Joint Commitment for Action on Inclusion and Diversity in Publishing: An Interview with Laura Norton and Nicola Nugent of the RSC

Laura Norton and Nicola Nugent of the Royal Society of Chemistry answer Alice Meadows’s questions about the RSC’s Joint Commitment for action on inclusion and diversity in publishing

The post Joint Commitment for Action on Inclusion and Diversity in Publishing: An Interview with Laura Norton and Nicola Nugent of the RSC appeared first on The Scholarly Kitchen.

Author Interview: Sacha Gómez Moñivas on student learning despite COVID-19 confinement


Using prior academic years as a control group, Sacha Gómez Moñivas and a group of fellow teachers and researchers found that despite the confinement caused by COVID-19, the learning habits of students became more continuous and ultimately led to better scores during assessments. Their study “Influence of COVID-19 confinement on students’ performance in higher education” was one of the highest viewed PLOS publications of 2020 with over 150,000 views. Read our interview with Sacha about his team’s initial response to the surprising results, the importance of providing details to replicate a study and the difficulties in collecting data on student learning.

Would you say this study is outside the scope of your normal research? How did you get involved in this study and why do you believe this research is important?

Our main research line since 2015 is related to new learning methodologies. Within this topic, we study in detail distant learning, among others. When the COVID-19 pandemic forced most of the students stay at home and change their learning strategies, we were completely prepared for this scenario because, by that time, we had already developed different tools and methods of distance learning already applied in our subjects.

We were involved in this study by analyzing and comparing the huge amounts of data obtained in previous years in our pilot experiences applying distant learning with the new data obtained during the COVID-19 pandemic. We were following the same research line as before, but in a new scenario.

This research is important because it is related to the Susta​inable Development Goal 4 of UNESCO. More specifically, this research helps us understand the impact of COVID-19 in education and students’ capability to change their learning strategies. It is also important because COVID-19 pandemic has many specific factors that can interact with the previously detected relevant characteristics of distant learning. For example, does student motivation behave in the same way in the pandemic as in a traditional distance learning setting?

I want to send an optimistic message in this case. We have demonstrated that, even in this very difficult situation, students and teachers were able to adapt their strategies in the learning process successfully

Read Sacha’s article

Did you find the results to be generally surprising, or were they relatively in line with your expectations?

Some results were in line with our expectations since, ultimately, distant learning is distant learning. For example, the limited access to technology by the students is a problem that was well-known before. Of course, it also appeared in the COVID-19 confinement. The problems that appear when preparing assessment tools are indeed also present in the pandemic.

There are, however, other elements that appeared and were a huge surprise. For example, the improvement in students’ performance was unbelievable. We spent a lot of time trying to justify it with arguments related to fraudulent behaviors, such as cheating or copying in different forms. For that reason, we discarded many subjects where we considered that we could not fully exclude the possibility of cheating. After that, we still had three subjects where we could be sure that only confinement was related to the increase in students’ performance.

Your Results state that “the new learning methodology is the main reason for the change in students’ performance during the confinement.” How important is it for leadership bodies at institutions and schools to provide teachers with resources to properly implement new teaching practices adapted for less face-to-face interactions?

It is crucial. The first step for a good teaching practice is having a good communication between teachers and students. If that fails, everything fails. In distant learning, teachers should have good multimedia resources and connectivity, at least. If not, it does not matter the amount of material developed by the teacher or how good the teacher is when explaining a lesson. I have seen a lot of very good attempts of developing new and very well-organized online courses that failed at the very beginning due to not having the adequate resources.

I note that you opted to publish a preprint when you initially submitted this paper for review, and that you published your peer review history alongside your PLOS ONE publication. What led you to these decisions and how important is scientific transparency to you?

We believe that scientific advances must follow FATE principles: fairness, accountability, transparency and ethics. Transparency is, actually, a key factor in the scientific method itself. If a scientific result must be replicable, it should include all details about experimental procedures, materials, etc. Obviously, transparency is a must. In the case of scientific publications, the whole peer review history is very important for two reasons. First, it demonstrates that the article followed a rigorous peer review process. Second, it gives valuable information about the questions raised by the reviewers and how they were answered by the authors, which could lead in additional criticism by the readers, which can be also valuable.

Do you think your study could be easily reproduced in other parts of the world by other researchers interested in using your methodologies, or were there specific pre-existing conditions that allowed for this study to take place? How helpful would it be to have data from classrooms in other parts of the world?

The bigger problem is getting data. There are many factors that must be considered. Because of potential cheating by the students when working at home, we had to discard 80% of our data to be sure that this did not influencing in the study. This is the first and maybe more important problem, but there are others. For example, researchers must also take into account the differences between countries in the sense that different countries faced the pandemic with varying levels of confinement. This is important because conclusions should be related to those conditions.

At the very beginning, when we did our study, not many groups had the opportunity to collect and analyze reliable data. Now, there are more and more very interesting studies from many different countries. Soon we will have enough data to get conclusions about the success of different strategies, which will be very helpful for planning distant learning at all levels in the future.

