innovation

Stone Basket Innovations, LLC v. Cook Medical, LLC

(United States Federal Circuit) - Affirming a district court order denying a motion for attorney fees following the dismissal of a patent infringement suit with prejudice because attorney fees are only available in exceptional circumstances and the court decision was not an abuse of discretion.




innovation

Conversations about Innovations in Teaching, Research and Technology

From pioneer in our field, Jeanne Brett: With the unprecedented and rapid need to switch from face-to-face to synchronous online classes, everyone using exercises and simulations has learned a lot.  iDG, NegotiateUP and NTR  are launching a series of Conversations about Innovations in Teaching Research and Technology held during three Fridays in June (5th, 12th, … Continue reading Conversations about Innovations in Teaching, Research and Technology




innovation

2021 Innovations in Freight Data

Convened by TRB, Innovations in Freight Data will be held on June 2-3, 2021 at the Beckman Center in Irvine, California. The workshop will bring together freight data users and decision makers to learn and share the latest applications of traditional and emerging freight data sources, development of value-added features, integration of data sets, and other innovations.




innovation

American tech goliaths decide innovation is the answer to Chinese 5G dominance, not bans, national security theater

Microsoft, Cisco, Google etc gang up to form Open RAN Policy Coalition

Some of America’s super-corps have remembered how the US became the dominant global technology force it is, and have vowed to use innovation over threats to counter Chinese dominance in 5G markets.…




innovation

IBM Reveals Five Innovations That Will Change Our Lives within Five Years

Today IBM unveiled the seventh annual IBM 5 in 5 – a list of innovations that have the potential to change the way people work, live and interact during the next five years.




innovation

IBM Reveals Five Innovations That Will Change Our Lives in the Next Five Years

Today IBM formally unveiled the fifth annual "Next Five in Five" – a list of innovations that have the potential to change the way people work, live and play over the next five years: • You'll beam up your friends in 3-D • Batteries will breathe air to power our devices • You won’t need to be a scientist to save the planet • Your commute will be personalized • Computers will help energize your city



  • Energy & Utilities

innovation

IBM optimise "Watson Anywhere" avec de nouveaux clients et des innovations conçues pour rendre encore plus facile la mise à l'échelle de l'intelligence artificielle sur tous les types de cloud

Reconnaissant que les entreprises mettent du temps à adopter l'intelligence artificielle, en partie à cause de la complexité croissante des données, IBM (NYSE : IBM) dévoile aujourd'hui de nouvelles innovations qui optimisent son approche Watson Anywhere pour mettre à l'échelle l'intelligence artificielle sur tous les types de cloud, et de permettre à une multitude de clients de tirer parti de la stratégie pour intégrer l'intelligence artificielle à leurs données, où qu'elles se trouvent.




innovation

Innovation activity slows in Australia according to Innovation Index

IBM Australia and the Melbourne Institute of Applied Economic and Social Research, University of Melbourne, today announced the launch of the IBM-Melbourne Institute 'Innovation Index of Australian Industry’ second edition. The Study revealed that the annual increase in the rate of innovative activity in Australia in 2006 was only 0.7 percent, with only four industries experiencing an increase in the annual rate of innovation in that period: communication services; mining; finance; and the insurance industry.



  • Energy & Utilities

innovation

Speech: Innovation for a sustainable future

My topic today is innovation for a sustainable future. This raises two questions:



  • Energy & Utilities

innovation

Southern Cross Computer Systems Wins IBM Beacon Award for Innovation in Green IT Data Center Solution

Southern Cross Computer Systems Pty Ltd has been named winner of the award for “Innovation in Green IT Data Center Solution” in the annual IBM Beacon Awards competition, honoring IBM Business Partners for their ingenuity, innovation, customer satisfaction and outstanding achievements in providing business solutions.




innovation

IBM study finds majority of Australian shoppers “apathetic” towards retailers, hungry for multi-channel innovation

An IBM (NYSE: IBM) study of 26,000 consumers from 14 countries -- including almost 2,000 Australians.-- found that over 60% of Australian consumers identify themselves as “apathetic” in their choice of primary retailer – almost double those who see themselves as advocates of a particular retailer. As such Australian retailers have a significant opportunity to capture shopper loyalty, but they need to capitalise on existing investments in multi-channel and accelerate customer engagement across all channels, including mobile devices and social media platforms in order to win in this globally competitive sector.



  • Services and solutions

innovation

Iriss and the Care Inspectorate explore risk and innovation

In 2015, Iriss launched a joint project with the Care Inspectorate to explore strategic innovation, resilience and risk in the context of the Care Inspectorate’s mandate of scrutiny and improvement.

