A stack of papers facedown on a table.

10 publications in 2019!!!

2019 has been a hectic year for my career, but I managed to turn lemons into peer-reviewed lemonade. For the first half of the year, my primary focus was writing and submitting manuscripts on a backlog of work. And it’s paid off, I have had 10 things accepted for publication this year! I don’t expect to repeat this feat, this was the culmination of many projects over the last 5 years which matriculated all at once. But, it feels great to be able to do it once.

Research Articles

Ishaq, S.L., Page, C.M., Yeoman, C.J., Murphy, T.W., Van Emon, M.L., Stewart, W.C. 2019. Zinc amino acid supplementation alters yearling ram rumen bacterial communities but zinc sulfate supplementation does not. Journal of Animal Science 97(2):687–697. Article.

blog post and project page for the zinc paper.


Ishaq, S.L., Lachman, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed.  PLoS ONE 14(6): e0215797. Article.

blog post and project page for the ‘particle size’ paper.


Stenson, J., Ishaq, S.L., Laguerre, A., Loia, A., MacCrone, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E.T., Van Den Wymelenberg, K. 2019. Monitored Indoor Environmental Quality of a Mass Timber Office Building: A Case Study. Buildings 9:142. Article.

Blog post for the buildings paper.


Seipel, T., Ishaq, S.L., Menalled, F.D. 2019. Agroecosystem resilience is modified by management system via plant–soil feedbacks. Basic and Applied Ecology. In press. Article.


Ishaq, S.L., Seipel, T., Yeoman, C.J., Menalled, F.D. 2020. Soil bacterial communities of wheat vary across the growing season and among dryland farming systems. Geoderma 358(15):113989. Article.

Blog post on the soil microbes paper.


Velazquez, S., Bi, C., Kline, J., Nunez, S., Corsi, R., Xu, Y., Ishaq, S.L. 2019. Accumulation of di-2-ethylhexyl phthalate from polyvinyl chloride flooring into settled house dust and the effect on the bacterial community. PeerJ. Accepted, anticipated out in early December

Reviews

Velazquez S., Griffiths W., Dietz L., Horve P., Nunez, S., Hu, J., Shen, J., Fretz, M., Bi, C., Xu, Y., Van Den Wymelenberg, K.G., Hartmann, E.M., Ishaq, S.L. 2019. From one species to another: A review on the interaction of chemistry and microbiology in relation to cleaning in the built environment. Indoor Air 26(6):875-1049. Impact 4.71. Article.


Garcia-Mazcorro, J.F., Ishaq, S.L., Rodriguez-Herrera, M.V., Garcia-Hernandez, C.A., Kawas, J.R., Nagaraja, T.G. 2019. Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. Animal: 1-9. Article.

Blog post for the yeast paper.


Horve, P.F., Lloyd, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCroneG., Van Den Wymelenberg, K., Ishaq, S.L. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology.  Article.

Essays

Ishaq, S.L., Rapp, M., Byerly, R., McClellan, L.S., O’Boyle, M.R., Nykanen, A., Fuller, P.J., Aas, C., Stone, J.M., Killpatrick, S., Uptegrove, M.M., Vischer, A., Wolf, H., Smallman, F., Eymann, H., Narode, S., Stapleton, E., Cioffi, C.C., Tavalire, H.. 2019. Framing the discussion of microorganisms as a facet of social equity in human health. PLoS Biology, Microbiomes Across Systems special issue. Accepted, will be released Nov. 26, 2019 at 2 pm EST

Blog post for the social equity paper.

Five new publications in June! (updated)

Update: on the very last day of June, I received word that two more papers had been accepted for publication, bringing the tally to five in the month of June alone!

I’ve previously discussed how many researchers end up with partially-completed projects in their wake, and I’ve made a concerted effort in the last 6-ish months to get mine across the finish line. I have five new publications which were accepted in June alone, with one reviews and one manuscript currently in review, and another three manuscripts in preparation. On top of that, I have a number of publications that are looming in the second half of 2019.