If the general public were to take one lesson from your study, what should that be?

I want to send an optimistic message in this case. We have demonstrated that, even in this very difficult situation, students and teachers were able to adapt their strategies in the learning process successfully. We are going through some very difficult times, but we have been able to adapt and we must have the courage and energy to continue fighting until we overcome this pandemic.

Thank you to Sacha and his research team for their important work and taking the time to answer these questions. Their work was founded by CRUE, CSIC and Banco Santander.

Citation

Gonzalez T, de la Rubia MA, Hincz KP, Comas-Lopez M, Subirats L, Fort S, et al. (2020) Influence of COVID-19 confinement on students’ performance in higher education. PLoS ONE 15(10): e0239490. https://doi.org/10.1371/journal.pone.0239490

The post Author Interview: Sacha Gómez Moñivas on student learning despite COVID-19 confinement appeared first on EveryONE.

Working together to improve the user experience: a conversation with Susan Stearns of the Boston Library Consortium

Working together to improve the user experience: a conversation with Susan Stearns of the Boston Library Consortium

Q. Can you tell us about your background and your current position? A. I’m a librarian by training and worked early in my career in both academic and corporate libraries.  However, the bulk of my career has been spent on the library software vendor side, working for companies such as Faxon Research Services, NorthernLight Technologies,…

Contextualizing the Hobbits

LB1

18,000 years ago, the remote Indonesian island of Flores was home to a population of tiny humans. They stood only about 3.5 feet tall on their large feet, and their skulls housed unusually small brains approximately the size of a grapefruit. The identity of these ‘hobbits’ has been hotly debated for years: Were they modern humans suffering a disease, or a new species, Homo floresiensis?

Biological anthropologist Karen Baab first studied a model of LB1, the only skull recovered from the site, at the American Museum of Natural History in 2005. In a recently published PLOS ONE study, she and other researchers compare this specimen to a range of other modern human and extinct hominin skulls to get closer to settling the identity of Homo floresiensis, or ‘Flores man’.

The origins of ‘Flores man’ have been debated for quite a while now. What are the possible origins that are being discussed, and why the uncertainty?

The primary debate has centered on whether LB1 (and possibly the other individuals found on Flores) represents a new species that descended from an extinct species of the genus Homo or whether it is instead a pathological modern Homo sapiens, i.e the same species as us. If the Flores remains do in fact represent a distinct species, then the next question is whether they descended from Homo erectus, a species that may be our direct ancestor, or an even more primitive species. The latter scenario implies an otherwise undocumented migration out of Africa.

What makes it so hard to settle the argument one way or the other?

One of the difficulties in settling this particular argument is that most studies have focused on one or the other of these ideas and compared the Flores remains to either fossil hominins or to pathological modern humans, each using a different set of features. This makes it challenging to compare the alternative hypotheses side-by-side.

What kind of diseases might have caused modern humans to have features similar to these ‘hobbits’?

The three that have been discussed most prominently (and the three we looked at) are microcephaly, endemic hypothyroidism (“cretinism”) and Laron Syndrome. Microcephaly is not a disease per se, but rather a symptom of many different disorders. It refers to having an abnormally small brain and therefore skull. “Cretins” suffer from a lack of thyroid hormone before and after birth, which leads to stunted growth and possibly a slight decrease in skull size. Laron Syndrome individuals produce growth hormone, but their bodies do not properly recognize it, again leading to stunted growth and other developmental issues.

Only a few specimens of this hominin have been found, and there’s only one known skull, from the specimen named LB1. Are there reasons why these specimens have not been discovered elsewhere?

If Homo floresiensis descended from Homo erectus, then their closest relative lived just “next door” on the nearby island of Java. In this case, the unique features of the Homo floresiensis species probably evolved in the isolated island environment of Flores. If, however, the ancestor was a more primitive species, and Homo floresiensis didn’t branch off from H.erectus, it is possible that they might have migrated earlier than known, and we could still find older sites in mainland Asia containing this ancestral species.

Liang Bua cafe

You compared the morphology of the LB1 skull to many hominin ancestors and modern human populations from around the world. What were some of the most striking similarities and differences?

The LB1 skull is very distinct from the typical modern human’s, as it has a lower,  more elongated silhouette when viewed from the side, , greater width at the rear of the braincase, and a flatter frontal bone (the bone underlying the forehead) with a more pronounced brow ridge. Interestingly, these are some of the same features that distinguish archaic species like Homo erectus from modern humans.

Specimens of Laron Syndrome and “cretin” skulls from modern Homo sapiens presented large, round, globular braincases, which are very different from the smaller, lower and less rounded braincase of LB1. The microcephalic human skulls present a closer comparison to LB1, but still show clear distinctions from LB1 in much the same way that they differ from species like Homo erectus or Homo habilis.

