Abstract.Relatively unstructured expression of some preliminary thoughts about how a priori explanatory models of dynamic complex systems might be constructed outside of a canonical approach.Body.A canonical approach consists of inference that strictly follows from precisely defined concepts, or spatio-temporal maps, the variation from which is some kind of confounding error to form a new hypothesis. If precision, whether of a concept, or a mathematical relation, is not retained from one state of a system to another, then the canonical approach does not capture what is relevant (if there is a sense in which a system incorporates a model of itself, so there is some kind of repetition or homeostasis that can't be explained through a continuous model).What might questions associated with a non-canonical approach be?Defining where an analogue representation of a system within itself is possible (different dependencies of variables tending to be separable).If there is no possibility that these are separable, and an analogue representation of a system within itself cannot occur, then a system of coded representation would be necessary for a system to maintain these characteristics of homeostasis or repetition.As such, if a coded representation of a system are necessary within the system this may be explained by a mathematical model which answers the question of when differing dependencies of variables are separable.The inferential relation between parameters affecting the model may provide a guide for which principal components to look for in the data from such a system (this guide being a mathematical rather than a conceptual heuristic)

It is our great pleasure to welcome you to NRM18 - ‘Mapping Neuroreceptors at Work’. The meeting, established by Prof Albert Gjedde in 1997, represents a vibrant community of in vivo brain researchers deciphering the mysteries of the living human brain: exploring how CNS molecule - protein recognition makes us human – for better or for worse – in sickness and in health. This year’s meeting is no exception and brings together delegates from around the globe to discuss the latest advances and controversies in this constantly evolving field. A record-breaking number of attendees (ca. 300) will be joining the 2018 meeting at KCL Waterloo Campus in central London.In addition to keynote talks on ‘The Neurobiology of Beauty’ (Prof. Semir Zeki) and ‘Of Psychotic Mice and Men’ (Prof. Oliver Howes), the programme includes an impressive collection of the latest scientific research in the field, scheduled as oral and poster presentations. In order to maximise exposure of the submitted abstracts, we have also implemented two ‘rapid-fire’ sessions during the meeting. Other programme additions include the NRM18 ‘Grand Challenge’, a session on ‘Opportunities and Challenges for Total Body Imaging’ and a status update on the ‘Data Sharing Initiative’.In addition to enjoying an excellent scientific program, the conference dinner and entertainment on Wednesday will be held aboard the ‘Dixie Bell’ for a cruise along the river Thames, details of which will be provided during the meeting.The organization of NRM18 would not have been possible without the dedicated efforts of many individuals, including the local organising committee and administration, scientific advisory board, reviewers, session chairs, presenters, sponsors, exhibitors and supporters for their invaluable contribution to the conference. Most importantly we would like to thank YOU, the delegates, who never fail to provide lively scientific (and non-scientific) debate during the meeting. We hope you have a stimulating and enjoyable NRM18.Book of abstracts: https://authorea.com/users/242183/articles/323425/master/file/Book_of_abstracts_NRM.pdf

In this experiment we will find that the wavelength of light from a laser can be measured fairly well with the clever use of a ruler. This is a fine way to introduce more advanced forms of error propagation, as well as some introductory statistical analysis tools, to students in an upper division physics lab who are looking to understand the appropriate ways to interpret and report data. The evaluation methods used come directly from John R. Taylor's "An Introduction to Error Analysis" 

ABSTRACT Preferential trade agreements are meant to promote trade within the targeted region. Once such agreements are put into effect, it is interesting to investigate the impact and effectiveness in the targeted region. This paper analyzes world trade network as a graph and introduces the measure to evaluate a change in strength or degree of regional integration. The measure or index introduced also captures the contribution of member countries in the regional integration. INTRODUCTION The Number of preferential trade agreements has been increasing since the 1990s and has increased more than four-fold . Do preferential trade agreements foster trade between the member countries? This question has been as important today as it was when such agreements were formed. This paper analyzes world trade network data to answer this question. The main aim of such agreements is to foster mutual trade in the region and they are considered helpful for promoting the regional economic competitiveness as well. Whereas the impact of such agreements is not homogeneous across countries, the impact is large for industrialized nations and small for developing nations. Several measures of regional integration are devised and found in the literature . Intra-regional trade share ( Si ) measures the ratio of regions i intra-regional trade to total trade . Intraregional Trade Share, Intraregional Trade Intensity Index, and Regional Trade Introversion Index measure the degree of trade interdependence in a certain region . This paper analyze Regional Trade Integration Index and introduce an index, which measures the individual contribution of member countries in the given region. METHODOLOGY This paper introduces an index to study regional trade integration and examines trade data before and after the formation of such agreements. Collection of countries around the world and their trade relationship is represented by graph G(W, E) . W represents a set of all countries and E represents a set of all directed edges or all possible exports. Let eij represents the amount of export from country i to j country. REGIONAL TRADE INTEGRATION INDEX (RTII): This index is the ratio of the sum of exports of all member nations within the region to the sum of export of member nations outside the region. The index range from 0 to 1. Index 0 indicates the member countries do not export within region index 1 indicates the members in a group export everything to other group members. Let g(W′, E′) be a subgraph of G(W, E) and W′ ⊆ W and E′ ⊆ E. In real world, graph G(W, E) all countries in the world and their export relationship. And, subgraph g(W′, E′) represent some preferential trade agreements e.g. NAFTA. Regional Trade Integration Index (RTII) for subgraph g is calculated as Ig. $$I_g=}}e_{ij}}} {}e_{ij}}$$ Individual contribution to the regional integration is computed as Individual Contribution Index (ICI) $$ICI_g^{i}=}e_{ij}}} {}e_{ij}}$$ Where, ICIgi is the ICI for a country i in subgraph g. The weighted sum of Individual Contribution Index is equal to Regional Trade Integration Index . $$I_g = \sum}ICI_g^{i}$$ INDIVIDUAL TRADE INTEGRATION INDEX (ITII): The index indicates how integrated a country is in a certain or group. The index compares the country’s export within the region to export outside the region. Or, the index calculates the ratio of the sum of the export of a country to all another member country in a region to the sum of export of the country to all nations around the globe. This index range from 0 to 1. Integration index 0 indicates the country export within the region is 0 or the country doesn’t export at all to the member countries in the region. Integration index 1 indicates the country’s whole export is within the region and exports nothing outside the region. This paper introduces an integration index Igi, which represents the integration of a country i in some region g or trade agreement or subgraph is given by $$I^{i}_{g} = }{e_{ij}}}{\sum{e_{ij}}}$$ DISCUSSION This paper analyzes and investigates the trend of regional integration for regional trade agreements NAFTA. The ITII of a country with respect to a particular region indicates the country’s contribution to regional integration and RTII represents a ratio of the region’s export within the same region to export to all other countries. Figure [109874] shows RTII for the NAFTA region and the ITII for all countries in the that region. The figure shows RTII for the NAFTA region is almost at the same level in 1990 and 2016 with some fluctuations in between. RTII shown by the red solid line in the figure indicates, the percentage of trade export that NAFTA does within the region compared to all around the world. The RTII trend indicates gradual increment from the inception of NAFTA to downward trend particularly during the global financial slowdowns around the year 2008. The RTII was 0.430114 when the group was formed and reached up to 0.576939 in 2002, then decreased to 0.487429 in 2009, eventually follows an increasing trend after the financial crisis of 2008. Downward trend before 2008 and the upward trend after 1999 is noticeable. If we look at the individual countries ITII, Mexico’s the ITII index is highest among the three countries followed by Canada and the USA. Notably, the ITII is moving parallel for three nations.