Ishaq, S.L., Lachman, M.M., Wenner, B.A., Baeza, A., Butler, M., Gates, E., Olivo, S., Buono Geddes, J., Hatfield, P., Yeoman, C.J. 2019. Pelleted-hay alfalfa feed increases sheep wether weight gain and rumen bacterial richness over loose-hay alfalfa feed.  PLoS ONE 14(6): e0215797. Article.

I’ve already done the blog post and project page for the ‘particle size’ paper, so I’ll move on.


Stenson, J., Ishaq, S.L., Laguerre, A., Loia, A., MacCrone, G., Mugabo, I., Northcutt, D., Riggio, M., Barbosa, A., Gall, E.T., Van Den Wymelenberg, K. 2019. Monitored Indoor Environmental Quality of a Mass Timber Office Building: A Case Study. Buildings 9:142. Article.

This was a case study on a newly (at the time of sample collection) constructed building in Portland, OR which was made using mass timber framing. Since building materials alter the sound, vibration, smell, and air quality of a building, the primary goals of the study were to evaluate occupant experience and indoor air quality. Dust samples were also collected to investigate the indoor bacterial community, as the effect of building materials on the whole microbial community indoors is unknown. For this project, I assisted with microbial sample processing and analysis, for which I taught Georgia MacCrone, an undergraduate Biology/Ecology junior at UO, bioinformatics and DNA sequence analysis.


Garcia-Mazcorro, J.F., Ishaq, S.L., Rodriguez-Herrera, M.V., Garcia-Hernandez, C.A., Kawas, J.R., Nagaraja, T.G. 2019. Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits. AnimalAccepted.

This review was a pleasure to work on. Last year, Dr. Jose Garcia-Mazcorro emailed me, as I am the corresponding author on a paper investigating protozoa and fungi in cows with acidosis. We corresponded about fungi in the rumen, probiotics, and diet, and Jose graciously invited me to contribute to the review. Last August, after having worked with Jose for months, we finally met in person in Leipzig, Germany at ISME. Since then, we’ve been discussion possible collaborations on diet, probiotics, and the gut microbiome.


Horve, P.F., Lloyd, S., Mhuireach, G.A., Dietz, L., Fretz, M., MacCrone, G., Van Den Wymelenberg, K., Ishaq, S.L. Building Upon Current Knowledge of Indoor Microbiology to Construct the Next Era of Research into Microorganisms, Health, and the Built Environment. Journal of Exposure Science and Environmental Epidemiology. Accepted.


Seipel, T., Ishaq, S.L., Menalled, F.D. Agroecosystem resilience is modified by management system via plant–soil feedbacks. Basic and Applied Ecology. Accepted.


And as a reminder, I’m a guest editor for the PLoS ” Microbiome Across Biological Systems” special issue call, which is accepting submissions into August!

The Fine Art of Finding Scientific Information

Not a day goes by that I don’t search for information, and whether that information is a movie showtime or the mechanism by which a bacterial species is resistant to zinc toxicity, I need that information to be accurate. In the era of real fake-news and fake real-news, mockumentaries, and misinformation campaigns, the ability to find accurate and unbiased information is more important than ever.

Yet, assessing the validity of information and verifying sources is an under-appreciated and under-taught skill. There are some great resources available for determining the reliability (if the same results are achieved each time), and validity (is it a real effect), of a dataset, as well as of the authors. Even with fact-evaluation resources available through The National Center for Complementary and Integrated Health (NCCIS), The University of EdinburghThe Georgetown University Library, or Michigan State University, like any skill, finding information takes practice.

Where do I go for Science Information?

Thanks to the massive shift towards digital archiving and open-access online journals, nearly all of my information hunting is done online (and an excellent reason why Net Neutrality is vital to researchers). Most of the time, this information is in the form of  scientific journal articles or books online, and finding this information can be accomplished by using regular search engines. In particular, Google has really pushed to improve its ability to index scientific publications (critical to Google Scholar and Paperpile).