Overall, the LB1 braincase is most similar in its overall shape to small-brained Homo erectus from Eurasia that are 1.8 million years old.

How does this analysis add to, or change, what we knew about Flores man? 

This analysis provides a unique opportunity to evaluate these evolutionary and pathological hypotheses side-by-side based on the same criterion – of cranial shape similarity. The results support a stronger affiliation of LB1 with fossil Homo than with any of the proposed pathologies. This study also offers an improvement over previous assessments of the microcephaly hypothesis by using a more extensive sample that better captures the variability in this disorder.

Do these results conclusively settle the discussion? What other possibilities still exist for the origins of H. floresiensis?

While very little in paleoanthropology is ever “settled,” I do think this study represents an important step forward in terms of putting the pathological hypotheses to rest. The question that remains to be answered definitively is which species of archaic Homo is the most likely ancestor of Homo floresiensisHomo erectus or an earlier and more primitive species of Homo?

Citation: Baab KL, McNulty KP, Harvati K (2013) Homo floresiensis Contextualized: A Geometric Morphometric Comparative Analysis of Fossil and Pathological Human Samples. PLoS ONE 8(7): e69119. doi:10.1371/journal.pone.0069119

Images: Homo floresiensis by Ryan Somma, Cave where the remains of Homo Floresiensis where discovered in 2003, Liang Bua, Flores, Indonesia by Rosino

 

Fixing siRNAs by creating an anti-siRNA

Small pieces of RNA in our cells can act like molecular switches that turn genes off by binding to them. These pieces, called small interfering RNAs (siRNAs) are also used by researchers to design experiments to understand what certain genes do.

Scientists can design siRNA molecules aimed at turning off specific genes they are trying to study. Though such siRNA ‘switches’ can be very useful, they are often non-specific, turning off hundreds of genes that they should not have an effect on. As a result, it is difficult for a biologist to conclude whether an experimentally observed effect is due to turning off the gene they meant to turn off or the hundreds that they didn’t (called “off-target effects”).  Eugen Buehler of the  National Center for Advancing Translational Sciences (NCATS), a new center at the NIH, describes an alternate approach to dealing with these off-target effects of siRNAs in his recent PLOS ONE paper. Read on to find out more about this research:

How did you become interested in improving siRNA experiments?

I’ve been working on siRNAs for about the last five years.  When I would talk to my wife (a cell biologist) about my research, I would go on and on about all the problems created by these non-specific effects. Since she uses siRNAs in her research, she would ask, “Well, what should I do to avoid it?”

I didn’t have an answer.  All the methods I had involved a statistical analysis of a large number of results from high-throughput screens, which look at several thousand genes at once. They couldn’t be applied to experiments that only involved one or a few genes, which is what many researchers do.  It frustrated me not being able to help her, and so this question of what to do about off-target effects in small-scale experiments kept nagging me, until I found an answer.

And what was that answer?

As is often the case, the answer involved looking at the problem a different way.  For years, people have been trying to solve the problem by getting rid of the non-specific effects. There are many ways to do this, but they still have a high incidence of these effects.

So, rather than trying to eliminate the off-target activity, we took the opposite approach. We changed three points (bases 9-11) where an siRNA makes contact with its target, so it couldn’t have the effect it was designed for. In this way, we created the C911 version, an anti-siRNA of sorts, which had all the off-target effects but none of the on-target effects.

So if an siRNA has an effect in a cell that is different from what the C911 version of the same siRNA has, we can conclude that the effect is because it silenced the intended target.

Which figure in the manuscript do you think best summarizes your results?

Definitely Figure 3B. Here, we compare siRNAs that appear to have specific effects but don’t (false positives), with ones that do have a specific action on a target gene. We took ten of each kind and created C911 versions for all twenty.

When we compared the two we found that for the false positives, the siRNA and the anti-siRNA had the same effects (left hand panel). But for the siRNAs which really did have an effect on their target, there was a big difference between the siRNA and its C911 version. As it happened, the C911 controls worked perfectly for all twenty siRNAs we had selected for the experiment.

Where do you hope to go from here?

For a tool as well established as siRNA, it will take a while to change the way we design our experiments.  The first step is for there to be a reasonable alternative, and that is what this paper is meant to supply.  The next is to make that alternative easy to choose.  Part of that will involve getting companies that manufacture siRNAs to eventually make negative controls like this, so that negative controls like C911 can be easily and affordably obtained for any siRNA.

My hope is that someday when a researcher orders an siRNA, they won’t even have to ask; they’ll get a tube with their siRNA and a tube with the appropriate negative control by default.

Read about Nobel-winning research on interfering RNAs, and explore more PLOS ONE research about siRNAs here and here

Citation: Buehler E, Chen Y-C, Martin S (2012) C911: A Bench-Level Control for Sequence Specific siRNA Off-Target Effects. PLoS ONE 7(12): e51942. doi:10.1371/journal.pone.0051942

Image: Target by Ivan McClellan on flickr