The project has comprised of an internal staff survey with 108 responses, two workshops with 18 staff members, and has sought to engage the wider Care Inspectorate workforce through the findings. 

read more




innovation

Collaboration and innovation will break down barriers to health and social care integration

Professor Lord Patel of Bradford OBE, former chair of the Mental Health Act Commission, makes the case for a radical new report that offers practical solutions to breaking integration barriers.




innovation

Thinking of the future: Innovations, & developments for social work practice: social media and digital technology for social work practice.

When: Mon Feb 8, 2016

Where: Stirling Court Hotel, University of Stirling
Event Status: confirmed
Event Description: https://www.eventbrite.co.uk/e/thinking-of-the-future-innovations-and-developments-for-social-work-practice-tickets-19249165773



  • http://schemas.google.com/g/2005#event

innovation

Expected Profits and The Scientific Novelty of Innovation -- by David Dranove, Craig Garthwaite, Manuel I. Hermosilla

Innovation policy involves trading off monopoly output and pricing in the short run in exchange for incentives for firms to develop new products in the future. While existing research demonstrates that expected profits fuel R&D investments, little is known about the novelty of the projects funded by these investments. Relying on data that describe the scientific approaches used by a large sample of experimental drug projects, we expand on this literature by examining the scientific novelty of pharmaceutical R&D investments following the creation of the Medicare Part D program. We find little evidence that the positive demand shock implied by this program prompted firms to undertake scientifically novel R&D activity, as measured by whether the specific scientific approach had been used before. However, we find some evidence that firms invested in products involving novel combinations of scientific approaches. These estimates can inform economists and policymakers assessing the tradeoffs associated with marginal changes in commercial returns from newly developed pharmaceutical products.




innovation

Immigration, Innovation, and Growth -- by Konrad B. Burchardi, Thomas Chaney, Tarek Alexander Hassan, Lisa Tarquinio, Stephen J. Terry

We show a causal impact of immigration on innovation and dynamism in US counties. To identify the causal impact of immigration, we use 130 years of detailed data on migrations from foreign countries to US counties to isolate quasi-random variation in the ancestry composition of US counties that results purely from the interaction of two historical forces: (i) changes over time in the relative attractiveness of different destinations within the US to the average migrant arriving at the time and (ii) the staggered timing of the arrival of migrants from different origin countries. We then use this plausibly exogenous variation in ancestry composition to predict the total number of migrants flowing into each US county in recent decades. We show four main results. First, immigration has a positive impact on innovation, measured by the patenting of local firms. Second, immigration has a positive impact on measures of local economic dynamism. Third, the positive impact of immigration on innovation percolates over space, but spatial spillovers quickly die out with distance. Fourth, the impact of immigration on innovation is stronger for more educated migrants.




innovation

Travel innovations that repel bugs and keep germs away

A wrap that also keeps mosquitoes away and a sheet that slips between you and the airplane seat are a couple of products that help keep you safe.




innovation

DSU offers new certificate, chooses new Atwood Innovation Plaza director

Dixie State University recently announced both a new educational certificate and a new director for its Atwood Innovation Plaza.

       




innovation

Great leaders inspire innovation and creativity from within their workforces

Rita J. King, co-director and EVP for business development at Science House, recently conducted a series of interviews with business leaders, exploring the challenges and hurdles companies face in evolving business landscapes. In this interview, King chats with James Jorasch, founding CEO of Science House, about the importance of innovation and how to inspire and […]



  • Future of the Firm
  • Big Systemic Thinking

innovation

CBD News: This year's World Cities Day theme, "Changing the world: innovations and better life for future generations", focuses on how urban governance can be used to achieve sustainable development.




innovation

NIH invests in rapid innovation and development for COVID-19 testing

(University of Massachusetts Lowell) UMass Medical School and UMass Lowell will perform a key role in a new National Institutes of Health initiative aimed at speeding innovation, development and commercialization of COVID-19 testing technologies via their Center for Advancing Point of Care Technologies collaboration.




innovation

A smart space for innovation

Entrepreneur Ricky Chan’s information technology company has been hard at work developing a virtual reality application that enables designers and their clients to walk through different versions of their home or office without having to physically move a single piece of furniture.

 

From the colour of the walls to the style of fixtures and fittings, Mr Chan’s app caters to all personal tastes and design ideas.

 

“We have customers who are interior designers or furniture retailers. Our virtual reality application brings their sketches to life. Designers in the past needed weeks to produce sketches. Now they can make designs instantly,” he explained.