En esta tarea se abordan problemas relacionados con los temas: vectores, momento de una fuerza y teorema de Varignon.

Popular culture has traditionally tended to paint a skewed image of the average marijuana user. The typical cannabis consumer – we've been led to believe by media imagery – is invariably a lazy, unmotivated millennial, often black, and typically living paycheck-to-paycheck. As cannabis becomes legalized and regulated across the nation, along with the implementation of seed-to-sale systems that track some consumer behavior at the point-of–sale, more information has become available to shed light on cannabis consumer behavior to help lawmakers and businesses make better informed decisions. What is so far resulting is a portrait of the cannabis industry retail landscape looking an awful lot like the same as the landscape for other retail generally.

This is a review of Carter, Helm et al. bioRxiv 374264; doi: https://doi.org/10.1101/374264 posted on July 23, 2018. In this paper, the authors showed that diverse barley cultivars are able to respond to the Pseudomonas syringae effector AvrPphB and they characterized  both the effector target (PBS1) and the receptor (PBR1) responsible for this recognition. Furthermore, their phylogenetic analyses revealed that the immune receptor involved in this response is not orthologous to a previously characterized receptor (RPS5) from Arabidopsis thaliana that has a functionally analogous AvrPphB recognition mechanism. This leads the authors to conclude that recognition of the AvrPphB protease has evolved independently in Arabidopsis and barley.

Hello, and welcome to Authorea!👋  We're happy to have you join us on this journey towards making writing and publishing smoother, data-driven, interactive, open, and simply awesome. This document is a short guide on how to get started with Authorea, specifically how to take advantage of some of our powerful tools. Of course, feedback and questions are not only welcome, but encouraged--just hit the comment icon to the right of this text 💬  (You can also highlight specific parts of the text to leave a comment on). (Ha. That's your first lesson!).The BasicsAuthorea is a collaborative document editor built primarily for researchers. It allows you to collaboratively write in real-time in normal text, LaTeX, and Markdown all within the same document. In addition to easily writing together, each article on Authorea is a git repository, which allows you to host data, interactive figures, and code. But first, let's get started! 1. Sign up.If you're not already signed up, do so at authorea.com/signup.  Tip: if you are part of an organization, sign up with your organizational email.  2. First stepsDuring the signup process you will be asked a few questions: your location, your title, etc. You will be also prompted to join a group. Groups are awesome! They allow you to become part of a shared document workspace. Tip: during signup, join a group or create a new one for your team. Overall, we suggest you fill out your profile information to get the best possible Authorea experience and to see if any of your friends are already on the platform. If you don't do it initially during sign up, don't worry; you can always edit your user information in your settings later on.Once you've landed on your profile page (see below). There are a few things you should immediately do:Add a profile picture. You've got a great face, show it to the world :) For reference, please see Pete, our chief dog officer (CDO), below. Add personal and group information. If you haven't added any personal information, like a bio, a group affiliation, or your location, do it! You might find some people at your organization already part of Authorea, plus it is a great way to build your online footprint, which is always good for getting jobs.Invite your colleagues. Click here to invite contacts from your Gmail. You'll get extra private documents in your account and you'll make Pete very happy!

The largest contributor to the planetary energy imbalance is well-mixed greenhouse gases (GHGs), which are partially offset by poorly-mixed (and thus northern mid-latitude dominated) anthropogenic aerosols (AAs). To isolate the effects of GHGs and AAs, we analyze data from the CMIP5 historical (i.e. all natural and anthropogenic forcing) and single forcing (GHG-only and AA-only) experiments. Over the duration of the historical experiment (1861-2005) excess heat uptake at the top of the atmosphere and ocean surface occurs almost exclusively in the Southern Hemisphere, with AAs canceling the influence of GHGs in the Northern Hemisphere. This interhemispheric asymmetry in surface heat uptake is eliminated by a northward oceanic transport of excess heat, as there is little hemispheric difference in historical ocean heat storage after accounting for ocean volume. Data from the 1pctCO2 and RCP 8.5 experiments suggests that the future storage of excess heat will be skewed towards the Northern Hemisphere oceans. PLAIN LANGUAGE SUMMARY Climate change is fundamentally an energy balance problem. Due to the influence of greenhouse gas (GHG) emissions, the amount of solar energy absorbed by Earth is currently greater than the amount of energy radiated to space. This energy imbalance is partially offset by particulate matter released into the atmosphere from burning fossil fuels (anthropogenic aerosols; AAs), which is most concentrated in the northern mid-latitudes. In this study, model simulations of the historical and future climate are compared to single forcing simulations that apply only GHG or AA emissions. We find that the historical uptake of excess heat is strongly skewed towards the Southern Hemisphere because AAs cancel the influence of GHGs in the Northern Hemisphere. The oceanic storage of that heat shows little difference between the hemispheres due to a strong northward transport of excess heat. In future, the models suggest excess heat storage will skew towards the Northern Hemisphere. KEY POINTS - Single forcing simulations of the historical (1861-2005) climate suggest anthropogenic aerosols cause most excess heat uptake to occur in the Southern Hemisphere - This interhemispheric asymmetry in heat uptake is eliminated (after accounting for ocean volume) by a northward oceanic transport of excess heat - In future, the storage of excess heat will be skewed towards the Northern Hemisphere

Writing with a purpose means that you need to make sure your writing communicates amessage. However, doing this effectively might mean taking a few extra steps as you write. Inthis article, we will look at seven ways you can improve your writing and communication skills.