However, it takes skill to compose your search request to find accurate results. I nearly always add “journal article” or “scientific study” to the end of my query because I need the original sources of information, not popular media reports on it. This cuts out A LOT of inaccuracy in search results. If I’m looking for more general information, I might add “review” to find scientific papers which broadly summarize the results of dozens to hundreds of smaller studies on a particular topic. If I have no idea where to begin and need basic information on what I’m trying to look for, I will try my luck with a general search online or even Wikipedia (scientists have made a concerted effort to improve many science-related entries). This can help me figure out the right terminology to phrase my question.

How do I know if it’s accurate?

One of the things I’m searching for when looking for accurate sources is peer-review.  Typically, scientific manuscripts submitted to reputable journals are reviewed by 1 – 3 other authorities in that field, more if the paper goes through several journal submissions. The reviewers may know who the authors are, but the authors don’t know their reviewers until at least after publication, and sometimes never. This single-blind (or double-blind if the reviewers can’t see the authors’ names) process allows for manuscripts to be reviewed, edited, and challenged before they are published. Note that perspective or opinion pieces in journals are typically not peer-reviewed, as they don’t contain new data, just interpretation. The demand for rapid publishing rates and the rise of predatory journals has led some outlets to publish without peer-review, and I avoid those sources. The reason is that scientists might not see the flaws or errors in their own study, and having a third party question your results improves your ability to communicate those results accurately.

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Kriegeskorte, 2012

Another way to assess the validity of an article is the inclusion of correct control groups. The control group acts a baseline against which you can measure your treatment effects, those which go through the same experimental parameters except they don’t receive an active treatment. Instead, the group receives a placebo, because you want to make sure that the acts of experimentation and observation themselves do not lead to a reaction – The Placebo Effect. The Placebo Effect is a very real thing and can really throw off your results when working with humans.

Similarly, one study does not a scientific law make. Scientific results can be situational, or particular to the parameters in that study, and might not be generalizable (applicable to a broader audience or circumstances). It often takes dozens if not a hundred studies to get at the underlying mechanisms of an experimental effect, or to show that the effect is reliably recreated across experiments.

Data or it didn’t happen. I can’t stress this one enough. Making a claim, statement, or conclusion is hollow until you have supplied observations to prove it. This a really common problem in internet-based arguments, as people put forth references as fact when they are actually opinionated speeches or videos that don’t list their sources. These opinionated speeches have their place, I post a lot of them myself. They often say what I want to say in a much more eloquent manner. Unfortunately, they are not data and can’t prove your point.

The other reason you need data to match your statements is that in almost all scientific articles, the authors include speculation and theory of thought in the Discussion section. This is meant to provide context to the study, or ponder over the broader meaning, or identify things which need to be verified in future studies. But often these statements are repeated in other articles as if they were facts which were evaluated in the first article, and the ideas get perpetuated as proven facts instead of as theories to be tested. This often happens when the Discussion section of an article is hidden behind a pay wall and you end up taking that second paper’s word for it about what happened in the first paper. It’s only when the claim is traced all the way back to the original article that you find that someone mistook thought supposition for data exposition.

The “Echo Chamber Effect” is also prominent when it comes to translating scientific articles into news publications, a great example of which is discussed by 538. Researchers mapped the genome of about 30 transgender individuals – about half and half of male to female and female to male, to get an idea of whether gender identity could be described with a nuanced genetic fingerprint rather than a binary category. This is an extremely small sample group, and the paper was more about testing the idea and suggesting some genes which would be used for the fingerprint. In the mix-up, comments about the research were attributed to a journalist at 538 – comments that the journalist had not made, and this error was perpetuated when further news organizations used other news publications as the source instead of conducting their own interview or referencing the publication. In addition, the findings and impact of the study were wrongly reported – it was stated that 7 genes had been identified by researchers as your gender fingerprint, which is a gross exaggeration of what the original research article was really about. When possible, try to trace information back to its origin, and get comments straight from the source.

How do I know if it’s unbiased?

This can be tricky, as there are a number of ways someone can have a conflict of interest.  One giveaway is tone, as scientific texts are supposed to remain neutral. You can also check the author affiliations (who they are and what institution they are at), the conflict of interest section, and the disclosure of funding source or acknowledgements sections, all of which are common inclusions on scientific papers. “Following the money” is a particularly good way of determining if there is biased involved, depending on the reputation of the publisher.