 

Up to 40% of the application was developed at Smart-Space 8 in Tsuen Wan, Cyberport’s first co-working space outside its main Pok Fu Lam campus.

 

“Cyberport provides funding that helps to lower our expenses and we can hold seminars here with a rental fee that is much lower than the market price,” Mr Chan added.
 

The 20,000 sq ft space launched last year was specifically designed with young entrepreneurs in mind and provides workshops and seminars for startups. For companies that wish to join the Smart-Space 8 community, one of its founders must be aged between 18 and 35 and the company itself should not have been in operation for longer than seven years.

 

Smart-Space 8 users are entitled to comprehensive entrepreneurial support and value-added services to accelerate their businesses such as the Cyberport Creative Micro Fund and Cyberport Incubation Programme.

 

Mr Chan, who lives in the New Territories, said the added bonus of setting up shop in Smart-Space 8 is the commute, as Cyberport in Pok Fu Lam is farther away for him and his clients.

 

Cyberport may be expanding beyond Pok Fu Lam, but some entrepreneurs like agriculture technology company CEO and founder Gordon Tam have opted to stay at the home campus because of the incentives available.

 

“The business network here is unique. There are so many startups and we encourage and learn from each other.”

 

Mr Tam’s company sells vegetables from an indoor farm to local supermarkets and is now exploring the overseas market. He credits the vibrant community and ecosystem at Cyberport for building up his business.

 

“Traditional agriculture comes with a host of problems and the efficiency of Hong Kong’s agriculture industry is relatively low. This is why we are looking into indoor agriculture. We want to grow plants in industrial buildings.”

 

When Mr Tam joined the Cyberport Incubation Programme, his firm was offered two years of rent reduction. But more importantly, he said, the space is a one-of-a-kind ecosystem where his team can brainstorm ideas and continue to innovate.

 

Other startup owners share the same sentiment. Information technology company CEO and founder Stark Chan noted that with Cyberport as a public body, it offers a lot of support and rents are more stable.

 

“We have been here since we first started up. My colleagues are familiar with this environment and the atmosphere is good for innovation,” Mr Chan said.




innovation

Quality Over Quantity: In A Financial Crisis, Innovation Is A Survival of the Fittest

Wednesday, May 6, 2020 - 11:45

NEW YORK – Innovation is at an all-time high, but the economic damage from the COVID-19 outbreak has the potential to stifle inventions and patents. But new research shows that financial crises are both destructive and creative forces for innovation.




innovation

St. Jude awarded federal grant for Emerging Frontiers in Research and Innovation

(St. Jude Children's Research Hospital) Funding will help expand collaboration across engineering and physical sciences to expand tools for studying pediatric diseases.




innovation

Water.org: Financial Innovation for Impact

Were credit guarantees, in partnership with the International Finance Corporation (IFC), the right path for Water.org to scale its water-related microfinance initiatives in emerging markets?




innovation

Virtual Issue: Technological Innovations

Anne-Claude Gingras
Apr 1, 2020; 19:572-573
Editorial




innovation

Combining Precursor and Fragment Information for Improved Detection of Differential Abundance in Data Independent Acquisition [Technological Innovation and Resources]

In bottom-up, label-free discovery proteomics, biological samples are acquired in a data-dependent (DDA) or data-independent (DIA) manner, with peptide signals recorded in an intact (MS1) and fragmented (MS2) form. While DDA has only the MS1 space for quantification, DIA contains both MS1 and MS2 at high quantitative quality. DIA profiles of complex biological matrices such as tissues or cells can contain quantitative interferences, and the interferences at the MS1 and the MS2 signals are often independent. When comparing biological conditions, the interferences can compromise the detection of differential peptide or protein abundance and lead to false positive or false negative conclusions.

We hypothesized that the combined use of MS1 and MS2 quantitative signals could improve our ability to detect differentially abundant proteins. Therefore, we developed a statistical procedure incorporating both MS1 and MS2 quantitative information of DIA. We benchmarked the performance of the MS1-MS2-combined method to the individual use of MS1 or MS2 in DIA using four previously published controlled mixtures, as well as in two previously unpublished controlled mixtures. In the majority of the comparisons, the combined method outperformed the individual use of MS1 or MS2. This was particularly true for comparisons with low fold changes, few replicates, and situations where MS1 and MS2 were of similar quality. When applied to a previously unpublished investigation of lung cancer, the MS1-MS2-combined method increased the coverage of known activated pathways.