Latar BelakangInstitut teknologi sumatera merupakan salah satu perguruan tinggi baru yang didirikan oleh kementerian riset dan teknologi pendidikan tinggi nasional. Dalam perkembangannya telah memiliki 5000 mahasiswa dan semakin bertambah sepanjang tahun. Dari perkembangan mahasiswa ini sarana dan pra sana perlu semakin bertambah pula. Dalam hal ini gedung dan penyediaan tenaga listrik. Saat ini ITERA telah memiliki lima gedung kuliah. Beberapa gedung masih mengandalkan generator sebagai sumber tenaga listrik. Energi terbarukan merupakan  sumber energi yang dapat diperoleh secara gratis terutama di ITERA. Seperti Sinar matahari dan angin yang mudah dikonversi untuk diubah menjadi energi. Proses perubahan tersebut membutuhkan teknologi yang nanti dapat memproses perubahan energi tersebut menjadi energi listrik. pemanfaatan energi listrik tersebut dapat diterapkan pada gedung kuliah yang masih mengandalkan energi non terbarukan seperti fosil yaitu diesel. Kebutuhan listrik ITERA per gedung dikonversikan adalah 1080 kW  per bulan karena pemakaian ruangan yang secara full dengan kondisi ruangan yang terbatas.teknologi energi terbarukan dapat mengatasi krisi energi seperti matahari dan angin.

This is a journal club review of Moderate developmental alcohol exposure reduces repetitive alternation in a zebrafish model of fetal alcohol spectrum disorders, posted on bioRxiv (DOI: 10.1101/370072)

Steven Burgess (0000-0003-2353-7794), Samuel Fernandes, Antony Digrado, Charles Pignon, Elsa de Becker, Naomi Housego Day, Lusya Manukyan, Stephanie Cullum, Isla Causon, Iulia Floristeanu, Young Cho, Freya Way, Judy Savitskya, Robert Collison, Aoife Sweeney, Pietro Hughes, Cindy Chan AbstractThis review is compiled from notes taken by the UIUC Plant Physiology preprint journal club during a one hour session on 2018-07-30. The review refers to the preprint "Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana" by Hannes Dittberner, Arthur Korte, Tabea Mettler-Altmann, Andreas Weber, Grey Monroe, and Juliette de Meaux ( doi: https://doi.org/10.1101/253021) published on BioRxiv.ReviewIn the paper “Natural variation in stomata size contributes to the local adaptation of Water use efficiency in Arabidopsis thaliana” Dittberner et al. (2018) investigated the genetic basis of water use efficiency using genome wide association analysis. Findings included (1) that there is substantial variation in stomatal size and patterning in A. thaliana accessions (2) decreased stomata size correlates with increased water use efficiency (3) two novel QTL affecting WUE independently of stomatal patterning (4) water use efficiency is a polygenic trait and (5) natural selection contributed to the establishment of variation in WUE in accordance with climatic conditions.The findings are in accordance with previous studies looking at genetic variation in stomatal size and patterning in A. thaliana (Delgado et al. 2011; Monda et al. 2016), the role of natural selection in WUE of tomato (Muir et al. 2014), analysis of genomic variation in WUE in A. thaliana (Easlon et al. 2014; Aliniaeifard and van Meeteren 2014) and the extensive literature correlating a decrease in stomatal size with increased water use efficiency in many species.We were impressed by the significant technical advance presented in the form of automated stomatal counting and suggest more could be made of this aspect of the paper. For example the we suggest inclusion of the term ‘high-throughput’ in the title, and think it would be helpful to include a picture of how the screening system works in the introduction.Further, we found the conclusion that water use efficiency is a polygenic trait very interesting. The implications are important for studies aimed at the improvement of photosynthesis/WUE through conventional breeding or genetic manipulation. We wonder if there are other papers which have already discussed the potential polygenic nature of stomatal traits? Yoo et al. (2011) mentions different genes involved in WUE and stomatal patterning. This kind of paper could have been worth-mentioning in the discussion.The identification of two novel QTL, not otherwise known to influence water use efficiency or to be related to stomatal patterning and regulation was particularly intriguing, and these two genes provide a great starting point for further analysis in future publications.Major commentsWe believe the kinship matrix accounts for relatedness, and is usually called the k model. To account for population structure one could use principal components, combining these two approaches is known as the Q+K model. It would be helpful to include a citation for calculating the kinship matrix as there are multiple methods available. It might also be worth providing QQplots to show whether including population structure is necessary or not for this study.We found the use of a Bonferroni correction in the analysis quite conservative, there are other options such as Benjamini-Hochberg adjusted p-values that could lead to declaring other SNPs as significant. Also, from the GWAS results, there seem to be other SNPs popping up - although, not significant. It might be worth using an alternative to p-values when investigating the possible biological significance of outstanding SNPs on a Manhattan plot - such as selecting the top 10 hits for investigation.Minor comments:Keywords: Consider revisiting, as many of the keywords are already on the title. Additionally, it would be helpful to include terms rather than acronyms which are not familiar to non-experts.Introduction: Would be good to include examples of some of the limitations to automated confocal microscopy approaches to orientate readers.Line 143: (Atwell et al., 2010). This citation doesn't seem to be right. If the author is referring to genomic heritability it could cite de los Campos et al. (2015).Methods: Would like to see further information on the methodology used for carbon isotope discrimination in the main textResults: Might consider using the term ‘genetic-heritability’ rather than ‘pseudo-heritability’Results: Direct comparison with previously reported dC13 values for accessions that have been demonstrated to differing WUE would be helpful.Figure 4: the text on the figure is likely to be too small to see properlyLine 505: “soil composition...” This is a really interesting point about the complexity of environmental effects on plant physiology. It might be helpful to provide some explanation for readers less familiar with soil content. (e.g. water holding content and effect on root structure - e.g.https://doi.org/10.1073/pnas.1721749115)Line 499-500. Repetition of text on 498-499Results: It would be helpful to share where the functional annotation for genes come from. This gene appears to be involved in mRNA decapping. There is only one publication, which found it is involved in PAMP triggered immunity, plants were dwarf in stature. TAIR does not annotate a role in cell differentiation (10.15252/embj.201488645)Discussion: It is interesting to see a comparison with a related species and how the observed pattern is consistent between the two.Data accessibility: This is excellent. Great to see that all data and code will be made available and deposited in a permanent repository!ReferencesAliniaeifard and van Meeteren (2014) J Exp Bot. 65(22): 6529–6542.de los Campos et al. (2015) PLoS Genet 11(5): e1005048. doi:10.1371/journal.pgen.1005048Delgado et al. (2011) Ann Bot.; 107(8): 1247–1258Easlon et al. (2014) Photosynth Res 119: 119. https://doi.org/10.1007/s11120-013-9891-5Monda et al. (2016) Plant Physiol, 170: 1435–1444Muir et al. (2016) Genetics. 2014 Dec; 198(4): 1629–1643.

