tag:beta.briefideas.org,2005:/all?page=30Journal of Brief Ideas: Ideas from the last week2015-11-21T01:18:52Ztag:beta.briefideas.org,2005:Idea/2562015-11-21T01:18:52Z2015-11-21T06:00:46ZHyperglycaemia: both cause and effect of diabeteshttp://dx.doi.org/10.5281/zenodo.34078Current thinking suggests diabetes has variable causes, is inevitably progressive, and causes hyperglycaemia. **Type 1** is an autoimmune disease causing β-cell (source of insulin) death, and **type 2** is an insulin activity deficiency (insulin resistance)<sup>[1](http://linkinghub.elsevier.com/retrieve/pii/S1538544212001149),[2](http://linkinghub.elsevier.com/retrieve/pii/S0140673613605917),[3](http://link.springer.com/10.1007/s00125-011-2204-7),[4](http://linkinghub.elsevier.com/retrieve/pii/S0026049515002565)</sup>. I propose that an excessive carbohydrate intake, inducing raised blood glucose (hyperglycaemia), is instead the starting point for both types. This modifies the accelerator hypothesis<sup>[5](http://www.nature.com/doifinder/10.1038/ijo.2009.97)</sup>, replacing insulin resistance with hyperglycemia.
Autoantibodies (probably derived from chronic raised demand for insulin, which is itself a significant antigen<sup>[6](http://perspectivesinmedicine.cshlp.org/lookup/doi/10.1101/cshperspect.a007658)</sup>) are only weakly predictive for diabetes<sup>[7](http://linkinghub.elsevier.com/retrieve/pii/S1074761310001251)</sup>. Hyperglycaemia directly reduces insulin production<sup>[8](http://www.nature.com/doifinder/10.1038/ncomms5639)</sup> and also induces β-cell death<sup>[9](http://diabetes.diabetesjournals.org/cgi/doi/10.2337/diabetes.50.6.1290)</sup>, suggesting other routes to loss of insulin production (type 1).
Cells become insulin resistant (unable to take up glucose) with high serum lipids (fats). These lipids are associated with high-calorie/high-carbohydrate diets<sup>[4](http://linkinghub.elsevier.com/retrieve/pii/S0026049515002565),[10](http://ajcn.nutrition.org/content/48/2/240.long),[11](http://www.jlr.org/content/39/6/1280.short)</sup>. Insulin resistance has been demonstrated to be reversible with low-carbohydrate and weight loss diets<sup>[3](http://link.springer.com/10.1007/s00125-011-2204-7),[12](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188071/),[13](http://diabetes.diabetesjournals.org/cgi/doi/10.2337/diabetes.54.3.603)</sup>.
Excessive carbohydrate (starch and sugar) intake, more than can be metabolised or stored as glycogen or lipids, leaves the excess glucose in the blood. This hyperglycaemia (initiated by intermittent or chronic excess carbohydrate) actually causes diabetes through a cascade of events leading to insulin deficiency (type 1) or impairment (type 2).
Nelson, Warricktag:beta.briefideas.org,2005:Idea/2552015-11-10T00:29:22Z2015-11-10T06:00:38ZAssessing 'ownership' of useful evidence for measuring impact and giving credithttp://dx.doi.org/10.5281/zenodo.33540An evidence synthesis, such as a systematic review, guideline or other evidence summary, will include collated and filtered data, typically from published reports of primary studies. Those studies were instigated, carried out, supported and to varying degrees 'owned' by, or associated with, individuals, teams, institutions, funders, publishers, and others. The 'ownership' includes intellectual and legal components. Stakeholders, driven by various incentives, wish to demonstrate impact of their output. Impact may reasonably include influence on evidence syntheses and other secondary outputs designed to summarise the status quo or make the case for change. But it would be interesting to look backwards from the starting point of, for example, a systematic review. The review itself has impact, by influencing guidelines, policy and practice, and that impact comes partly from the people and organisations responsible for that synthesis work, and partly from the data and analysis that formed the basis of the review. Impact is therefore linked with an array of individuals and academic and commercial organisations (including publishers), with varying degrees and types of rights or responsibilities for the work. What kinds of formulae or rules could be applied to the array to present a reasonable statement about the 'ownership' of impact?Hilton, Johntag:beta.briefideas.org,2005:Idea/2522015-11-01T06:41:42Z2015-11-02T06:00:40ZRabies Virus: Toward Ante-Mortem, Sub-Clinical Diagnosis by Electron Microscopyhttp://dx.doi.org/10.5281/zenodo.33000According to the Centers for Disease Control and Prevention (CDC), Rabies is the cause of approximately 59,000 deaths annually worldwide. Rabies is 100% fatal and with no approved treatment or survivability upon clinical symptom presentation. With the low-efficacy and general irreproducibility of the “Milwaukee protocol,” post-exposure prophylaxis (PEP) is essential in preventing disease onset through multiple rounds of vaccine alongside rabies immunoglobulin. There remains no single test to diagnose rabies infection sub-clinically in humans, with the gold standard being brain tissue analysis via animal host necropsy.
