This is a preprint review of An empirical test of the temperature dependence of carrying capacity by Joey Bernhardt, Jennifer M. Sunday, and Mary I. O'Connor. The preprint was originally posted on bioRxiv on October 28, 2017 (DOI: https://doi.org/10.1101/210690).

This is a preprint journal club review of K-Means Method for Clustering Water Quality Status on The Rivers of Banjarmasin by Tien Zubaidah and Nieke Karnaningroem. The preprint was originally posted on INArxiv on December 21, 2017 (link: https://osf.io/g6wkp/). The article is now in review in the ARPN Journal of Engineering and Applied Sciences (submitted December 20, 2017). Original abstract: The surface river water quality in Banjarmasin city tends to decline constantly as the result of direct and indirect waste disposal from various human activities along the river body. This study aimed to determine the vulnerability points against pollution in the rivers of Banjarmasin using clustering techniques with K-means algorithm. The parameters observed include Biological Oxygen Demand (BOD), Chemical Oxygen Demand (COD), Total Suspend Solid (TSS) and Dissolved Oxygen (DO). The data were collected at eight water monitoring stations on various rivers in Banjarmasin city. With the K-means method, four water quality status were clustered. The result showed that 6 stations observed during the period April to October 2016 were categorized into the heavy polluted cluster with major pollution point of sources came from the domestic and industrial activities.

Hello everyone! In this post we will detail our beta testing phase, hopefully clarifying what it means to be a beta tester for PREreview and guiding you on how to best contribute. Thank you for taking the time to help us in our mission to make journal clubs worth any researchers' time!

We are proud to introduce you to the members of our Advisory Committee. These fantastic people have been unofficially supporting us throughout the launch of PREreview, and we are honored that they have agreed to continue their support in a more official fashion. We look forward to building and improving PREreview together.

In our journal club this week, we went a little more experimental and selected a BioRxiv paper yet to be published - it can be found at https://www.biorxiv.org/content/early/2017/07/13/163402 and currently bears the title "Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age".  We were inspired by the eLife Labs article on PREReview to give this a go and hopefully the authors and wider biological community benefit from this interaction.As mentioned above, this was our first attempt at discussing a preprint paper from BioRxiv so we had a few opening questions and general discussion about the concept between the 15 or so members of the journal club.  Our groups (Laurenti and Kent) are based at the WT / MRC Cambridge Stem Cell Institute in Cambridge, UK (https://www.stemcells.cam.ac.uk/) and the opinions and comments found below are a summary of the group discussion rather than the opinion of any single researcher partaking in the journal club.First question:   Was reading this any different than a normal paper?Some people had worried that a pre-publication paper would suffer from major gaps in organisation or presentation and this was not the case here.  Overall, there was not a substantial difference from published papers and people agreed that the structure of the paper was good and the content relatively easy to follow.  That said, one cynical comment was raised, querying whether the peer review process prohibited authors from telling their version of the story (e.g., one interpretation), that might actually diverge from the interpretation of the broader field (i.e., peer review makes the article "less readable" but also "more accurate").  Second question: Would you continue to explore pre-print servers for new content?Resounding "yes" from majority of researchers (many of whom had not heard of preprint servers prior to the discussion)---We then entered the discussion phase and came up with the following "review" based on the discussion:In their manuscript, "Heterogeneous Responses of Hematopoietic Stem Cells to Inflammatory Stimuli are Altered with Age", Mann et al., identify and transcriptionally profile at the single cell level a novel subset of aged cells primed to respond to  inflammatory stimuli.  Overall, the manuscript read very well, had a logical progression and was easily considered to be "publication standard" with respect to these aspects (i.e., it was in better shape from an editing perspective than some manuscripts!).  The data were presented nicely and generally supported the statements in the abstract, but several areas of concern were identified through our discussion and a number of questions arose that might be considered by the authors: Concerns:1) Unknown LT-HSC frequency of cells isolated from aged animals:  LSK SLAM is a well-described phenotype for functional HSCs in young mice (~35-50% functional HSCs), but it remains unknown what the precise frequency of functional HSCs in that phenotype in aged mice would be.  Perhaps the best evidence comes from the de Haan group (http://jem.rupress.org/content/208/13/2691.long) where they studied LSK SLAM 34- EPCR+ cells and showed that there was at least 2-fold less functional activity on a per HSC basis and this arguably is a much more stringent sorting criteria.  Therefore, the cells being isolated as "aged LT-HSCs" in this current manuscript are likely less than 10% functional HSCs, making interpretation of all downstream data difficult to ascribe to "LT-HSCs".  Moreover, the frequency of phenotypic LT-HSCs is highly variable (from 100 to 4300 per million cells), making the number of input mice (n=4) concerning, since they might represent a large proportion of one single mouse (e.g., 100-fold more phenotypic HSCs).  Overall, our discussion group agreed that the data presented re: inflammatory signatures were still interesting - it was just that the claims that it was a functional LT-HSC specific (or myeloid-biased LT-HSC specific) signature were less robust.2) Proportional, not absolute, changes in chimerism:  Figure 1 appears to display the proportion of cells that were T, B, gran, or myeloid without showing the absolute levels of chimerism.  It therefore precludes any reviewer from appropriately determining whether a "myeloid bias"really exists (e.g., an absolute increase in myeloid cell production) or whether it is an absence of lymphoid cell production (lymphoid deficient).  Without differences in the absolute myeloid cell number, it changes the interpretation of the data since both cell types would produce the same number of cells and young myeloid progenitors would be present (but not responding) to the stimulus.3)  in vitro 2h stimulus vs. in vivo effect:  The in vivo effect of a single dose treatment seems to be temporary (Figure 1 B-E), whereas the in vitro effect (from a 2 hr stimulation) is sufficient to change the fate of the aged LT-HSCs that get transplanted.  It remains unclear how the progeny of these LT-HSCs continue to self-renew in a way which creates progeny HSC with the same properties for sustaining long term hematopoiesis.  A few items came up in discussion:  1) Is there selective killing of balanced/lymphoid biased HSCs?  2)Are secondary transplantations "myeloid-biased" as well (e.g., how strong is the continuation of the pattern?)Additional questions arising in discussion:1)  Could the authors speculate on the origin of the HSC expansion?  It has been described by several groups that the HSC subtype balance shifts with age but nobody has clearly addressed whether the lymphoid deficient HSCs that accumulate with age are "old" balanced HSCs that have lost lymphoid potential or an accumulation of "lymphoid deficient (or alpha / My-biased)" HSCs.  2)  Would young HSCs from malignant mouse models (or patient samples) also bear the aged/inflammatory signature?minor items:the mega-biased HSCs were first described by the Jacobsen and Nakauchi groups, not the de Haan and Graf groups as mentioned in discussion.