This is a review of Maekawa et al. bioRxiv 293050; doi: https://doi.org/10.1101/352278 posted on June 20, 2018. In this paper, the authors mined the transcriptomes of 50 different accession of wild barley, generating a rich library of natural variants of the MLA immune receptor—a classical nucleotide-binding domain and leucine-rich repeat-containing (NLR) protein. They grouped the MLA variants in two subfamilies with all receptors known to be effective against the powdery mildew fungus grouping in one subfamily.

Title: Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia. Authors: Gerard Minuesa, Steven K Albanese, Arthur Chow, Alexandra Schurer, Sun-Mi Park, Christina Z. Rotsides, James Taggart, Andrea Rizzi, Levi N. Naden, Timothy Chou, Saroj Gourkanti, Daniel Cappel, Maria C Passarelli, Lauren Fairchild, Carolina Adura, Fraser J Glickman, Jessica Schulman, Christopher Famulare, Minal Patel, Joseph K Eibl, Gregory M Ross, Derek S Tan, Christina S Leslie, Thijs Beuming, Yehuda Goldgur, John D Chodera, Michael G Kharas Date of submission to bioRxiv: May 14, 2018 __________________________________________________________________________________ Dear Authors, Thank you for posting your manuscript titled Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia as a preprint on bioRxiv! We reviewed this work at our journal club at the Structural Genomics Consortium, University of Toronto. Compiled comments from the attendants are below. To structure the feedback, we used the quick worksheet guidelines published on PREreview. We hope this feedback will be useful to improve the manuscript. Kind regards, PreReview Journal Club  Members, Structural Genomics Consortium, University of Toronto__________________________________________________________________________________ What is the main question the study attempts to answer?Can chemical inhibition of Musashi2’s RNA-binding function be used to selectively target myeloid leukemia cells?How does Ro 08-2750 inhibit MSI RNA-binding activity? What is (are) the hypothesis?Small molecule antagonism of the RNA binding domain of MSI2 has therapeutic potential in the treatment of acute myeloid leukemia. Ro-08-2750 binds at an RNA-interacting site and competitively inhibits RNA binding of MSI2. What techniques/analyses do the researchers adopt to test their hypothesis(es)? The authors use biophysical assays, computational structural biology, cell biology techniques, and an animal model. These methods are all common to preclinical drug development and are appropriate to address the outlined hypothesis and in most cases adequately address the question being asked. Why is this study relevant? Understanding of RNA biology and its importance in human health has expanded greatly in recent years. While proteins with RNA binding domains have been implicated in disease, they are typically thought of as “undruggable” as they often lack defined pockets. MSI2 overexpression is common in AML patients with poor clinical prognosis. This study highlights that (1) RRM domains can be targeted by a small molecule antagonist and (2) that this approach may have therapeutic value in the treatment of AML. Write here any general comments you might have about the research approach. Structural studiesThe structure-activity-relationship was clearly described considering a lack of a co-crystal structure.Given that residues F66, F97 and R100 of MSI2 are also conserved in MSI1, it would have been interesting to see how Ro 08-2750 compares between both proteins. Biophysical AssaysIt would be interesting to see measurements of compound binding to MSI2, for example ITC or thermal shift assays. Cell BiologyThe assays used appeared to be well thought out and provided good evidence for target engagement and therapeutic potential in cellular models of AML. However, given the genetic diversity of AML, it would be informative to include a sentence to describe why MOLM13 and K562 cells were selected for these studies. Write here any specific comment you might have about experimental approaches and methods used in the study.In the discussion the authors state that Ro 08-2750 is the first “selective MSI inhibitor”. MSI2 was compared to SYNCRIP for selectivity; however, given the extensive repertoire of RNA binding domains found in the human genome, we feel that a more extensive characterization is warranted to make a definitive statement. This could be accomplished by either utilizing a biotinylated compound for pulldowns and MS-id or by measuring binding to a panel of RRMs.It would be interesting to see KD/KO studies alongside compound treatment to evaluate to what degree this compound may phenocopy genetic perturbation of MSI2 in AML. In addition, it would also be cool to see how the mutants deficient in Ro binding are functional in cells, which may hint at potential mechanisms of resistance. For the mouse data presented it would be informative to the reader to include both survival and tumour volume data. Additionally, have the authors done any experiments to test the suitability of this compound for in vivo use (ex. What is the PK of Ro?).Additional biophysical assay to measure direct binding of the compound to MSI2’s RRM domain would be informative, ex. ITC or thermal shift assay.Structural studiesWe found that the molecular dynamics analysis greatly complemented the structural data and enabled a thorough description of the potential binding mechanism for the Ro compounds. It would be useful to note whether co-crystallization of MSI2 and Ro was attempted, though the mutagenesis experiments provided evidence of the importance of interactions with F66, R100, and F97. It is unclear why YANK was selected to perform alchemical analysis given that the program has not yet been extensively validated and carries a “Use at your own risk!” warning. It would have been reassuring to see these calculations carried out with a more validated software.Write here any specific comment/note about figures in the paper (this could be related to the way data are displayed and your ability to understand the results just by looking at the figures).Extended figure 7 appears to be mislabeled in text and extended figure 8 is missing.For figure 3d, we felt it would be easier to interpret if annexin V + cells were normalized to the DMSO control.For the RNA-IP experiments, we would suggest that this data be presented as % input, akin to a ChIP experiment.  This would account for any changes in gene expression that may confound the interpretation of this result as well as allow the authors to probe RNAs that should not change in response to compound (ie. negative control) Write here any additional comment you might have (this includes minor concerns such as typos and structure of the manuscript).On line 216: what does “proximal” mean here?Classically, the term inhibitor would be reserved for a compound disrupting an enzymatic activity. Here, antagonist may be a more appropriate term. Any supplementary tables listed in the text should be included for readers/reviewers.  

