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Biophysics: Geometry supersedes simulations

Ludwig-Maximilians-Universitaet (LMU) in Munich physicists have introduced a new method that allows biological pattern-forming systems to be systematically characterized with the aid of mathematical analysis. The trick lies in the use of geometry to characterize the dynamics.

Many vital processes that take place in biological cells depend on the formation of self-organizing molecular patterns. For example, defined spatial distributions of specific proteins regulate cell division, cell migration and cell growth. These patterns result from the concerted interactions of many individual macromolecules. Like the collective motions of bird flocks, these processes do not need a central coordinator. Hitherto, mathematical modelling of protein pattern formation in cells has been carried out largely by means of elaborate computer-based simulations. Now, LMU physicists led by Professor Erwin Frey report the development of a new method which provides for the systematic mathematical analysis of pattern formation processes, and uncovers the their underlying physical principles. The new approach is described and validated in a paper that appears in the journal Physical Review X.

The study focuses on what are called ‘mass-conserving’ systems, in which the interactions affect the states of the particles involved, but do not alter the total number of particles present in the system. This condition is fulfilled in systems in which proteins can switch between different conformational states that allow them to bind to a cell membrane or to form different multicomponent complexes, for example. Owing to the complexity of the nonlinear dynamics in these systems, pattern formation has so far been studied with the aid of time-consuming numerical simulations. “Now we can understand the salient features of pattern formation independently of simulations using simple calculations and geometrical constructions,” explains Fridtjof Brauns, lead author of the new paper. “The theory that we present in this report essentially provides a bridge between the mathematical models and the collective behavior of the system’s components.”

The key insight that led to the theory was the recognition that alterations in the local number density of particles will also shift the positions of local chemical equilibria. These shifts in turn generate concentration gradients that drive the diffusive motions of the particles. The authors capture this dynamic interplay with the aid of geometrical structures that characterize the global dynamics in a multidimensional ‘phase space’. The collective properties of systems can be directly derived from the topological relationships between these geometric constructs, because these objects have concrete physical meanings — as representations of the trajectories of shifting chemical equilibria, for instance. “This is the reason why our geometrical description allows us to understand why the patterns we observe in cells arise. In other words, they reveal the physical mechanisms that determine the interplay between the molecular species involved,” says Frey. “Furthermore, the fundamental elements of our theory can be generalized to deal with a wide range of systems, which in turn paves the way to a comprehensive theoretical framework for self-organizing systems.”

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Materials provided by Ludwig-Maximilians-Universität München. Note: Content may be edited for style and length.

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ScienceDaily

Novel analytic approach enhances nuclear magnetic resonance signal detection in previously ‘invisible’ regions

First introduced into wide use in the middle of the 20th century, nuclear magnetic resonance (NMR) has since become an indispensable technique for examining materials down to their atoms, revealing molecular structure and other details without interfering with the material itself.

“It’s a broadly used technique in chemical analysis, materials characterization, MRI — situations in which you do a non-invasive analysis, but with atomic and molecular details,” said UC Santa Barbara chemistry professor Songi Han. By placing a sample in a strong magnetic field and then probing it with radio waves scientists can determine from the response from the oscillating nuclei in the material’s atoms the molecular structure of the material.

“However, the problem with NMR has been that because it’s such a low-energy technique, it’s not very sensitive,” Han said. “It’s very detailed, but you don’t get much signal.” As a result, large amounts of sample material may be needed relative to other techniques, and the signals’ general weakness makes NMR less than ideal for studying complex chemical processes.

One remedy to this situation lies in dynamic nuclear polarization (DNP), a popular technique in which energy is “borrowed” from nearby electrons to enhance the signal emanating from the nuclei.

“Electrons have much higher energy than nuclei,” Han explained. Built into specially-designed “radical” molecules, these unpaired electrons’ polarization is transferred to the nuclei to improve their signal.

