Science Startups meet at Le Web 2014

Axon

Since becoming Elsevier’s VP of Strategy, Mendeley Co-founder and CEO Victor Henning has been up to a lot of exciting stuff. Here he tells us a bit about his latest project, Axon, which is stirring things up by bringing together the best and brightest new startups in the fields of Science and Research at Le Web 2014.

Over the last few years, I have watched something interesting happen in the world of science: Tech startups and VCs suddenly care about scientists. Strangely, this wasn’t always the case.

When the World Wide Web was invented at CERN, its original purpose was to help manage and share scientific information about particle accelerator experiments. Yet, with the exception of a few search engines, document repositories, and journal databases, the web remained barren of well-designed tools and applications engineered for scientists.

Instead, the last 15 years witnessed the explosion of the consumer web and mobile apps, fueled by advertising revenue. Jeff Hammersbacher, an early Facebook data science employee (and now founder of Cloudera), summed it up as:

“The best minds of my generation are thinking about how to make people click ads. That sucks. If instead of pointing their incredible infrastructure at making people click on ads, they pointed it at great unsolved problems in science, how would the world be different today?”

How indeed? We might be watching hilarious cat gifs on the screens of our flying cars.

Around 2008, things started to change: A small wave of bootstrapped startups began building document management tools, social networks, and recommendation engines for scientists. Among them was Mendeley, my own company. Grown out of our own frustrations as researchers, my co-founders and I built Mendeley to make science more open, more efficient, and more collaborative. Getting started wasn’t easy – many VCs turned us down because they saw research as a “niche”. We nonetheless managed to convince a couple of angel investors (among them the founders of Skype) to invest in us.

After launching in 2009, we came to LeWeb to participate in the startup competition. I have the fondest memories of the event – a freezing, pre-Christmas Paris in December, and Dave McClure, the famously foul-mouthed Silicon Valley angel investor, tweeting his sexual arousal at seeing our pitch:

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Events like LeWeb helped put us on the map with international investors, press, and potential users. From there, Mendeley grew to a research platform connecting more than 3.5 million researchers in 180 countries, with institutional customers like Stanford, Harvard, and MIT. In April 2013, we were acquired by Elsevier, the world’s largest publisher of science and health information.

Without wanting to claim undue credit, quite a few Ph.D. students and Postdocs who became entrepreneurs themselves have told me that Mendeley was an inspiration for them: It proved that tools for researchers could go from garage to global audience, and it proved to potential investors that the “niche” could also deliver sizeable exits.

We are now seeing the emergence of a second wave of venture-backed research startups, offering a much wider range of scientific workflow tools. They help scientists keep electronic versions of lab notebooks, organize and share experimental data, order lab materials, write papers collaboratively, outsource experiments to other labs and to the cloud, get credit for peer reviews, launch their own journals, and even raise crowdfunding for their research projects.

It’s time to give this movement more visibility. Elsevier and LeWeb 2014 are teaming up to run a half-day event called Axon@LeWeb (in case you’re wondering – in the brain, axons are the fibres that carry impulses from neurons to other nerve cells). We want to bring together the most exciting science and research startups – the ones that build tools for the best minds of our generation, to help them crack those great unsolved problems.

Startups can apply online here, and we already have applications from amazing companies in the US, Canada, Sweden, France, the UK, and Germany. The 15 best startups will receive a free ticket to LeWeb 2014, as well as the opportunity to present at Axon@LeWeb and network with the hottest companies in this space. Even if your startup is not among the 15 selected to present, Elsevier is sponsoring a €200 discount on the regular startup ticket for all science and research startups that want to join us at LeWeb.

Applications for Axon@LeWeb close on Sunday, 16th November, at midnight CET, and the winning startups will be announced by Tuesday, 18th November.

Hope to see you in Paris in December!

Mendeley Debates At Cambridge : Do We Need A ‘Right To Be Forgotten’ ?

GabeHughes 1

By: Gabriel Hughes, VP Web Analytics at Elsevier

Images © Chris Williamson, courtesy of the Cambridge Union Society 

Should we have the right to require websites to ‘forget’ or ‘delete’ stories and posts about us which we find embarrassing or just don’t want other people to see? Should people be able to force search engines to remove links to information like that? Do individuals need more legal powers to control their personal data online?

As a growing technology company based in London, Mendeley finds itself drawn into many of the great debates facing the technology sector in Europe today, and we take this responsibility very seriously.

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This October, we were proud to sponsor the prestigious Cambridge Union Society as it debated the ‘The Right To Be Forgotten’, a contentious issue following recent legal developments in Europe.