Diurnal active photolocation enhances predator detection in a marine fishMatteo Santon, Pierre-Paul Bitton, Jasha Dehm, Roland Fritsch,  Ulrike K. Harant, Nils Anthes,  Nico K. Michielsdoi: https://doi.org/10.1101/324202     Who we are:We are a group of zoologists at different career stages with a diverse background. We have started a preprint review journal club in order to discuss topics across our different areas of concentration to stay up-to-date with the latest research and get practice writing reviews. We selected this preprint, “Diurnal active photolocation enhances predator detection in a marine fish,” by Matteo Santon et al. due to the interesting experimental design and general interest of the topic. This manuscript built upon a body of previous work in a logical, easy-to-read way. The authors demonstrate experimentally that diurnal active photolocation exists in diurnal fish and that it aids in predator detection. We were generally impressed by the experimental design and the thorough treatment of the topic. We do, however, have a few questions that we could not answer by reading the manuscript and also some comments on the presentation of the information. Questions:For the lab experiment: a. What kind of glass was used for the partition between the triplet and the predator? This is explicitly stated for the field experiment (spectrally neutral Evotron Plexiglas), but we were wondering if the same glass was used in the laboratory experiments?b. What is the purpose of the “sub-optimal substrate” strip of gravel along the long side of the tank and why is it not included in the schematic drawing of the setup? c. In lines 200-201, the authors state, “Both stimuli were simultaneously present in the tank, but only one was visible to the triplefins.” Here we would like to know how they prevented visibility of one stimulus and suggest that the spatial relationship be stated or illustrated more clearly.

“In silence and movement you can show the reflection of people.”  Marcel Marceau

“Beyond a doubt truth bears the same relation to falsehood as light to darkness.”Leonardo da Vinci

Well known Dirichlet series include: \zeta(s) = ^\infty {k^s}\\ {\zeta(s)} = ^\infty {k^s}\\ {\zeta(s)} = ^\infty {k^s} If we define the inverse Dirichlet transform to map like \zeta(s) \to 1 \\ {\zeta(s)} \to \mu(k) \\ {\zeta(s)} \to \lambda(k) then we can track less standard variations by creating ratios of zeta functions: {\zeta(s)}\to A210826(k) \\ \zeta(s)^2 \to d(n) = \tau(n) \\ {\zeta(s^2)} \to (k)\\ {\zeta(s^2)} \to {k^q} \\ {2})}{\zeta(s+{2})} \to {k} \\ = ? Consider the duality of ζ(s)→Γ(s) with inverse Mellin transform... DIRICHLET SHIFT OPERATOR We could consider an operator O− (O+) which shifts the argument of a zeta function by −1 (+1). Then use something like the product and quotient rules, to define this on Dirichlet generating functions O^-[\zeta(s)] = \zeta(s-1) \\ O^-[\zeta(s)\zeta(s-1)] = \zeta(s-1)^2 + \zeta(s)\zeta(s-2)\\ O^-[{\zeta(s)}] = {\zeta(s)^2} we can then define the ’number theoretic derivative’ of a function for this latter one we appear to have {\zeta(s)} \to \lambda(n)*A000188(n)\\ {\zeta(s)^2} \to A074722(n) so as ζ(2s)/ζ(s)→λ(n) we could say $$ \delta \lambda(n) = \lambda(n)*A000188(n) - A074722(n) = 0,-1,-2,0,-4,1,-6,-4,-2,1,-10,-4,-12,1,-2,-2,-16,\cdots $$ where clearly, we have every prime, δλ(p)=1 − p, this is nice. We have depending on definition \delta \mu(n) = -A007431(n) \mu(n)-A007431(n) this is $$ \delta \mu(n) = - \phi(d) \mu({d}) $$ and therefore $$ \phi(n) = - \delta \mu(d) $$ then \delta |\mu(n)| = \delta {\zeta(2s)} = {\zeta(2s)^2} = {\zeta(2s)} - {\zeta(2s)^2} \\ \delta |\mu(n)|= A063659(n) - H(n) where H(n)=1 unless n = 9, 16, 18...?, and 2 otherwise. It seems that $$ {\zeta(s)} = ^\infty {(k^2)^s} = ^\infty }(k)\phi()}{k^s} $$ then there is the convolutions $$ {\zeta(2s)^2} = |\mu(n)|*_D }(n)\phi() = |\mu({d})|}(d)\phi() = }(n)\phi() + (1-}(n)) = H(n) $$ we have \delta \tau(n) = 2 \sigma_1(n)\\ \delta \sigma_1(n) = n \tau(n) + \sigma_2(n)\\ \delta \sigma_2(n) = n \sigma_1(n) + \sigma_3(n)\\ \delta \sigma_k(n) = n (n) + (n) noting that σ−1(n)=σ₁(n)/n, also then \delta n\tau(n) = 2 \sigma_1(n) \\ \delta \tau(n) = 2 \sigma_1(n)\\ \delta^2 \tau(n) = 2n \tau(n) + 2 \sigma_2(n) \\ \delta^3 \tau(n) = (4+2n)\sigma_1(n) + 2 \sigma_3(n) By thinking carefully about the linearity of derivatives and implying the δ is a linear operator, then we can easily show that \delta ^k \log(n) = n^k \log(n) for all integer k. In fact in general $$ \delta ^k \log^l(n) = n^k \log^l(n) $$ A stunning result appears to be $$ \delta \Lambda(n) = \log(n^{\phi(n)}) $$ for which the DGF is $$ {\zeta(s)^2} - {\zeta(s)} $$ FURTHER OPERATORS Consider the operator $$ \kappa = [{\zeta(s)} \delta \zeta(s)] $$ such that a factor of ζ(s) is applied, the derivative taken, and then the factor removed. $$ \kappa \zeta(s) = {\zeta(s)} \delta \zeta(s)^2 = {\zeta(s)} 2 \zeta(s)\zeta(s-1) = 2 \zeta(s-1) $$ therefore $$ \kappa 1 = k $$ we also have \kappa \zeta(s-1) \to {\zeta(s)} + \zeta(s-2) \\ \kappa k = P(k) + k^2 where P(k) is A018804(k). We can consider more complicated operators $$ \epsilon = 1 + \delta + \delta^2 + \delta^3 + \cdots $$ then $$ \epsilon \zeta(s) \to \zeta(s) + \zeta(s-1) + \zeta(s-2) + \cdots $$ which implies $$ \epsilon 1 = 1 + k + k^2 + k^3 + \cdots = {1-k} $$ KERNEL GUIDED TRANSFORM For the Lambert transform we have the nicve property that $$ ^\infty a_n {1-x^n} = ^\infty b_n x^n $$ where the relationship is $$ b_n = a_n $$ but we can generalise this by realising that $$ ^\infty a_n f(x^n) = ^\infty b_n x^n $$ where $$ f(x) = ^\infty \kappa(n) x^n $$ generates a new transform, we then know for κ(n)=1, we have the Lambert transform. RATIO OF SIGMA If we let $$ \kappa(n)={\sigma_1(n^2)} $$ then it seems if an bn ζa ζb ------- ------------------ ------------------------------- ------------------------------- μ(n) nϕ(n) 1/ζ(s) ${\zeta(s)}$ ϕ(n) n² ${\zeta(s)}$ ζ(s − 2) μ(n)² A034444(n)=d*(n) ζ(s)/ζ(2s) ζ(s)²/ζ(2s) σ₁(n) ... ζ(s)ζ(s − 1) ζ(s − 2)ζ(s)² n σ₂ ζ(s − 1) ζ(s)ζ(s − 2) If we let $$ \kappa(n)=\phi(n) $$ then it seems if an bn ζa ζb ------ ------------------------- ------------------------------- ----------------------------------- ϕ(n) ∑d|nϕϕ ${\zeta(s)}$ ${\zeta(s)^2}$ μ(n) ∑d|nϕμ ${\zeta(s)}$ ${\zeta(s)^2}$ 1 n ζ(s) ζ(s − 1) n $^n gcd(n,k)$ ζ(s − 1) ζ(s − 1)²/ζ(s) If we let $$ \kappa(n)=\mu(n) $$ then it seems if an bn ζa ζb ------ -------- ------------------------------- --------------------------------- ϕ(n) ∑d|nϕμ ${\zeta(s)}$ ${\zeta(s)^2}$