Since recent technological developments continue to increase the quality of MS1 signals (e.g. using the BoxCar scan mode for Orbitrap instruments), the combination of the MS1 and MS2 information has a high potential for future statistical analysis of DIA data.




innovation

Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics [Technological Innovation and Resources]

Top-down proteomics studies intact proteoform mixtures and offers important advantages over more common bottom-up proteomics technologies, as it avoids the protein inference problem. However, achieving complete molecular characterization of investigated proteoforms using existing technologies remains a fundamental challenge for top-down proteomics. Here, we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. Notably, the described UVPD setup applies multiple laser pulses to induce ion dissociation, and this feature can be used to optimize the fragmentation outcome based on the molecular weight of the analyzed biomolecule. When applied to complex proteoform mixtures in high-throughput top-down proteomics, 213 nm UVPD demonstrated a high degree of complementarity with the most employed fragmentation method in proteomics studies, higher-energy collisional dissociation (HCD). UVPD at 213 nm offered higher average proteoform sequence coverage and degree of proteoform characterization (including localization of post-translational modifications) than HCD. However, previous studies have shown limitations in applying database search strategies developed for HCD fragmentation to UVPD spectra which contains up to nine fragment ion types. We therefore performed an analysis of the different UVPD product ion type frequencies. From these data, we developed an ad hoc fragment matching strategy and determined the influence of each possible ion type on search outcomes. By paring down the number of ion types considered in high-throughput UVPD searches from all types down to the four most abundant, we were ultimately able to achieve deeper proteome characterization with UVPD. Lastly, our detailed product ion analysis also revealed UVPD cleavage propensities and determined the presence of a product ion produced specifically by 213 nm photons. All together, these observations could be used to better elucidate UVPD dissociation mechanisms and improve the utility of the technique for proteomic applications.




innovation

Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands [Technological Innovation and Resources]

The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.




innovation

MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity [Technological Innovation and Resources]

Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link information from both MS2 and MS3 level. However, the current cross-link search algorithm available for MS2-MS3 strategy follows a "MS2-centric" approach and suffers from a high rate of mis-identified cross-links. We demonstrate the problem using two new quality assessment metrics ["fraction of mis-identifications" (FMI) and "fraction of interprotein cross-links from known interactions" (FKI)]. We then address this problem, by designing a novel "MS3-centric" approach for cross-link identification and implementing it as a search engine named MaXLinker. MaXLinker outperforms the currently popular search engine with a lower mis-identification rate, and higher sensitivity and specificity. Moreover, we performed human proteome-wide cross-linking mass spectrometry using K562 cells. Employing MaXLinker, we identified a comprehensive set of 9319 unique cross-links at 1% false discovery rate, comprising 8051 intraprotein and 1268 interprotein cross-links. Finally, we experimentally validated the quality of a large number of novel interactions identified in our study, providing a conclusive evidence for MaXLinker's robust performance.




innovation

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation [Technological Innovation and Resources]

The use of protein biomarkers as surrogates for clinical endpoints requires extensive multilevel validation including development of robust and sensitive assays for precise measurement of protein concentration. Multiple reaction monitoring (MRM) is a well-established mass-spectrometric method that can be used for reproducible protein-concentration measurements in biological specimens collected via microsampling. The dried blood spot (DBS) microsampling technique can be performed non-invasively without the expertise of a phlebotomist, and can enhance analyte stability which facilitate the application of this technique in retrospective studies while providing lower storage and shipping costs, because cold-chain logistics can be eliminated. Thus, precise, sensitive, and multiplexed methods for measuring protein concentrations in DBSs can be used for de novo biomarker discovery and for biomarker quantification or verification experiments. To achieve this goal, MRM assays were developed for multiplexed concentration measurement of proteins in DBSs.

The lower limit of quantification (LLOQ) was found to have a median total coefficient of variation (CV) of 18% for 245 proteins, whereas the median LLOQ was 5 fmol of peptide injected on column, and the median inter-day CV over 4 days for measuring endogenous protein concentration was 8%. The majority (88%) of the assays displayed parallelism, whereas the peptide standards remained stable throughout the assay workflow and after exposure to multiple freeze-thaw cycles. For 190 proteins, the measured protein concentrations remained stable in DBS stored at ambient laboratory temperature for up to 2 months. Finally, the developed assays were used to measure the concentration ranges for 200 proteins in twenty same sex, same race and age matched individuals.




innovation

Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome [Technological Innovation and Resources]

Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.




innovation

A Compact Quadrupole-Orbitrap Mass Spectrometer with FAIMS Interface Improves Proteome Coverage in Short LC Gradients [Technological Innovation and Resources]

State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.




innovation

A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities [Technological Innovation and Resources]

We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm. After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.