When in doubt, try asking a librarian

There are a lot of resources online and in-person to help you find accurate information, and public libraries and databases are free to use!

Figure 7; Guadamillas Gómez, 2017.

 

How is manuscript editing like roulette?

Because you play another round until your number wins!

Manuscript writing seems like it should be a straightforward ordeal. You explain the current body of research on the subject and identify the knowledge gap that your hypothesis fills, explain the rationale and objectives for the study, describe all the methods you used, present the data results, and then interpret them in the discussion. Oh and don’t forget the bibliography. Simple!

Oh contraire. Many manuscripts grow and then end up splitting into two or more, or you add a collaborative project on after the fact using the samples you’ve already collected. Sometimes you just say “let’s test these and see what happens”, and you don’t have a specific hypothesis except for “it could be cool”. Moreover, when you work in a very novel, difficult, unpopular, or boring field, there often isn’t a lot of previous research for you to read up on.  It makes it more challenging to write what should be the easiest section, the Introduction, because you don’t have much background to introduce.  While this does justify your work and the need for more research, it also makes it difficult to plan an experiment because you don’t know what outcomes or problems will crop up, and it can make your interpretation of the data problematic.

Methods: probably the worst section.

Sometimes you end up with more or less data than you planned. And most often, you didn’t just use commercial kit instructionDSCN1272s, you probably had to piece together methods from two to ten different journal articles, many of which were not verbosely described to maintain a sort of proprietary hold on the procedures, until you end up with a heavily-citationed Frankenstein’s monster of a Methods section. Not to mention that you probably had to mess around with procedures to find just the right settings on your equipment, so you have to go back through your lab notebook and try to tease apart what you did months or years ago. My suggestion: write the Methods while you are running the experiment. Whenever you finish a procedure that worked, type it up, especially if you are stuck waiting for something to process or grow anyway.

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In 2015, I worked on the DNA sequencing section of a project that had begun four years earlier when the original animal feeding trials were run, and which had been sequenced nearly a year prior to my taking over the data. Not only did the original Principal Investigator (PI) have trouble digging up the project files from four years ago, but the technician who had sequenced the data was no longer a member of the lab. Between the two, it was very difficult to track down what had been done, and which sequencing file name corresponded to which sheep sample. Even if you think the project will never be published, TAKE GOOD NOTES. Really specific, legible ones, trust me- you’ll thank me later.

 

Results and Discussion: Let’s be honest, the only two sections anyone actually reads.

exopolysaccahride
Exopolysaccharide production (white) prevents colonies from being ctained by red dye in the media.

Results is the easiest section to write, but possibly the most difficult to make appealing and understandable to a general scientific audience. Naturally, you need to know how to properly summarize your data and how to graph it. Seems easy: something about means and standard deviations, liberally sprinkle in some p-values…  But in reality, there are lots of ways to statistically validate or measure something, and most of these are minor variations on each other to accommodate slightly different data or situations. Maybe your data has a bell-curve normal distribution like people’s height in North America; maybe it’s heavily skewed to one side, like my preference for maple-frosted donuts over celery. Or you need an ordination plot that takes non-Euclidean distance samples and graphs their relationship to each other by plotting one point, then rotating the axis and plotting another until you’ve plotted all your points. No matter how sophisticated your presentation techniques, if someone can’t look at your graph and the graph summary out of context and understand what you are measuring, you haven’t done your job well. I’ve heard many scientific authors complain that a reviewer demanded changes to the manuscript because they did not under the results or statistical analysis. That can be frustrating, and sometimes it feels like the reviewer is just being obtuse, but as scientific authors it’s our job to properly explain what we did.

acid production
Acid production from different carbohydrates by Streptococcus gallolyticus shown by a pink color change.

The Discussion section is always my favorite, because now you interpret your results into the context of other findings and speculations- in short, you finally get to tell the story of what is happening and why in a more interesting way.