A preprint review of "Explanation implies causation?" by Myint, Leek, & Jager. Posted on bioRxiv, November 13 2017. doi: 10.1101/218784

Hello! Thank you to all who came to our preprint workshop at UCL 30th October, 2017. We thoroughly enjoyed the discussion and we hope it was useful to you too. Due to the superb note-taking skills of Naomi Penfold, I am able to provide a detailed summary of the event as a refresher for those who came, and as info for those who couldn't make it. If you are interested in hosting your own preprint event and would like some help, please let me know ([email protected]). Enjoy!

Metabolic Interactions Between Dynamic Bacterial Subpopulations  Adam Z Rosenthal, Yutao Qi, Sahand Hormoz, Jin Park, Sophia Hsin-Jung Li, Michael ElowitzVersion reviewed: V1. October 25, 2017. bioRxiv 208686; doi: https://doi.org/10.1101/208686Note: This review incorporates input from attendees to the ITQB Preprint Journal Club on November 9, 2017.Overview:Rosenthal et al. demonstrate that stochastic changes between metabolic gene expression states underlie the population-averaged progression through acetate production to acetoin detoxification during exponential growth of B. subtilis. They show that the probabilities of cells being in the slow-growing, acetate-producing (sucC+) and acetoin-producing (alsS+) states depend upon competence regulators (comK) as well as environmental acetate concentration. The work combines population averaged experiments with single-cell fluorescence snapshot and timelapse microscopy experiments to conclusively prove the claims in the abstract. The work was very interesting for members of our journal club coming from several different fields. We were particularly interested in the the implications of the final gel-pad timelapse experiment and its discussion in the main text—the possibility that competence, toxic-product secretion, and subsequent detoxification could be coupled to give B. subtilis an advantage in a complex environment will be a great problem to investigate in the future.

[Compensatory evolution via cryptic genetic variation: Distinct trajectories to phenotypic and fitness recovery]  [Sudarshan Chari, Christian Marier, Cody Porter, Emmalee Northrop, Alexandra Belinky and Ian Dworkin   , october 10, 2017, version 1, BioRXiv] 

The following notes were taken by Naomi Penfold, eLIFE Innovation Officer, during our session at MozFest 2017. Here is a link to our short slide deck. Welcome everyone! We are excited to see you and we hope you are having a fantastic time at MozFest 2017. Who are we?* Daniela Saderi, neuroscientist at OHSU. I love organising community events, including Science Hack Day Portland. Originally from Sardinia (it's beautiful!)* Samantha Hindle, "post"-postdoc at UCSF, from scarborough, UK. I'm a neuroscientist too.We are ASAPbio ambassadors! We advocate for preprints in the life sciences, and have built PREreview to enable researchers to review preprints in their journal clubs and online.* Naomi Penfold, eLife - I'm here to help Dani and Sam to encourage the adoption of preprints.

In the summer of 2017, we conducted a survey to assess scientists' opinions on the value and potential barriers related to reading and reviewing preprints at journal clubs. In this short article we present and discuss the results of the survey as well as how these results helped us shape our approach at PREreview.