As hot a topic as DNP has become in the past decade, however, Han thinks we’re still just scratching the surface.

“Despite DNP fundamentally changing the landscape of NMR, at the end of the day, only a handful of designer polarizing agents have been used,” Han said. “A polarizing agent has been used to polarize hydrogen nuclei, but the power of DNP is greater than that. In principle, many other sources of electron spin can polarize many other types of nuclear spin.”

In a paper published in the journal Chem, Han and colleagues push the boundaries of NMR with the first demonstration of dynamic nuclear polarization using the transition metal vanadium (IV). According to Han, their new approach — dubbed “hyperfine DNP spectroscopy” — offers a glimpse into the typically obscure local chemistry around transition metals, which are important for processes such as catalysis and reduction-oxidation reactions.

“Now we may be able to use endogenous metals that are present in catalysts and in many other important materials,” Han said, without having to add polarizing agents — those radical molecules — to produce a stronger NMR signal.

The irony with transition metals such as vanadium and copper, Han explained, is that those atoms tend to tend to be functional centers — places where important chemistry takes place.

“And those exact action centers and functional centers have been very difficult to analyze (with NMR) because they tend to become invisible,” she said. The electron spins in the transition metal tend to shorten the lifetime of the NMR signal, she explained, making them disappear before they can be detected.

This wouldn’t be the first time chemistry around transition metals has been observed, Han said, pointing to studies that looked at the chemical environments around gadolinium and manganese. But the commercially-available instrument used in those studies offered “a very narrow view.”

“But there are many more metals that are much more important for chemistry,” she said. “So we developed and optimized instrumentation that enhances the frequency range from the very narrow scope of a commercial instrument to a much broader range.”

With their hyperfine DNP spectroscopy the researchers also found that the signal is indeed wiped out within a certain region around the metal called the spin diffusion barrier, but if the nuclei are located outside that zone the signal becomes visible.

“There are ways to lighten up that environment, but you need to know how and why,” Han said, adding that the paper’s co-lead authors, Sheetal Kumar Jain of UC Santa Barbara and Chung-Jui Yu of Northwestern University will continue to explore and apply this new method as they pursue their academic and research careers.

Other contributors to the research on this paper include Christopher Blake Wilson and Tarnuma Tabassum of UC Santa Barbara; and Danna E. Freedman of Northwestern University.

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ProgrammableWeb

IBM’s OpenAPI Comment Parser Brings API Reference and Code Development Together

IBM has introduced OpenAPI Comment Parser. The new offering brings API reference creation and code development into the same environment. The theory is that API references will improve, and stay updated, if developers don’t have to bounce back and forth between their code and the API reference that tells developers how to use that code.

“When the [API reference] lives inside the code, developers are much more likely to keep it up-to-date as their code changes,” IBM’s Nicholas Bourdakos commented in a blog post announcement. “It gets broken up into smaller, more manageable pieces. It lives next to the code that it’s describing.”

More specifically, the Comment Parser enables developers to generate an OpenAPI spec from the parser itself. The OpenAPI Specification is an open standard for defining and documenting an API. Using the parser to create OpenAPI specs, IBM reports that it has been able to reduce the size of API references by 50% on average. Given the typical size of API references, this is significant.

The library is open source and written in Node.js. However, the CLI will work with any language using the following comment style:

/**
 * GET /users/{userId}
 * @summary Returns a user by ID.
 * @pathParam {int64} userId - The user's ID.
 * @response 200 - OK
 */

To learn more, visit the OpenAPI Comment Parser at GitHub.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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ProgrammableWeb

FXCubic Introduces Real-time Markup API

FXCubic, a trading technology provider, has introduced a real-time bridge markup API. The API targets high volume brokers and traders. Through the API, users gain access to market data calculations and can adjust their markups in real-time according to an algorithm of choice.