Electron Microscopy (EM) appears a reliable option for early diagnostics given its ability to image Rhabdoviridae. Limitations include equipment size, expense, and technical expertise essential for operation. This can be partially addressed by the use of the Low-Voltage electron microscope (6-25kV). Such is functionally compact and does not require staining given its enhanced contrast, provided tissue samples are thin enough for examination (20-65nm).
Rabies virus is known to initially replicate in infected muscle tissue of bite wounds. This could be the basis for aforementioned diagnosis via muscle biopsy by simple viral load presence. Combined with EM (having been used in rabies imaging previously), further research is necessary to determine the viability of this approach.
Cobb, Travistag:beta.briefideas.org,2005:Idea/2502015-10-14T04:27:46Z2015-10-23T06:00:41ZUse Real-time MRI to Track Nitric Oxide in Our Brainhttp://dx.doi.org/10.5281/zenodo.32532We have already known that nitric oxide plays a important part in long-term potentiation as a neurotransmission in our brain, especially in hippocampus, and consequently plays an important role in both short-term memory and long-term memory. Thank to the physic basis of magnetic resonance imaging(MRI), any nucleus with a net nuclear spin, including nitrogen, could potentially be imaged with MRI, and the appearance of real-time MRI gives us a chance to obtain movies of the physiological activity in real time. Accordingly, we can use specialized real-time MRI technology to watch how nitric oxide act in our hippocampus or even in the whole brain when a human is learning something and trying to remember them. It is obvious that it can enrich our knowledge about how our memory is formed, or even how we study.Zhou, Yijiatag:beta.briefideas.org,2005:Idea/2492015-10-08T17:24:12Z2020-08-09T00:09:46ZFrom Budapest via San Francisco to The Hague: a bird's eye view of two dozen scholarly communication charters.http://dx.doi.org/10.5281/zenodo.31943Idea: speeding up the transition towards a scholarly commons by summarizing and reviewing existing charters and pinpointing where there’s still work to be done.
Science is in transition. But in what direction, demanded by whom, accepted by whom and realised where and how? This is what we would like to find out in a review of scholarly communication charters, manifestos and roadmaps drawn up over the last 15 years. We have identified some 30 of these charters, from famous ones such as the Berlin Declaration on Open Access to more niche ones such as the Leiden Manifesto on Research Metrics.
Our idea is to classify these charters according to what part of the research cycle they address, and compare them on their demands and acceptance. Then, we'll try to determine to what extent the demands put forward have been implemented in tools, included in written norms and applied by stakeholders such as research institutions, funders, publishers, libraries, and research evaluation organisations. For this, we propose to collect quantitative impressions available in the literature and on the charter websites. The research will hopefully contribute to priority setting and cooperation by organisations working towards more open, efficient and reproducible science.
