfaces of the hairs so that they can interact with sensory dendrites.  But for terrestrial hermit crabs in air, the diffusion of odor molecules is so much faster in air that they don’t need to hold on to a sample the way marine crabs do, which has likely caused a shift in the morphology of the hairs themselves.
The way fluid interacts with a structure depends a lot on how big the structure is, how fast it moves, and the properties of the fluid it’s in. So the scaling of a structure like a chemosensory hair during growth that operates in water is a big deal. Size changes that crabs experience between when they settle as juveniles (~4 mm in body length) to their adult size (~30-40 mm in body length) could drastically change the way their antennae interact with the odor-containing fluid. We know that marine crabs scale their antennae allometrically – that is the antennae of small juveniles are relatively much bigger than the antennae of adults. This helps them continue to capture odor samples when they are small. But since terrestrial hermit crabs have antennae that capture odors in air and a different odor-capture mechanism, it was unclear how being small would impact a juvenile hermit crab’s ability to capture odor molecules. Our study looks at how the antennae of juvenile hermit crabs scale and uses a simple odor-capture model to determine how the scaling impacts odor capture.

PJ: Do you have any anecdotes about this research?

LW: [spoiler alert: gross but funny] I collected the animals used in the study from a very tiny island off the coast of Moorea, French Polynesia. I went out at night (because that is when the large hermit crabs are the most active) with a few other scientists who were collecting other animals, one of whom was collecting moths with a very bright headlamp. His light accidentally flashed me in the eyes, which triggered the very first migraine headache I ever had, not a very fun experience. I threw up as a result, and tried to sit in the dark without moving so that my head would hurt less. As my eyes adjusted to the dark, I looked down and saw tiny things start to cluster around my vomit. They were the hermit crabs that I was there to collect, and they were quite happily munching away on my former dinner. So I can add human vomit to the list of food sources for terrestrial hermit crabs, along with detritus, rotting plant matter, dead animals, and human excrement!

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Terrestrial hermit crabs. Photo: Lindsay Waldrop

PJ: What kinds of lessons do you hope the public takes away from the research?

LW: When someone asks me what I study, I say “I study how crabs sniff!” which almost always makes someone smile and think. They have often never heard of such a crazy thing – sniffing crabs! – much less that someone has studied it for years. It’s often the first time they have really considered what it must be like to be a crab, what sort of challenges a crab has to face in daily life and how they could go about it all. I hope that public takes away that if you stop and look closely at nature, to consider how plants and animals do all the amazing things they do just to survive, and that they will always find something brilliant that will make them smile!

PJ: Where do you hope to go from here?

LW: Our mathematical model of odor capture in the paper is extremely simple but it gave us some interested trends to investigate with a better model. I’m currently working with a mathematician to take a more realistic antennae geometry, based on the antennae morphology reported in the paper, and solve advection-diffusion equations to get a more accurate idea of how odor capture varies during growth. With a more accurate model, we hope to validate some of the trends that the simple model produced.

PJ: Why did you choose to reproduce the complete peer-review history of your article?

LW: I chose to release my peer-review history because first and foremost, I think the history shows how the paper has progressed to something that we’re really proud of. Our reviewers were very thorough and took us to task over the weaknesses of the odor-capture model and the interpretation of our results, but did it in ways that were deeply constructive and helpful. In the end, the finished paper is far higher quality than the preprint, and for that, I have my reviewers and the academic editor to thank.

Second, I think it’s a great example for people to see how the process of peer review really works. It’s a term that’s thrown around a lot, but I think the public has very little understanding of what it’s like to go through the process as a researcher. This is a very concrete example that I can point to when I teach students about constructive peer-review or when an interested layperson wants to know what the phrase really means. I really think this is a great example of how peer review ought to work.

PJ: How did you first hear about PeerJ, and what persuaded you to submit to us?

LW: I heard about PeerJ from colleagues on Twitter, where you seem to be very active! I am a strong proponent of open access research and wanted to be part of the movement to publish in journals where that was an option. However, I did my graduate work without a big grant, I funded it entirely with small grants pieced together, so I didn’t have the budget to pay the thousands of dollars in fees for open access. PeerJ allows me, as a former graduate student who independently funded their research, to publish open access. 
In addition to that, your wonderful policy on waiving fees for undergraduate researchers really helped out. My two coauthors, Roxanne Bantay and Quang Nguyen, where both undergrads at UC Berkeley that help through the Undergraduate Research Apprenticeship Program to conduct the research. They did a brilliant job, and I was delighted that I could include them as authors on the paper for free to recognize their contribution to the work. I will continue to have an active undergraduate research program, so I anticipate sending more papers with undergrad authors your way in the future.

PJ: How would you describe your experience of our submission/review process?

LW: I enjoyed my experience published with PeerJ. The staff are very friendly and work quickly. The academic editor and reviewers were extremely constructive and professional. I was genuinely shocked by how fast I received a first decision on my manuscript. As an early career scientist, it is critical for me to get papers out in a timely manner, so the fact that the turn-around was so fast is a huge plus!

PJ: Would you submit again, and would you recommend that your colleagues submit?

LW: I will absolutely submit to PeerJ again, and I have already recommended to colleagues, particularly those with active undergraduate research programs, to submit as well.

PJ: In conclusion, how would you describe PeerJ in three words?

LW: Fast, Open, and Affordable!

PJ: Many thanks for your time!

Join Lindsay Waldrop and thousands of other satisfied authors, and submit your next article to PeerJ.

A TEXT POST

DNA sequencing in the middle of the Pacific Ocean – Video



A group of researchers including scientists at San Diego State University overcame equipment failure, space constraints and shark-infested waters to do real-time DNA sequencing in a remote field location. Check out this video to find out how they did it!

Today we published the article in which they describe the sequencing and informatics pipelines established during the 2013 Line Islands research expedition, release the data generated during the expedition, and discuss some of the unexpected challenges in remote sequencing.