Under a ruling made in May, in a case brought against Google, European citizens may now demand that search engines remove links to online public information about them. This is the current legal interpretation of the ‘right to be forgotten’, a concept which has been debated for some years and is outlined in the EU’s Data Protection Directive drafted back in the 1990s. This ethical and legal issue is still evolving and whatever finally emerges is likely to have far reaching implications for the internet for many decades to come.

I entered the debate from my personal position, one that is also informed by my experience working at Google, which is of course the company most significantly affected by this new ruling. My fellow teammates in opposition were the MP for Cambridge Julian Huppert,  Mariam Cook, CEO of Position Dial, and Alistair McCapra, CEO of Chartered Institute of Public Relations. The side in proposition of the motion was led by David Smith, Deputy Commissioner at the Information Commissioner’s Office, and also included Jon Crowcroft,  Professor of Communications Systems at Cambridge, Gavin Phillipson, Chair of Law at Durham University and also Emma Carr, Director of Big Brother Watch. Each of these expert speakers brought considerable depth of knowledge and unique perspectives to this complex issue.

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My argument in opposition was based not on a disagreement with the right to privacy or control over one’s personal information, quite the contrary. It focused on the deep flaws in the recent European court ruling, which targeted search engines and technology companies, who are not responsible for what publishers and individuals post online. A perverse outcome of the ruling is that in asking Google to delete a link to something you do not like, they are put in a position where they alone have to judge whether it is in fact right for them to do so, leaving the publisher under no obligation to delete the offending post itself. The information remains online, and search engines are forced into a censorship role which few can defend.

In my opinion, search engines are just a part of the navigational infrastructure that enables the internet to function, together with social networks, wiki pages, feeds and the hypertext link itself, and this ‘right to be forgotten’ ruling confuses navigational linking technology with the content that it points to. Nobody seems to think it is a good idea to force Google into this new Big Brother role where it now tries to arbitrate what websites can share online, and this new right turns the neutral and automated role of a search engine on its head.

The opposing team also pointed out that many of the worst cases where private or embarrassing information has been posted online are already covered under data protection, harassment and privacy laws. New laws have a habit of creating unintended consequences that could lead us down a dark path of censorship and excessive regulation, they warned.

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In the end, this team opposing the right to be forgotten won the debate. Before entering the debate chamber 40 per cent of the audience indicated they supported the motion ‘this house supports the right to be forgotten’, but after hearing the debate, the balance of the vote had shifted against, with the ‘nay’ side winning by 35 per cent to 30.

Yet the debate highlighted the complexity of the issue and this was reflected in how close the vote ended and in how many felt compelled to abstain. Indeed, one audience member spoke up ask whether the debate was about the principle of the Right To Be Forgotten, or the actual right in law now defined by the Court of Justice of the European Union. Some of those arguing in support of the proposition did not seem to think search engines should be targeted and distanced their arguments from the court ruling. Likewise, those speaking against the motion acknowledged the real concerns of many people about how their data is used online.

It seems a balance has to be struck between opposing demands. An absolute right to be forgotten, allowing everyone complete control over what information about them should be published online, makes no sense. There are too many politicians who have over-claimed expenses, doctors who have been sued for malpractice, and bankers who have been convicted of fraud. If there are to be more legal powers to control what information about you is out there, then everyone accepts there have to be counter-balancing limitations in defence of freedom of speech and freedom to know.

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At the same time, we all have to recognise that our society is going through a period of enormous change, whereby more data than ever is collected about our day-to-day life. We are moving too close to the point where almost every waking moment of our lives is recorded online, and can potentially be shared or made public. The volumes of data about us that are being collected and stored are truly immense and unprecedented in our history.

Given this, the truth is that our society does need to evolve new mechanisms, both technical and maybe even legal, to ensure that individuals are empowered to better manage their privacy and identity online. The challenge will be doing this in such a way that we do not introduce censorship, and an Internet plagued by legal disputes over what should or should not be online. Reflecting on the debate, it looks very much like we do need new solutions, but perhaps just not this one.

Jan Reichelt

As Jan Reichelt, President and Co-founder of Mendeley, made clear in his introduction, we have a firm ethical policy to preserve data protection and privacy for our users. We also believe in the power of technology innovation to solve the very toughest problems, often powered by data that our researchers and the scientific community creates. We will continue to support the great debate about to balance these interests, so we can support both freedom of speech and the right to privacy.