“We believe this is truly groundbreaking, as this kind of technology has never been accessible to the vast majority of brokers, Ege Kozan, FXCubic CEO, commented in a press release. “When used right, such technology can have a big impact on a broker’s profitability, so we are expecting our clients to take full advantage of this new tool and apply it to their business very rapidly.”

With the API, users can react to market changes in their books automatically. Exposure is monitored and calculated on an ongoing basis. When certain thresholds and predefined metrics are hit, markups are adjusted for each independent instrument.

FXCubic has not currently published public API docs for the new API. For an overview of all FXCubic’s technology, visit its technology site. Those interested can see more details at the platform and architecture sites.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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ProgrammableWeb

Solo.io Introduces Gloo Federation Adding Multi-Cluster Control Feature

Solo.io has introduced Gloo Federation. It is the next step in the company’s development of Gloo, its envoy proxy based API gateway. With its continued focus on scalability, Solo.io sought a better way to allow its users to operate multiple “Gloos”. Gloo Federation became the answer.

“Today we are excited to announce the next evolution of Gloo, with the release of Gloo Federation, giving enterprises the ability to scale their API gateway and management capabilities across clusters, sites and regions,”. Idit Levin, Solo.io CEO, commented in a blog post announcement. “Gloo Federation has two goals: to simplify and globalize your management of multiple Gloo instances across multiple clusters, and to provide you with advanced multi-cluster control features.” 

According to Levine, Gloo Federation offers “a single pane of glass” to view all services. That includes services across all clusters and clouds. In turn, users enjoy consistent configuration, unified debugging, and automated Gloo discovery. Further, users can configure Gloo instances in a manner that brings failover and location-based routing across instances.

Features of note in Gloo Federation include a global dashboard (a read-only UI that provides quick status view of all Gloo instance configurations), federate configuration (the ability to configure all Gloo instances from a single point), multi-cluster failover routing (enables application resilience through failover capabilities in traffic routing), location-based routing (a global view that enables rerouting to alternative clusters), and role-based access control (user-based permissions at multi-cluster level). Solo.io will host an upcoming webinar for those interested in learning more.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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ProgrammableWeb

Vericred Adds ICHRA Affordability Calculator API to ICHRA Development Kit

Vericred, an insurance and benefits data services company, recently introduced its ICHRA Affordability Calculator API. The service expands the company’s ICHRA Development Kit that companies use to build Individual Coverage Health Reimbursement Arrangement (ICHRA) solutions for brokers, employees and employees.

“There is considerable momentum for companies, large and small, to adopt ICHRAs as an alternative to traditional employer-sponsored coverage,“ Michael W. Levin, Vericred co-founder and CEO, commented in a press release. “Our ICHRA Affordability Calculator is yet another element of the infrastructure necessary for developers to create great ICHRA experiences for brokers, employers and employees.”

At its core, the ICHRA Affordability Calculator API allows employers to calculate the minimum contributions it must make to employees’ health insurance costs in order to comply with various laws. Additionally, it calculates how much subsidy an employee would receive if the employee opts out of an ICHRA to purchase a plan through a federal or state-based exchange. The calculators give programmatic and automatic access to the applicable options so that employers and employees alike can compare options and make informed decisions.

The calculator adds to the existing development kit which already includes a number of robust features including group and individual quoting APIs, group and individual disruption analysis APIs, shop by doctor, and shop by drug. Those interested in the new API, or any feature of the ICHRA Development Kit should visit the Vericred website and reach out to the sales team.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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3D Printing Industry

Farsoon debuts its FS621M large-format metal 3D printer at TCT Asia 

Chinese SLM and SLS 3D printer manufacturer Farsoon, has introduced it’s latest Laser Beam Powder Bed Fusion (LPBF) large-format metal 3D printer, the FS621M.  Developed with industry partner and manufacturing service provider Falcontech, the new system has been designed to address the productivity challenges of metal 3D printing including size constraints, powder management and process […]

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Author: Paul Hanaphy

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ProgrammableWeb

Ireland Launches COVID-19 Tracker App

This week, Ireland introduced a COVID-19 Tracker app. The app uses the Exposure Notification API built by Apple and Google. The app is intended to help contact trace and slow the spread of coronavirus. The app is now available from the App Store and Google Play.