This is a review of the preprint entitled " On the overlap between scientific and societal taxonomic attention - insights for conservation", by Ivan Jarić, Ricardo A. Correia, David L. Roberts, Jörn Gessner, Yves Meinard, and Franck Courchamp. The preprint was originally posted on bioRxiv on June 3, 2018 (http://dx.doi.org/10.1101/334573). Our journal club reviewed this preprint in the meeting of July 6, 2018.

A document by Benedict Irwin. Click on the document to view its contents.

This is a journal club review of Differential encoding of predator fear in the ventromedial hypothalamus and periaqueductal grey, posted on bioRxiv (DOI: 10.1101/283820)

Preface This article provides a discussion about knowledge and how the University practice of and ideology behind knowledge dissemination to the public fits within our current Economy of Knowledge Abundance. Here, I suggest that University methods for knowledge delivery to the public need to be reconsidered and approached in a different way. I begin to discuss how faculty can start to think and address the problem of knowledge dissemination to the public in a knowledge abundance economy. In the last two sections, I also provide a way for how Presidents, Vice Presidents or Chancellors of Research (VPR’s/VCR’s), Provosts, and other Upper Administrative leaders of Universities can support this approach in conjunction with State Regents/Education Boards/Board of Trustees. Introduction Knowledge dissemination is a phrase that is used ubiquitously across the academic landscape. Originally, knowledge dissemination practices were based on the pre-Knowledge Abundance Economy Era or the Era of Knowledge Scarcity. In the Era of Knowledge Scarcity, Universities were considered by many to be a beacon of knowledge and thus it was imperative that Universities and the individuals in them set up mechanisms to provide knowledge to the public. As more knowledge was provided and technological acuity increased it prompted the use and development of technological “Knowledge Systems”, (a.k.a. knowledge-based systems) - especially in the context of knowledge management (KM). In this context, a knowledge-base is defined as a collection of complex structured and unstructured information used by a computer system. This term, knowledge base (KB), was originally employed in connection with expert systems (a.k.a. experts). So, it is not surprising to hear in Academic circles KB being used frequently in this way – “That we, individuals in the University, are contributing to the knowledge base”. Which is an approach that works very well within the context of traditional academic knowledge dissemination practices and ideology.* From an Academic perspective, there is a knowledge base/s and someone in the Academy will add to it. Again, this assumes that knowledge is stable, knowledge is wanted or needed, and that it is valued by the public.  Our Changing World However, we no longer live in the Era of Knowledge Scarcity. Universities and Industries along with their corresponding knowledge management systems have had to wrestle with this scenario for at least the last three decades. “Knowledge Systems”, (a.k.a. knowledge-based systems), now must account for a knowledge base (KB) that approaches infinity. In addition, there are now mechanisms that the public recognizes and uses like a KB. Examples of these would be Facebook, Twitter, LinkedIn, Tumbler, Snap Chat. In many cases, even the Google Search Engine is being used like a KB for the public. There are now more than 200 social media sites and by other estimates there are more than 800 social media sites that are and can be used as a KB. This does not include the numerous websites and webpages that the public is using as KBs. The total global population in January 2018 was estimated to be 7.593 Billion. A summary of the 2018 Global Social Media Research Summary Report shows that the number of people using social media went up by 13% in 2018 to 3.196 Billion since last year. The number of internet users world-wide went up by 7% in 2018 to 4.021 Billion compared to last year. The number of active mobile phone social users went up by 4% to 2.958 Billion since last year. All of this suggests that there has been a change in what and how the public obtains, envisions, prioritizes, and counts as knowledge.   Defining Knowledge in the New Economy Our understanding of what constitutes knowledge has changed in the last 10 to 15 years for the public. Meaning that the ideology and practice of knowledge dissemination to the public is now a little bit of a misnomer. Because knowledge, especially for the public, implies a use function. This must not only be of use to the individual providing it but also to those who receive it. For example, if someone claims that they have knowledge of a subject and cannot demonstrate/show that knowledge to someone else, then the knowledge claimed is put into question. Knowledge must have a multi-user function. Most dictionaries describe knowledge as facts, information, and skills acquired by a person through experience or education; or, as the theoretical or practical understanding of a subject or awareness or familiarity gained by experience of a fact or situation. For western philosophers and scholars of knowledge, defining knowledge appears to have been debated for centuries. Some older known philosophers and scholars known for these debates include but are not limited to Kant, Locke, Plato, Kripke, Gettier, Blackburn, Nozick, Kirkham, Wittgenstein, and Moore. Aspects of this debate over what is knowledge still goes on today.** Currently under a western perspective, there is wide-spread agreement on three conditions, but not consensus, on what constitutes knowledge. They are: if the person believes the statement to be true; the statement is in fact true; and if the person is justified in believing the statement to be true. These three conditions embody Justification, Truth, and Belief or JTB for short. One can find a short synopsis on JTB by clicking here. Both the dictionary and scholarly definitions of knowledge are correct. Showing how both definitions are correct is a topic for another discussion. However, in the context of the public and our current (new) knowledge abundance economy, synthesis of the dictionary and scholarly definition of knowledge can be best understood in general through the following definition. Knowledge can be described as useful, or recognized as being useful, coherent well-organized packets or containers of information that embody at least the three JTB conditions. When this packet or container (of information) is used by the receiving individual, the container is opened, and the organized information inside is interpreted under JTB conditions into some usable form called knowledge. The reason that a particular container would be used can be as simple or basic as an individual wanting to understand a little more about a topic. Note: Above, the phrase, “some usable form called knowledge”, was used because one hundred percent (100%) knowledge transfer is a persistent myth. Corruption, perversion, and misinterpretation of knowledge happens among individuals