innovation

Virtual Issue: Technological Innovations [Editorials]




innovation

MaxQuant software for ion mobility enhanced shotgun proteomics [Technological Innovation and Resources]

Ion mobility can add a dimension to LC-MS based shotgun proteomics which has the potential to boost proteome coverage, quantification accuracy and dynamic range.  Required for this is suitable software that extracts the information contained in the four-dimensional (4D) data space spanned by m/z, retention time, ion mobility and signal intensity. Here we describe the ion mobility enhanced MaxQuant software, which utilizes the added data dimension. It offers an end to end computational workflow for the identification and quantification of peptides and proteins in LC-IMS-MS/MS shotgun proteomics data. We apply it to trapped ion mobility spectrometry (TIMS) coupled to a quadrupole time-of-flight (QTOF) analyzer. A highly parallelizable 4D feature detection algorithm extracts peaks which are assembled to isotope patterns. Masses are recalibrated with a non-linear m/z, retention time, ion mobility and signal intensity dependent model, based on peptides from the sample. A new matching between runs (MBR) algorithm that utilizes collisional cross section (CCS) values of MS1 features in the matching process significantly gains specificity from the extra dimension. Prerequisite for using CCS values in MBR is a relative alignment of the ion mobility values between the runs. The missing value problem in protein quantification over many samples is greatly reduced by CCS aware MBR.MS1 level label-free quantification is also implemented which proves to be highly precise and accurate on a benchmark dataset with known ground truth. MaxQuant for LC-IMS-MS/MS is part of the basic MaxQuant release and can be downloaded from http://maxquant.org.




innovation

DEqMS: a method for accurate variance estimation in differential protein expression analysis [Technological Innovation and Resources]

Quantitative proteomics by mass spectrometry is widely used in biomarker research and basic biology research for investigation of phenotype level cellular events. Despite the wide application, the methodology for statistical analysis of differentially expressed proteins has not been unified. Various methods such as t-test, linear model and mixed effect models are used to define changes in proteomics experiments. However, none of these methods consider the specific structure of MS-data. Choices between methods, often originally developed for other types of data, are based on compromises between features such as statistical power, general applicability and user friendliness. Furthermore, whether to include proteins identified with one peptide in statistical analysis of differential protein expression varies between studies. Here we present DEqMS, a robust statistical method developed specifically for differential protein expression analysis in mass spectrometry data. In all datasets investigated there is a clear dependence of variance on the number of PSMs or peptides used for protein quantification. DEqMS takes this feature into account when assessing differential protein expression. This allows for a more accurate data-dependent estimation of protein variance and inclusion of single peptide identifications without increasing false discoveries. The method was tested in several datasets including E.coli proteome spike-in data, using both label-free and TMT-labelled quantification. In comparison to previous statistical methods used in quantitative proteomics, DEqMS showed consistently better accuracy in detecting altered protein levels compared to other statistical methods in both label-free and labelled quantitative proteomics data. DEqMS is available as an R package in Bioconductor.




innovation

Immunopeptidomic analysis reveals that deamidated HLA-bound peptides arise predominantly from deglycosylated precursors [Technological Innovation and Resources]

The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Whilst immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens.




innovation

Accelerating Innovation for a Circular Economy

Invitation Only Research Event

12 July 2016 - 9:30am to 5:30pm

Chatham House, London

Over the next two decades, a combination of ‘circular economy’ approaches and distributed manufacturing methods such as 3D printing raise the prospect of fundamental changes to the nature of production, the reconfiguration of supply chains and changes to patterns of resource consumption – with profound implications for sustainability. This roundtable will bring together expert participants from companies, government, civil society and academia to discuss the state of innovation in the ‘circular economy,’ with a particular focus on the approaches and activities of entrepreneurs and investors, what is needed to scale up and accelerate innovation, how to track and measure progress, and how to ensure that innovation in the ‘circular economy’ makes a significant contribution to the meeting of short and medium term climate and sustainability goals.

Attendance at this event is by invitation only. 