The App Store version utilizes the iOS version of the Exposure Notification APITrack this APITrack this API. The Google Play version utilizes the Android version of the Exposure Notification APITrack this API. The app is published by Ireland’s Health Service Executive, Ireland’s federal agency responsible for the provision of health and personal social services of all living in Ireland. Primary functions include contact tracking, symptom monitoring, and consistently updated facts and figures about the virus in Ireland.

Contact tracing is a core functionality of the app. This feature allows individuals to identify if they were in close contact with someone who has contracted the virus. By contact tracing, users can reduce the time required to alert others of potential contact, notify contacts who may have forgotten a potential exposure, and open communication streams between people who may not actually know each other.

To implement contact tracing, the app and underlying APIs use Bluetooth and anonymous IDs to track phones users have come into contact with (if those phones also have the app installed), the distance between a user’s phone and the other phones, and the length of time a phone is near another phone. The app downloads these tracked metrics every two hours and updates accordingly. IDs are anonymous, the entire system is opt-in, and tracing data is limited to each user’s personal device. Check out the apps on the App Store and Google Play.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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ProgrammableWeb

Hasura Introduces Hasura Cloud

Hasura, a data access infrastructure company, recently introduced Hasura Cloud. Hasura Cloud provides secure and instant access to data across hybrid and multi-cloud environments. It uses the unified GraphQL API to achieve this cross-cloud capability. Because it utilizes GraphQL, Hasura Cloud helps businesses achieve their cross-cloud goals without investment in expensive IT investments.

Hasura Cloud was borne out of Hasura’s existing enterprise product: Hasura Pro. Hasura Pro is amplified in Hasura Cloud with the addition of cloud-specific functionality. Features include data caching, auto-scaling, global availability and consumption-based pricing.

The goal of Hasura Cloud is to help data owners unlock data that is trapped in silos. Whether businesses face problems with fast-moving operational data, or static data warehouses and lakes, Hasura cloud was built to provide assistance. The primary method lying behind Hasura cloud is an approach that connects applications by federating access to where the underlying data lies. Hasura does this with an API approach that has security, governance, and scalability baked in.

Early testers of Hasura Cloud have had nothing but good things to say with the new offering. Hasura introduced the product at Hasura Con ’20. This year’s version was a virtual event that brought Hasura developers and collaborators together for six straight days of working together. To learn more, visit Hasura site.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>

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ProgrammableWeb

Hasura Introduces New GraphQL Data Federation Feature: Remote Joins

Hasura, a GraphQL data and services company, has introduced a new data federation feature: Remote Joins. Remote Joins allows developers to treat data across sources as a single database. The existing data sources do not need to be modified in order to utilize Remote Joins. With a point and click, a relationship across the sources is created and unified access is created through the GraphQL API.

“Being able to access existing related data across independently owned systems of record is a game changer for developer teams,” Tanmai Gopal, Hasura co-founder and CEO, commented in a press release. “Developers can build and ship capabilities that add value to their users within minutes by leveraging relationships in their user data where it is right now, even if the data they need spans multiple independent domains.”

The vast variety of data sources that currently exist often cause problems with integration as they expose different interfaces (e.g. GraphQL, REST, native protocols, etc.). Remote Joins allows these disparate types to be joined together through GraphQL. The underlying data sources maintain their existing forms but gain unified access through the GraphQL API. Accordingly, developers continue to maintain their existing data as originally built and maintained.

Remote Joins is current in public beta. Hasura will showcase the new feature at Hasura Con ’20, which is still waiting for a new date after being postponed. Learn more about this feature at GitHub.

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Author: <a href="https://www.programmableweb.com/user/%5Buid%5D">ecarter</a>