and groups – regardless of educational attainment. Aspects of these coherent well-organized packets or containers of information can also be just useful enough for someone to reject or modify. This would still constitute knowledge. Rejection or modification of knowledge could be based on a number of things, for example - religion, ignorance, illness, stupidity, and the Dunning-Kruger Effect. Discussion points that would generate much debate between philosophers and other scholars of knowledge. If all these points are considered, this could imply any knowledge disseminated, under academic traditional practices, to the public would be considered disseminated potential-stored knowledge or organized information rather than knowledge itself. This would be somewhat analogous to potential energy and the idea behind a photon (in general, a packet of energy). Disseminated knowledge is similar to potential energy because it has yet to be acquired, used, or put into motion by the public user within the context of a system. The system here includes: individuals mental models; distributors, sharers, and users of the disseminated potential-stored knowledge; a medium; type of delivery; and already existing information external and internal to the distributors, shares, and users.   Disseminated knowledge is also like a photon, because disseminated knowledge acts and behaves as a subatomic “Conceptual” particle. It has a certain frequency, speed, velocity, and transfer potential. Just like there could be wasted packets of energy (photons) there could be wasted packets of organized information (potential knowledge).   University Knowledge Dissemination and the Public in the Era of Knowledge Abundance What has happened and is currently happening, is that many coherent well-organized packets of information, when released (disseminated), don’t get used, and stay in their most basic form (that is, they’re untapped). The basic form of knowledge is useful coherent well-organized packets of information. Traditional academic knowledge dissemination practices become increasingly limited in an abundance environment. This occurs in an abundance paradigm because the knowledge base exponentially approaches infinity. Under these circumstances, formal knowledge representation (formal knowledge bases and their systems) are easily converted into constantly changing semi-formal, formal, and informal ways of knowing by the public to depict the world. These depictions are based on the cultural norms of the individual, group, or subgroup represented in the public. More importantly with the wide use of mediums like Facebook, LinkedIn, Google preferences, and etc., individuals, groups, and subgroups can either create or house their own knowledge base or pseudo-knowledge base systems. Result being, that for better or for worse, individuals or groups in the public are increasingly accessing knowledge from sources other than the University or well-established and tested knowledge systems. This also allows individuals, groups, or subgroups to pick and use the first pieces of coherent well-packaged information (knowledge) available that works for them. Even if it is wrong. Thus, in this abundance economy, knowledge may not be seen by the public as stable (such as coming from a stable fact-checked knowledge base), knowledge may no longer be needed or wanted, and there is enough knowledge that at any point in time that different types of knowledge can be viewed as having little to no value. Reconsidering Our Approach Disseminating knowledge to the public in an abundance of knowledge economy does not guarantee its use. Knowledge disseminated to the public without the public being able to use it, is waste. In fact, it might not be considered knowledge at all, just more information. In a knowledge abundance economy, knowledge must have a receiver/user to be knowledge. This suggests that knowledge is also finite and not indefinite. In other words, for the public, knowledge has an expiration date. In addition, universities and faculty in them are increasingly being forced to reconsider how they interact with the public. This has been due to several changes in the national and international landscape (e.g. state funding, governmental funding, politics, usefulness of the University conversations initiated by the public, declining enrollment, increasing ethnic and gender diversity, proliferation of social media, and national and international wicked societal problems). One critical step that would help universities successfully navigate this new landscape and economy would be to tweak how individuals/faculty in the University approach a community. This would require universities and faculty to change their ideological values about and practice concerning, “disseminating knowledge to the public”. Individuals/faculty would need to highly value and embrace some new perspectives, like “sharing, communicating, mobilizing, translating, managing, and propagating knowledge with and for the public”. Such a suggestion implies a more strategic approach. It implies understanding and working with those whom the information will be most relevant before the sharing, communication, translation, management, propagation, and mobilization process begins. This requires individuals and universities to know and develop relationships with the public outside the context of a recruitment mindset, a project need, or a requirement to get funding. It may also mean that it might be required, in some cases, that knowledge be co-constructed with the relevant individuals or groups in the public. Full or partial infrastructure needed to advance and support these approaches are already in place at many universities nationally and internationally. This infrastructure is typically comprised of Societal Benefit Professionals (SBPs). A few examples of SBPs at universities that could be better utilized for this endeavor are: community engagement and engaged scholarship professionals; broader impacts professionals (for the National Science Foundation, other agencies, and in general); and knowledge mobilizers, brokers, and translators. There are also a number of Societal Benefit Organizations (SBOs) that act as “boundary organizations” that could be used for this purpose to help share, communicate, translate, propagate, and mobilize University knowledge with and for the public. Boundary organizations sit either inside or outside the University and work with individuals in the Academy and in the public. In addition, several different types of University technology transfer centers, marketing offices, and communication departments and colleges could be employed with numerous types of SBPs and SBOs to support this proposed approach. However, for universities to fully embrace these new perspectives there must be high-level administrative support, a change in University culture, and a revaluing of what matters in departments concerning tenure. This starts with Presidents, Vice Presidents and Chancellors for Research (VPR/VCR), Provosts, and other Upper Administrative leaders embracing this change through formal University structures. Approach for Vice Presidents and Vice Chancellors of Research (VPR/VCR) For VPR’s and VCR’s, this means to create Assistant or Associate Vice President or Chancellor for Research, Society, and Impact (VPRSI/VCRSI) positions in their organizations. These VPRSI/VCRSI positions would support, engage, and work with and for “ALL” researchers and society to help an institution, VPR/VCR office, graduate and undergraduate students, and specifically faculty navigate their research with, for, and in the context of the public domain to maximize research impact. In addition, VPRSI’s/VCRSI’s and their offices would help individuals/faculty evaluate the effectiveness of their research impact endeavors and the research impact for an entire University.  