Johanna Lehne

Research Associate, Energy, Environment and Resources
+44 (0)20 7314 3629




innovation

Reversing our preconceptions about where innovation comes from

Reverse innovation may sound like some attempt to return to the dark ages - but it has a specific meaning, especially when it comes to med-tech. It’s about where we look for innovation - and overturning our preconceived ideas of where new ideas come from. Mark Skopec, and Matthew Harris - both from Imperial College London are two of the authors...




innovation

Embarking on the Next Journey: Innovations in Predeparture Orientation Programs for Refugees

This MPI Europe webinar examines innovative ways to better design and implement predeparture orientation programs for resetttling refugees. The discussion features observations from a refugee who went through an orientation program before being resettled in the Netherlands, and a resettlement agency official in Norway.




innovation

Social Innovation for Refugee Inclusion: A Sense of Home

The third Social Innovation for Refugee Inclusion conference in Brussels, co-organized by MPI Europe with the U.S. and Canadian Missions to the European Union and the European Economic and Social Committee, explored how innovations in living situations for refugees can promote community-driven inclusion, overcome divisions, facilitate economic opportunities, and foster a sense of "home."




innovation

Dental schools, industry team up to create innovation centers

The Center for Research & Education in Technology is encouraging dental schools to find out how to participate in its program and learn about the benefits to the school and its students.




innovation

Social Innovation for Refugee Inclusion: From Bright Spots to System Change

In the three years since the European migration and refugee crisis vividly captured public attention, a wave of innovative initiatives has emerged to help newcomers settle into receiving societies. Now, as the sense of crisis abates, this report explores what these initiatives will need to do to outlast the hype and produce lasting change on key integration issues such as housing, economic inclusion, and community building.




innovation

Social Innovation for Refugee Inclusion Conference Report: Maintaining Momentum and Creating Lasting Change

Fostering the social and economic inclusion of refugees has long been the domain of governments and NGOs. In the wake of the 2015–16 European migration and refugee crisis, however, new actors have emerged and taken on important roles in integrating newcomers. This report describes key discussions and takeaways from an MPI Europe conference on these developments.




innovation

Start-Up Visas: A Passport for Innovation and Growth?

Over the last decade, a number of governments have launched start-up visa programs in the hopes of attracting talented immigrant entrepreneurs with innovative business ideas. With the track record for these programs a mixed one, this report explains how embedding start-up visas within a broader innovation strategy could lead to greater success.




innovation

The Innovation Dilemma

"If it ain't broken, don't fix it."Sound advice, but limited to situations where "fixing it" only entails restoring past performance. In contrast, innovations entail substantive improvements over the past. Innovations are not just corrections of past mistakes, but progress towards a better future.

However, innovations often present a challenging dilemma to decision makers. Many decisions require choosing between options, one of which is both potentially better in the outcome but markedly more uncertain. In these situations the decision maker faces an "innovation dilemma."

The innovation dilemma arises in many contexts. Here are a few examples.

Technology. New and innovative technologies are often advocated because of their purported improvements on existing products or methods. However, what is new is usually less well-known and less widely tested than what is old. The range of possible adverse (or favorable) surprises of an innovative technology may exceed the range of surprise for a tried-and-true technology. The analyst who must choose between innovation and convention faces an innovation dilemma.

Investment. The economic investor faces an innovation dilemma when choosing between investing in a promising but unknown new start-up and investing in a well-known existing firm.

Auction. "Nothing ventured, nothing gained" is the motto of the risk-taker, while the risk-avoider responds: "Nothing ventured, nothing lost". The innovation dilemma is embedded in the choice between these two strategies. Consider for example the "winner's curse" in auction theory. You can make a financial bid for a valuable piece of property, which will be sold to the highest bidder. You have limited information about the other bidders and about the true value of the property. If you bid high you might win the auction but you might also pay more than the property is worth. Not bidding is risk-free because it avoids the purchase. The choice between a high bid and no bid is an innovation dilemma.

Employer decision. An employer must decide whether or not to replace a current satisfactory employee with a new candidate whose score on a standardized test was high. A high score reflects great ability. However, the score also contains a random element, so a high score may result from chance, and not reflect true ability. The innovation dilemma is embedded in the employer's choice between the current adequate employee and a high-scoring new candidate.

Natural resource exploitation. Permitting the extraction of offshore petroleum resources may be productive in terms of petroleum yield but may also present officials with significant uncertainty about environmental consequences.

Public health. Implementation of a large-scale immunization program may present policy officials with worries about uncertain side effects.

Agricultural policy. New technologies promise improved production efficiency or new consumer choices, but with uncertain benefits and costs and potential unanticipated adverse effects resulting from use of manufactured inputs such as fertilizers, pesticides, and machinery, and, more recently, genetically engineered seed varieties and information technology. (I am indebted to L. Joe Moffitt and Craig Osteen for these examples in natural resources, public health and agriculture.)

An essay like this one should - according to custom - end with a practical prescription: What to do about the innovation dilemma? You need to make a decision - a choice between options - and you face an innovation dilemma. How to choose? All I'll say is that the first step is to identify what you need to achieve from this decision. Recognizing the vast uncertainties which accompany the decision, choose the option which achieves the required outcome over the largest range of uncertain contingencies.