This is a preprint journal club review of "Age-related decline in behavioral discrimination of amplitude modulation frequencies compared to envelope-following responses" by Jesyn Lay, Edward L. Bartlett. The preprint was posted on bioRxiv on Sep 28, 2017 (DOI: http://dx.doi.org/10.1101/193268).Our group reviewed this paper on October 13, 2017 and used the PREreview quick participant worksheet.

The following guidelines and email templates are meant to help you start a PREreview journal club at your institution. The first two email templates are for you to send to your department to invite colleagues to your journal club; the last one is for you to send to the authors to let them know you have reviewed their preprint on PREreview. Please let us know if these materials helped you, or suggest changes by emailing us at [email protected]. Thank you! 

Where you can find preprints:There are various preprint repositories (see below) and also website platforms where you can search all/most of the preprint repositories, including Prepubmed, Publons, The Winnower, and Academic Karma (please let us know at [email protected] or leave a comment on this page if we missed any). You can search the Research Preprint Servers List to find a preprint server in your field.Below is a list of the most common preprint repositories that post findings in the biological sciences:AgriXiv: a preprint repository for agriculture and allied sciencesarXiv q-bio: a preprint repository for quantitative biology operated by the Cornell University Library. This repository includes manuscripts in the following categories: Biomolecules, Cell Behavior, Genomics, Molecular Networks, Neurons and Cognition, Subcellular Processes, Populations and Evolution, Tissues and Organs, Quantitative Methods, and Other Quantitative BiologybioRxiv: a preprint repository for the biological sciences operated by Cold Spring Harbor Laboratory. This repository includes manuscripts in the following areas: Animal behavior and Cognition, Biochemistry, Bioengineering, Bioinformatics, Biophysics, Cancer Biology, Cell Biology, Clinical Trials, Developmental Biology. Ecology, Epidemiology, Evolutionary Biology, Genetics, Genomics, Immunology, Microbiology, Molecular Biology, Neuroscience, Paleontology, Pathology, Pharmacology and Toxicology, Physiology, Plant Biology, Scientific Communication and Education, Synthetic Biology, Systems Biology, and ZoologyOSF PREPRINTS: a preprint server that hosts preprints from a broad range of disciplines, including the Life Sciences, and Medicine and Health Sciences  PeerJ Preprints: a preprint repository for the biology and computer sciencesPreprints.org: a preprint repository that posts manuscripts covering many areas of the biology and biomedical science (and other sciences, arts and humanities), including Behavioral Sciences, Biology, Life Sciences, and Medicine and PharmacologyWellcome Open Research: a preprint repository for research funded by the Wellcome Trust mainly in areas of the biological sciences, population health, applied research, humanities and social scienceINARxiv: the preprint server for Indonesia powered by OSF Preprints hosting preprints from a broad range of disciplines, including the Life Sciences, and Medicine and Health SciencesEarthArXiv: the preprint server for Earth Sciences powered by OSF Preprints

What are preprints?Preprints are complete pieces of scientific work that have not yet undergone editorial peer reviewed. Preprints are often the same manuscripts that are submitted to a journal for peer review, but are stored on freely accessible public servers (repositories) such that they become available to the whole web community within 1-2 days from submission. Usually preprints are posted on preprint repositories (see below) either before or at the same time as submission to a journal. Most journals will accept manuscripts that have previously been submitted to a preprint repository. A list of copyright and self-archiving polices can be found on Wikipedia and SHERPA/RoMEO.

At the top write: Title of the preprint, authors, date of submission, version number, preprint server, and digital object identifier (DOI)Start a new document and invite to your preprint journal club others  who want to collaboratively write the preprint review – they will have to sign up on PREreview to be able to edit. Below are a short list of questions that you can have journal club attendants answer (PREreview short participant worksheet, example here), followed by more detailed guidelines on how to structure a more formal and complete peer review (PREreview peer review, example here). Answering the first set of questions will be faster and still povide useful feedback to the authors. However, if the main purpose of the preprint journal club is to train early-career researchers on how to write a peer review, recommend you write the full review as if you were a reviewer for a journal.  You can use the comments from the first one to construct the preprint peer review. After you are done writing your your PREreview, you can click on "Document" (top left), "Publish" so that your preprint review will be public and will be assigned a DOI that you can use to advertise your review on social media, email to the authors, and post on the comment section on the server that hosts the preprint you chose for your JC. Additionally with a DOI, your preprint review will be citable! If you got this far, GREAT JOB! Thank you for supporting open science and helping science move forward faster!

This is a preprint journal club review of Cortical Representations of Speech in a Multi-talker Auditory Scene by Krishna C Puvvada, Jonathan Z Simon. The preprint was originally posted on bioRxiv on April 10, 2017 (DOI: https://doi.org/10.1101/124750). The authors have responded to this review, and you can find the comments on bioRxiv. The article is now published in The Journal of Neuroscience (DOI: 10.1523/JNEUROSCI.0938-17.2017).  

This is a step-by-step guide on how to create your own Preprint Journal Club on PREreview.