Interested to contribute to the debate ? Tweet us at @Mendeley_com or @gabehughes #RTBF

Crowdfunding to develop healthcare matching technology

Utilize health

A technology platform is helping to match paraplegic patients and those with neurological disabilities with the best healthcare providers available. They now want to use crowdfunding to develop this service even further, and their Indiegogo campaign has already reached over half of their initial $60,000 goal. Here’s their story, which began over 10 years ago…

By Jessica Harthcock, Founder and CEO of Utilize Health

I was 17 when I was paralyzed practicing gymnastics with the goal of bettering my skills for the springboard diving team. From the beginning, my prognosis was very grim; doctors said I would never regain function. This was certainly not what I thought my life would look like at age 17. My family and I wanted options – we wanted a treatment or therapy we could TRY. So for the next several years, my family and I traveled in search of highly specialized rehabilitation treatments. We went everywhere – Mayo Clinic, Vanderbilt, facilities in Chicago, Miami and Louisville. I tried anything and everything I could get my hands (or legs) on. I tried Lokomat therapy, e-stem, underwater treadmill training, vestibular therapy, hippo therapy (and the list goes on). After several years of hard work, I learned to walk again. Today, I still don’t have sensation below T3, but I walk by sight (and with the help of my service dog, Ozzie). It’s been a journey, one that’s never really over.

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This experience has taught me a lot about myself, but also about the gaps in the healthcare system. It was extremely difficult to learn about all of the existing and new treatments. Googling only gets one so far. Once I found a treatment or therapy I wanted to try, no one could tell me where to go to get it. Locating a facility with a particular therapy sometimes took months. After experiencing difficulties in finding resources and therapies, I knew there had to be an easier way, so I vowed to create a tool that could help other patients find the resources they needed without wasting time, energy and financial resources. Thus, Utilize Health was born.

Utilize Health is a platform that matches patients with neurological disabilities to the therapies and facilities they need to maximize their potential for recovery. Think OpenTable or Hotels.com, but for patients and facilities/therapies.

My husband and I started the company in May 2013. We were accepted into a top-ranked business accelerator program called Jumpstart Foundry. Through the program, we developed the idea into a sustainable business.

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In December of 2013, Utilize Health was very fortunate to unexpectedly receive national press from USA Today. Patients, families, facilities and equipment manufacturers all started reaching out to see if they could use our service. But there was a BIG problem… the website didn’t exist yet. We were in the process of raising funds to build the web application.

I lost sleep… a lot of sleep. What do we do? People need this and they need it NOW. Patients don’t want to wait. Every email, phone call, and social media request seemed more urgent than the next.

The Utilize Health team rallied. We created a plan. We started to manually match patients to therapies and facilities across the country. Manual matching is completed by essentially looking at spreadsheets and other paper databases. Manual matching is time consuming. It takes anywhere from 7-10 days, sometimes longer.

In April, the Utilize Health team had successfully matched more than 100 patients to therapies and facilities across the country. Patients and their loved ones were thrilled with the resources Utilize Health was able to provide them.

Unfortunately, there are still patients and their families on the waitlist waiting to be matched. More patients sign up daily. With a wait list a mile long, we need to automate the matching process. This is when we decided to ask the public for help through crowdfunding.

Crowdfunding has given us an opportunity to gain support within the community. In less than 48 hours, we raised more than $20,000. We were completely blown away by people’s generosity.

https://www.indiegogo.com/project/utilize-health-matching-patients-to-the-care-they-need/embedded

All the funds pledged will do directly towards the development and creation of the web application to automate the matching process. Perks and prizes are offered such as Utilize Health swag and patient advocate subscriptions. Our campaign is live until August 22nd. Click on the link below to check out the campaign.

We are so thankful to everyone who has contributed thus far. We truly hope to make an impact for those individuals who have neurological conditions. As we say at Utilize Health, No One Walks Alone.

If you’re interested in the subject, why not join the Mendeley Crowdfunding group, or let us know in the comments below if you have any experiences to share with the community!

 

 

 

JoVE Guest Blog Post – Visualising Scientific Experiments

JoVE October blog

This is the first in a series of guest posts from JoVE, the Journal of Visualized Experiments. Each month we’ll be featuring a different peer-reviewed video article with insights from their team. Like Mendeley, JoVE is using technology to make science more open, and we were really happy to have their Director of Marketing Rachel Greene join us at Social Media Week London for the Mendeley Masterclass on How Technology is Changing Research. You can watch the video of her presentation, talking about how visualising experiments enhance reproducibility on the Mendeley YouTube channel, and as usual let us know what you think in the comments below!

MALDI-TOF MS, an Adaptable Method for Protein Characterization, Visualized in a JoVE-Chemistry Video Article

(J. Vis. Exp. (79) e50635, doi:10.3791/50635 (2013))

By Val Buntrock, Ph.D.