Bosman, JeroenKramer, Bianca tag:beta.briefideas.org,2005:Idea/2472015-10-01T01:45:58Z2016-05-14T05:04:12ZTeen-Driven Open Sciencehttp://dx.doi.org/10.5281/zenodo.31944Through the [Hive Mapping Cooperative](http://bit.ly/hivemapping), five youth-serving organizations in Chicago have been working to develop shared systems for teens to collect, analyze, visualize, and share georeferenced data using free and open source tools for mobile data collection, data visualization, and digital mapping. With these tools, we aim to enhance cross-program, teen-driven inquiry into human ecology and urban ecosystems, and foster an open science ethos among teens. This ongoing project was partially [conceived at MozFest 2013](http://hivenyc.org/2013/12/11/mozfest-science-web/) and has been through various iterations since that time. We've been piloting a range of tools for data collection and visualization to varying degrees of success, as well as integration of [Contributorship Badges](https://www.mozillascience.org/projects/contributorship-badges) using the [Chicago City of Learning platform](https://chicagocityoflearning.org/workshop-detail?id=6701) to recognize collaboration and contribution, but we've struggled to identify *accessible* tools for teens to actually collaborate across programs on shared inquiries.
Through this project, teens (and everyone else) will have access to flexible digital technologies and a networked system to develop, share, and contribute to inquiry projects across programs. With open access to teen-designed research protocols and data, there is the potential for youth to inspire and be inspired by their peers following divergent paths of inquiry, and enlist peers in collecting/interpreting data and developing narratives around locally-relevant issues and topics. Bild, Davidtag:beta.briefideas.org,2005:Idea/2462015-09-30T21:04:51Z2015-10-01T06:00:27ZBionode - Modular and universal bioinformaticshttp://dx.doi.org/10.5281/zenodo.31637> Highly reusable tools and code for bioinformatics, focused on
* [Node.js](http://nodejs.org)/JavaScript to be *"write once, run anywhere"*
* Node.js [Streams](https://nodejs.org/api/stream.html) and [Events](https://nodejs.org/api/events.html) for scalable and reactive pipelines
* CLI for easy integration with other tools and languages
The [huge decrease in sequencing cost](https://upload.wikimedia.org/wikipedia/commons/b/b7/DNA_Sequencing_Cost_per_Genome_Over_Time.jpg) and consequent [explosion of data](https://www.nlm.nih.gov/about/image/2014CJ_fig_5.png) is reinforcing the need for well tested and scalable tools in biology. It is also causing a [boom in biological web services and databases](https://en.wikipedia.org/wiki/List_of_biological_databases) that often require some data to be processed in the browser. [Bionode](http://bionode.io) provides bioinformatics tools written in Node.js. Bionode is an improvement on other [bio* libraries](http://www.open-bio.org/wiki/Projects#Main_projects) because it can be run anywhere (browsers or servers), it is streamable, and it can be integrated with other projects and programming languages (each tools is a Node.js module but also comes with a [CLI](https://github.com/bionode/bionode-ncbi#usage)). Bionode tools follow the UNIX philosophy "do one thing and do it well".
All the development is public and transparent. The code is [MIT](https://opensource.org/licenses/MIT) licensed on [GitHub](http://github.com/bionode), and discussions happen on [Gitter](http://gitter.im/bionode/bionode) and IRC ([freenode #bionode](http://irccloud.com/#!/ircs://irc.freenode.net:6697/%23bionode)). We welcome all kinds of contributions (code, ideas, etc) and we collaborate and integrate with existing projects, such as [Dat](http://dat-data.com) (e.g., [Mozfest 2014 workshop](http://try-dat.com/guide/08-extra-credit.html
)), [BioJS](http://biojs.net) (e.g., [applied together for GSoC 2015](http://biojs.net/gsoc/2015/projects/bionode_biojs.html
)), and [CWL](http://common-workflow-language.github.io
) (e.g., [brainstormed and hacked together at #biohack15 Japan](https://github.com/dbcls/bh15/wiki/Software#reproducible-and-distributable-software-and-data
)). We apply the best practices from web development startups (e.g., [testing, coverage, CI, etc](https://github.com/bionode/bionode-template#principles)) into developing scientific software. Our best practices have [already inspired other projects](https://github.com/hydronode). We have a [small community](https://www.dropbox.com/s/njgeis4e1urolud/Screenshot%202015-09-30%2015.06.19.png?dl=0) but need more contributors.