The rest is just details. The Conflict of Interest section is always very interesting. Here you must disclose any conflicts you have, anything from a funding source that paid for your work and may or may not have had input in the experimental design (sometimes commercial companies will contract researchers to do a specific experiment that they more-or-less designed), or that the commercial lab you sent your samples to be tested at has you on the payroll. The Conflict of Interest is usually blank for studies coming out of academic universities, but it’s a good way to track down researchers who might be biased towards or against something.

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You have an acknowledgements section where you can thank personnel that may have assisted you in some small way, someone who you bounced ideas off of in planning and interpretation, someone who gave you samples to work with free of charge. In my case, I most often thanked the hunters who had dutifully collected a jar of rumen (stomach) contents, and sometimes colon contents, from moose while they were field dressing. Or the numerous undergrads that helped feed my newborn lambs five times a day until they were weaned.

Last but not least, the Bibliography or References Cited. Sounds easy enough. But you’d be surprised how pesky it can be. Different journals often want different formatting for your submission, some want authors lists to look like “Last, First; Last, First”, or maybe “Last, F., Last, F.”, or even “Last F, Last F”. Some want years in parentheses, others don’t. Some want issue number, or the journal name to be abbreviated, or a certain part of the reference to be bolded. Trying to reformat 50-100 references for submission to a different journal can be a nightmare. Luckily, there are plenty of citation managers that will create a digital library for your references, and allow you to search for citations while you are writing. Then, you hit “Insert Bibliography” and it numbers or alphabetizes it, and puts them into the desired format. That is, assuming you had put all the correct bibliographic information in. I like Mendeley because I can import references from my web browser; however, on older PDFs sometimes it can’t pick up the info it needs and you have to do it manually. I’ve gotten some interesting inputs for authors’ names when it gets confused.

Manuscript writing can take months, especially with complicated projects or those with many co-authors, as all co-authors need to approve the final version before it can be submitted. Once submitted, a Journal Editor will send the manuscript out to two or three Journal Reviewers, who are researchers in academia or industry that are in that field of expertise and can opt to volunteer to read and review the article. Nearly always, the authors do not know who the reviewers are, and in many cases the reviewers do not know who the authors are, although it is helpful for reviewers to see the authors’ names. If they have a conflict of interest with the author, such as they  don’t get along personally, they might be married, or they are currently working on another project together (anything that might bias them for or against), the reviewers are supposed to decline to review. Reviewers have two to four weeks, depending on the journal, but some will submit their reviews late. The Editor considers all the reviews and makes their final decision to accept as is, accept with minor revisions, accept with major revisions, decline with major revisions (authors may edit and submit a new manuscript for consideration), or decline.  It takes a few weeks to find reviewers, several more to get the revisions in, and another one or two for the editor to make a decision, so this can take anywhere from six weeks to four months.

Often journals will decline without reviewing if they are not interested in the subject material or feel it is outside the scope of the journal. If you have revisions, some journals request that you submit two new versions of the manuscript- one with the changes highlighted. Additionally, you need to address each reviewer comment by explaining what you did. For spelling mistakes, this is as simple as writing “corrected” after the comment. For more complex things, you need to explain the change along with quoting the new text, or explain why you aren’t changing things. If the Editor and Reviewers do not feel that you made all the changes, they may reject the re-submission or send you more edits. Usually they send you more edits that they didn’t notice the first time.

Eventually, a journal might accept your manuscript, and then you only have to approve the author proofs – unless your figures don’t have 18746_603831005730_3060064_na high enough resolution, and then you need to remake them or figure out how to increase your dpi.  Typically it takes between six months to a year to complete the whole peer-review process, depending on the study results and the journal’s internal process.

While tedious and arduous, the manuscript peer-reviewing procedure works very well. Experts in your field can assess the validity of your work, and experts in related fields can give you an outside perspective, especially when you have gotten used to using a very specific jargon or not completely explaining things. Most importantly, it improves the quality of the writing and presentation, and it maintains a standard of integrity and excellence. By the end of the submission process, you are dizzy and you want to get off the ride. But by the time you get through the next project, or eat a soft pretzel, you’ll be ready to climb back on that carousel horse.