If you want more of an answer than that, consult your favorite decision theory (like info-gap theory, for instance).

I will conclude by drawing a parallel between the innovation dilemma and one of the oldest quandaries in political philosophy. In The Evolution of Political Thought C. Northcote Parkinson explains the historically recurring tension between freedom and equality.

Freedom. People have widely varying interests and aptitudes. Hence a society that offers broad freedom for individuals to exploit their abilities, will also develop a wide spread of wealth, accomplishment, and status. Freedom enables individuals to explore, invent, discover, and create. Freedom is the recipe for innovation. Freedom induces both uncertainty and inequality.

Equality. People have widely varying interests and aptitudes. Hence a society that strives for equality among its members can achieve this by enforcing conformity and by transferring wealth from rich to poor. The promise of a measure of equality is a guarantee of a measure of security, a personal and social safety net. Equality reduces both uncertainty and freedom.

The dilemma is that a life without freedom is hardly human, but freedom without security is the jungle. And life in the jungle, as Hobbs explained, in "solitary, poor, nasty, brutish and short".




innovation

Squirrels and Stock Brokers, Or: Innovation Dilemmas, Robustness and Probability

Decisions are made in order to achieve desirable outcomes. An innovation dilemma arises when a seemingly more attractive option is also more uncertain than other options. In this essay we explore the relation between the innovation dilemma and the robustness of a decision, and the relation between robustness and probability. A decision is robust to uncertainty if it achieves required outcomes despite adverse surprises. A robust decision may differ from the seemingly best option. Furthermore, robust decisions are not based on knowledge of probabilities, but can still be the most likely to succeed.

Squirrels, Stock-Brokers and Their Dilemmas




Decision problems.
Imagine a squirrel nibbling acorns under an oak tree. They're pretty good acorns, though a bit dry. The good ones have already been taken. Over in the distance is a large stand of fine oaks. The acorns there are probably better. But then, other squirrels can also see those trees, and predators can too. The squirrel doesn't need to get fat, but a critical caloric intake is necessary before moving on to other activities. How long should the squirrel forage at this patch before moving to the more promising patch, if at all?

Imagine a hedge fund manager investing in South African diamonds, Australian Uranium, Norwegian Kroners and Singapore semi-conductors. The returns have been steady and good, but not very exciting. A new hi-tech start-up venture has just turned up. It looks promising, has solid backing, and could be very interesting. The manager doesn't need to earn boundless returns, but it is necessary to earn at least a tad more than the competition (who are also prowling around). How long should the manager hold the current portfolio before changing at least some of its components?

These are decision problems, and like many other examples, they share three traits: critical needs must be met; the current situation may or may not be adequate; other alternatives look much better but are much more uncertain. To change, or not to change? What strategy to use in making a decision? What choice is the best bet? Betting is a surprising concept, as we have seen before; can we bet without knowing probabilities?

Solution strategies.
The decision is easy in either of two extreme situations, and their analysis will reveal general conclusions.

One extreme is that the status quo is clearly insufficient. For the squirrel this means that these crinkled rotten acorns won't fill anybody's belly even if one nibbled here all day long. Survival requires trying the other patch regardless of the fact that there may be many other squirrels already there and predators just waiting to swoop down. Similarly, for the hedge fund manager, if other funds are making fantastic profits, then something has to change or the competition will attract all the business.

The other extreme is that the status quo is just fine, thank you. For the squirrel, just a little more nibbling and these acorns will get us through the night, so why run over to unfamiliar oak trees? For the hedge fund manager, profits are better than those of any credible competitor, so uncertain change is not called for.

From these two extremes we draw an important general conclusion: the right answer depends on what you need. To change, or not to change, depends on what is critical for survival. There is no universal answer, like, "Always try to improve" or "If it's working, don't fix it". This is a very general property of decisions under uncertainty, and we will call it preference reversal. The agent's preference between alternatives depends on what the agent needs in order to "survive".

The decision strategy that we have described is attuned to the needs of the agent. The strategy attempts to satisfy the agent's critical requirements. If the status quo would reliably do that, then stay put; if not, then move. Following the work of Nobel Laureate Herbert Simon, we will call this a satisficing decision strategy: one which satisfies a critical requirement.