Journal Development Editor, JoVE

A recent video-article published in JoVE, the Journal of Visualized Experiments, by a research group at the Centre National de la Racherche Scientifique (CNRS) captures the process of analyzing intact proteins using mass spectrometry (MS). In their video article, Signor et al. demonstrate how to accurately measure large proteins using matrix assisted laser-desorption ionization time-of-flight (MALDI-TOF) MS. Often, when describing MALDI-TOF MS procedures in text, essential information is omitted, leading to poor reproducibility. Part of a new trend in publishing, this video demonstration records the subtleties and nuances of this complex technique. Employing proper technique and variable consideration, this research group identifies an intact, large protein (> 100 kDa) with high sensitivity using a small amount (0.5 pmoles) of protein sample. Using these video instructions, research groups around the globe can modify this flexible technique to identify an infinite number of large proteins.

Phosphoregulation

Characterizing proteins is important for determining the current state of the protein, which has severe implications to several biological processes. The significance of proteins switching between active and inactive forms via protein kinase phosphorylation events has been recognized and applied to cellular and molecular research for several decades. Researchers have gone on to show that protein folding, as determined by phosphorylation, either exposes or protects structural motifs that serve as binding sites for effector molecules. Further, the binding between protein and effector molecule controls protein function. Therefore, the initial protein phosphorylation event regulates the activity level of the protein.

Protein activity or function plays a role in switching on or off a large number of cellular processes, such as cell communication and cell replication. As structural biologists identify a growing number of disease states related to malfunctioning protein modifications and subsequent de-regulation, understanding and identifying the differences between the two states of the protein (active or inactive) has become a priority.

Protein Characterization

A simple, fast, and common method of determining the presence or absence of phosphorylation in proteins is by determining their mass using mass spectrometry (MS). MS ionizes the molecule of interest, generating a charged species, and measures its mass-to-charge or m/z ratio.  The m/z ratio is determined by the isotopic distribution of each element present, meaning that each molecule or protein has its own unique isotopic pattern or fingerprint.

Two MS techniques are typically used to ionize heavy and labile biomolecules, such as proteins: electrospray ionization (ESI MS) and matrix assisted laser-desorption ionization time-of-flight (MALDI-TOF MS). ESI MS analysis requires dissolution of the sample in a pure solvent for direct ionization from the solution mixture. MALDI-TOF MS utilizes a co-crystallization method wherein the protein is crystallized with an ultraviolet (UV) absorbing organic species. This organic molecule is referred to as the matrix molecule or substance.

While ESI MS is more sensitive and accurate, the instrument compatible solvents or buffers typically contain significant amounts of substances, such detergents and salts, which interfere with the desired protein pattern. Additionally, ESI MS data is more difficult to interpret given that ESI MS spectra are riddled with multiple overlapping charge states from a single protein. A more gentle technique, MALDI-TOF MS produces fewer multiply-charged species, leading to a much cleaner spectra that is easier to analyze. This is especially true for larger biomolecules, such as proteins, which can fragment into numerous multiply charged species using ESI MS. For these reasons, MALDI-TOF MS is the preferred technique for protein analysis.

Optimizing MALDI-TOF MS Technique

Matrix

Purity at every stage of MALDI-TOF MS analysis is crucial to obtaining the highest quality MS spectra or protein fingerprint. For this reason, Signor et al. provide detailed instructions for how to effectively 1) clean the MALDI plate that holds the matrix and protein of interest and 2) purify the matrix substances using standard recrystallization techniques. Further, they employ two different matrix systems to compare which one yields the best results for the protein of interest. A single matrix and a mixed matrix system are used, demonstrating the influence of the matrix on the resulting spectra. In their work, Signor et al. found that the mixed matrix system yielded a higher signal to noise and a greater sensitivity than the single matrix system.

Deposition Method

The deposition method is another technique variable that impacts the quality of MALDI-TOF MS results. The two most commonly employed deposition methods are the droplet and thin layer method. Using a droplet technique, a mixture of the protein analyte and matrix solution is “dropped” onto the target substrate, and the solvent is evaporated, yielding a crystalline mixture of the matrix and protein. Slightly more controlled, the thin layer technique is composed of layers of matrix sandwiching the protein analyte layer. While the droplet method suffers from poor resolution and an inability to observe larger proteins (> 100 kDa), the thin layer deposition yields a protein fingerprint for large proteins, sharper peaks, and a higher signal to noise.

As protein analysis becomes a more vital component of studying protein modifications, mastering protein characterization techniques is increasingly important. In this video-article, Signor et al. provide a detailed overview of the steps involved in utilizing MALDI-TOF MS to analyze proteins. They also provide essential considerations and modifications to guide beginners and experts alike through tailoring this powerful technique to study different target proteins. Shown in video format, the necessary level of details, such as how to properly perform multiple deposition methods, is captured and relayed to the viewer for increased transparency.