This position would also allow University systems and VPR/VCR offices to effectively take advantage of the relationship between increased researcher public positive engagement and increased University funding. This relationship between public engagement and funding is a phenomenon that has not been adequately explored in the United States (US). However, as research funding is challenged, the relationship between public engagement and research expenditures is becoming a greater focus in the US and internationally.  Funding for research is not the only driver for increased institutional, office of VPR/VCR, and faculty/researcher engagement with the public. A culture change is beginning to happen throughout the world in which the society is requiring Universities to provide, work for, and with the public to increase the impact of University research. This impact implies an emphasis on the end user and not solely the researcher and University. There are now several national and international mechanisms bringing together individuals and organizations in the non-profit sector, government, Academy, and Industry to support and better address the public call for a Societal-Centric Research University Impact Culture. A few examples of these national and international mechanisms include the: National Alliance for Broader Impacts Summit in the US; Knowledge Mobilization Forum in Canada; and the International Impact of Science Conference. Note: The Impact of Science Conference is not just focused on the impact of science. It is concerned with the impact of social science, arts, humanities, and all aspects of research impact in the public domain.   Approach for Presidents, Provosts, Other High-Level Administrators, and Governance Boards For Presidents, Provosts, and other Upper Administrators this means to modify the University tenure guidelines and/or mandate an increased departmental and faculty value on being “Public Facing” in tenure considerations. A way that State Regents and other boards that perform similar functions could support this approach is by providing a public proclamation on the value of “Public Facing”. Public facing is when an individual/s, group, organization, entity, company, or University decides through their procedures, actions, professional responsibilities, and policies to have and encourage better: relationships; interactions; sharing; attention; mobilization; and communication (could be with the help of others) so that they can be more reciprocally involved and open to and with the public.*** “Public Facing” is used to accomplish at least three major objectives. These three major goals are to: create large positive public impacts; allow the public access and more equitable and effective use of information; and help individual, groups, and universities emphasize outcomes and outputs rather than only outputs and activities in the public sphere. In the context of knowledge dissemination to the public, most University tenure guidelines are either non-existent or outdated – based on 13th – mid 20th century values on knowledge. Times when knowledge scarcity was considered the norm. These outdated values on knowledge have shaped University departmental and faculty beliefs and values on what matters for tenure. Many departments and the faculty in them still adhere to an “Ivory Tower Approach” on knowledge as the primary indicator of tenure worthiness. This is evident by the low value put on “Public facing” by Committee A’s/tenure committees, already tenured faculty, and departmental/school chairs in departments across the nation.   Summary Times have changed, the world has changed, we have moved past the Era of Knowledge Scarcity, and are not going back. We are now in the Age of Knowledge Abundance. It is time for our University, departmental, and faculty tenure policies and values to reflect the current times, the current age, and how the public currently deals with knowledge. In a public domain, “Knowledge is art, a useful gift, it needs to be shared, and those who successfully share it in a way that it gets used are well-respected and highly esteemed artists”. These well-respected and highly-esteemed individuals embody public facing. After all, knowledge dissemination from the public’s perspective, equates to just providing more information if it has no use or perceived as useful. Simply because anyone can provide information in this age. How useful is that?     Notes* In health fields and medical universities in the US and around the world, there has been increased movement away from traditional University knowledge dissemination practices. Knowledge dissemination is now being shifted and/or equated to knowledge translation practices. Knowledge translation is more in line with knowledge mobilization depending on the field of study, profession, or industry. This is especially salient in Canada. Like knowledge mobilization, knowledge translation also seeks to put knowledge into action with the end user in mind. Many times, with emphasis on impact in terms of the non-academic user. **It is important to recognize that there are other notions and thoughts to what constitutes knowledge. Many of these notions come from civilizations well-established before European Western Civilizations. These civilizations influenced western scholarly thought on knowledge. Examples of these are Asian, Indigenous, and African civilizations. For the purposes of this article, this will be discussed in further detail at another time. *** Public Facing was a phrase used by Dr. Karlos Hill in a conversation he and I had that summarized my advice on how institutions, organizations, individuals, and faculty could be more impactful in today’s knowledge abundance environment.

We can transform functions in the summands of an Engel expansion to sequence terms and or generating functions. A list gives E\left[{G(1+n)G(2+n)(2,2)_n}\right] \to A273935 = n!(n-1)!(2^n-1) \\ E\left[{G(1+n)G(2+n)}\right] \to A010790 = n!(n-1)! \\ E\left[{G(1+n)G(3+n)}\right] \to A129464 = -n(n+1)(n-1)!^2 \\ E\left[ 2^{-n^2-n+{24}} \pi ^{{2}+{4}} G(n+3)}{A^{3/2} G\left(n+{2}\right)}\right] = C(n) = {(n+1)!n!} \\ E\left[{\Gamma(n+1)}\right] \to 1,1,2,3,4,5,6,7,8,9, \cdots \,n \\ E\left[{\Gamma(n+1)^2}\right] \to 1,1,4,9,16,25,36,49,\cdots \,n^2 \\ E\left[{G(1+n)}\right] \to 1,1,1,2,6,24,120,720, \cdots \, n! \\ this is generated by the product of the reciprocals of the sequence terms ^n {a(k)} = E^{-1}(a(n))