* [Bionode website](http://bionode.io)
* [Wurmlab website](http://wurmlab.github.io)
* [Bionode GitHub repository](http://github.com/bionode)
* [Bionode Gitter chat room](http://gitter.im/bionode/bionode)
* [Online shell to try Bionode](http://try.bionode.io)
* [Dat Mozfest14 workshop with Bionode chapter (8)](http://try-dat.com)
* [BioJS GSoC15 page with Bionode project ideas](http://biojs.net/gsoc/2015/)
* [Recent talk at biocoders meetup in Cambridge](http://bmpvieira.com/biocoders15a)
Vieira, Brunotag:beta.briefideas.org,2005:Idea/2452015-09-30T19:06:17Z2020-09-22T10:09:30ZPromoting Open Research among future scientists.http://dx.doi.org/10.5281/zenodo.31629It’s easier to mold a human at his childhood days than at later part of his life. The proposed idea is based on this simple fact.
**Idea:**
Imagine creating an online platform that acts an incubator for Open Research. The platform could be anything such as a simple mobile app or website. The primary aim of this platform is to teach and spread awareness about Open Research among young students while simultaneously developing the habits of doing open research in them. The platform can be developed in two parts:
1.The platform contains information and prospects of Open Research. The information may be provided in the form of online courses or tasks. Upon completion of certain courses/tasks the user’s can be awarded with Open Badges and scores.
2. Once the user has received a minimum no of points, allowing him to submit his research proposal. The platform can be developed in such a manner that it connects the proposed idea organizations supporting Open Research or the ones offering fellowships for the same.
It’s important to start the habit of doing open research at early days in one’s life as the next Stephen Hawking’s lies in between the kids.
Agarwal, Priyanktag:beta.briefideas.org,2005:Idea/2442015-09-30T17:36:38Z2020-08-09T06:00:50ZminiReproducibility Projecthttp://dx.doi.org/10.5281/zenodo.31626A valuable but hidden set of data: research trainees spend months to years confirming previously published data. These experiments are not considered publishable. Other trainees in the same field “reinvent the wheel” due to lack of publicly available information.
A simple idea: Imagine the savings in time and resources, reduction in retractions and the impact of each experiment if we knew the following: 10 labs repeated it, 7 found a phenotype and 3 did not. What if a single click could highlight differences in methodology between each experiment?
Our vision is to create a gamified portal for researchers (initially focused on students and postdocs) to publish replicated data, compare methodology and provide reproducibility statistics for individual experiments. A user ladder with increasing prestige (pioneer-->scholar--->catalyst), reviewing and commenting rights, and goodies donated by biotech (antibodies, kits etc.), coupled with the real benefit of having publications and peer-reviewing experience will attract trainees and encourage return usage.
The act of comparing several submissions and associated methodologies itself has received overwhelming support from a large network of fellow trainees and mentors (~100). We request a technical partnership to allow single experiment submission, review by several “players” and assessment of reproducibility.goyal, girijatag:beta.briefideas.org,2005:Idea/2422015-09-29T20:59:58Z2015-11-24T16:25:36ZModify and run other people's research code in your browserhttp://dx.doi.org/10.5281/zenodo.31598Science makes progress by reusing results and building on them. For research software this is pretty hard (the people writing it often do not have the time to make slick installers like big libraries do). As a result there is not as much reuse as there could be. With [`everware`](//github.com/everware/everware) we are changing this.
With `everware` you can edit and run code from a git repository with one click, in your browser. This significantly reduces the barrier to entry for trying out other people's code on a whim. As a result you will try out and decide to reuse other people's code more often, instead of rolling your own. Furthermore, if reuse is possible, reproducibility comes for free.
Interest in big discoveries like the Higgs boson is massive, imagine how many lay-people would love to be able to run (parts of) the analysis software that discovered the Higgs.
As the author of a research code all you have to do for your repository to be `everware`-ready is provide a `Dockerfile` that describes how to setup all the dependencies. Once this is done other's can launch your code from their browser and experiment with it.
`Everware` builds on [github](//github.com), [docker](//docker.io) and [project jupyter](//jupyter.org). It started as a project at the [CERN webfest 2015](//webfest.web.cern.ch/). You can find [project everware](//github.com/everware/everware) on github.Head, Tim