"Prediction is always difficult, especially of the future." - Robert Storm Petersen

Now let's consider a different decision strategy that squirrels and hedge fund managers might be tempted to use. The agent has obtained information about the two alternatives by signals from the environment. (The squirrel sees grand verdant oaks in the distance, the fund manager hears of a new start up.) Given this information, a prediction can be made (though the squirrel may make this prediction based on instincts and without being aware of making it). Given the best available information, the agent predicts which alternative would yield the better outcome. Using this prediction, the decision strategy is to choose the alternative whose predicted outcome is best. We will call this decision strategy best-model optimization. Note that this decision strategy yields a single universal answer to the question facing the agent. This strategy uses the best information to find the choice that - if that information is correct - will yield the best outcome. Best-model optimization (usually) gives a single "best" decision, unlike the satisficing strategy that returns different answers depending on the agent's needs.

There is an attractive logic - and even perhaps a moral imperative - to use the best information to make the best choice. One should always try to do one's best. But the catch in the argument for best-model optimization is that the best information may actually be grievously wrong. Those fine oak trees might be swarming with insects who've devoured the acorns. Best-model optimization ignores the agent's central dilemma: stay with the relatively well known but modest alternative, or go for the more promising but more uncertain alternative.

"Tsk, tsk, tsk" says our hedge fund manager. "My information already accounts for the uncertainty. I have used a probabilistic asset pricing model to predict the likelihood that my profits will beat the competition for each of the two alternatives."

Probabilistic asset pricing models are good to have. And the squirrel similarly has evolved instincts that reflect likelihoods. But a best-probabilistic-model optimization is simply one type of best-model optimization, and is subject to the same vulnerability to error. The world is full of surprises. The probability functions that are used are quite likely wrong, especially in predicting the rare events that the manager is most concerned to avoid.

Robustness and Probability

Now we come to the truly amazing part of the story. The satisficing strategy does not use any probabilistic information. Nonetheless, in many situations, the satisficing strategy is actually a better bet (or at least not a worse bet), probabilistically speaking, than any other strategy, including best-probabilistic-model optimization. We have no probabilistic information in these situations, but we can still maximize the probability of success (though we won't know the value of this maximum).

When the satisficing decision strategy is the best bet, this is, in part, because it is more robust to uncertainty than another other strategy. A decision is robust to uncertainty if it achieves required outcomes even if adverse surprises occur. In many important situations (though not invariably), more robustness to uncertainty is equivalent to being more likely to succeed or survive. When this is true we say that robustness is a proxy for probability.

A thorough analysis of the proxy property is rather technical. However, we can understand the gist of the idea by considering a simple special case.

Let's continue with the squirrel and hedge fund examples. Suppose we are completely confident about the future value (in calories or dollars) of not making any change (staying put). In contrast, the future value of moving is apparently better though uncertain. If staying put would satisfy our critical requirement, then we are absolutely certain of survival if we do not change. Staying put is completely robust to surprises so the probability of success equals 1 if we stay put, regardless of what happens with the other option. Likewise, if staying put would not satisfy our critical requirement, then we are absolutely certain of failure if we do not change; the probability of success equals 0 if we stay, and moving cannot be worse. Regardless of what probability distribution describes future outcomes if we move, we can always choose the option whose likelihood of success is greater (or at least not worse). This is because staying put is either sure to succeed or sure to fail, and we know which.

This argument can be extended to the more realistic case where the outcome of staying put is uncertain and the outcome of moving, while seemingly better than staying, is much more uncertain. The agent can know which option is more robust to uncertainty, without having to know probability distributions. This implies, in many situations, that the agent can choose the option that is a better bet for survival.

Wrapping Up

The skillful decision maker not only knows a lot, but is also able to deal with conflicting information. We have discussed the innovation dilemma: When choosing between two alternatives, the seemingly better one is also more uncertain.

Animals, people, organizations and societies have developed mechanisms for dealing with the innovation dilemma. The response hinges on tuning the decision to the agent's needs, and robustifying the choice against uncertainty. This choice may or may not coincide with the putative best choice. But what seems best depends on the available - though uncertain - information.

The commendable tendency to do one's best - and to demand the same of others - can lead to putatively optimal decisions that may be more vulnerable to surprise than other decisions that would have been satisfactory. In contrast, the strategy of robustly satisfying critical needs can be a better bet for survival. Consider the design of critical infrastructure: flood protection, nuclear power, communication networks, and so on. The design of such systems is based on vast knowledge and understanding, but also confronts bewildering uncertainties and endless surprises. We must continue to improve our knowledge and understanding, while also improving our ability to manage the uncertainties resulting from the expanding horizon of our efforts. We must identify the critical goals and seek responses that are immune to surprise. 




innovation

Animal agriculture : sustainability, challenges and innovations

9780128170526




innovation

New Engineering X Pandemic Preparedness programme to support global innovation and knowledge sharing