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Gene Editing Modifies Tree Genomes to Reduce Lignin

Red stem from gene-editing and original green stem

Poplar plants produced from a gene-editing experiment at University of Georgia, left, had red-colored wood compared to the original green. Red stem is a known side effect of lignin modification. (University of Georgia)

5 June 2015. Plant scientists at University of Georgia used an emerging technique for gene editing to modify the genomes of poplars and related trees to make those varieties better suited for biofuels. The team from the lab of plant biologist Chung-Jui Tsai in Athens published its findings in a recent letter to the journal New Phytologist.

Poplars and related species in the genus Populus, such as aspen and cottonwood, are fast-growing trees used in packing boxes, industrial pallets, and musical instruments. Poplars also grow on marginal land, thus do not compete with food crops. These species, however, have quantities of lignin, a polymer material in trees and other plants that gives strength to the cell walls. That same quality in lignin, however, makes it difficult to break down, thus adding considerable effort and cost when processing poplar wood for commercial products, such as biofuels and pulp for making paper.

Tsai and colleagues sought to edit the genomes of poplars to reduce the concentrations of lignin, as well as tannins, a type of chemical in Populus and other plants that generate proteins poisonous to deer and livestock. The team applied the genome editing technique Crispr, short for clustered, regularly interspaced short palindromic repeats, adapted from a natural process used by bacteria to protect against attack by viruses, where a protein that deactivates or replaces genes binds to targeted RNA molecules generated by the genome. The RNA molecules then guide the editing protein, known as Crispr-associated protein 9 or Cas9, to specific genes needing changes.

Using Crispr, the researchers found they could reduce concentrations of lignin in the plants by 20 percent and condensed tannins by half, compared to trees grown in the wild.  An indicator of reduced lignin levels is a change in the color of the wood from green to red. Red stem, say the authors, is a known side effect of lignin modification in poplars and other Populus varieties, as well as maize, sorghum and pines.

Tsai notes that Crispr is simpler and and more direct than other gene editing techniques. “Compared to some other gene editing techniques,” says Tsai in a university statement, “this is incredibly simple, cost-effective and highly efficient, and it could serve as the foundation for a new era of discovery in plant genetics.” She adds that Crispr “is a mechanism that evolved naturally, but we can borrow the bacteria’s gene-cutting abilities and use it to edit very specific genes in all kinds of organisms, including plants and animals.”

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Life Sciences Commercialization Firm to Crowdfund IPO

NASDAQ display

(bfishadow, WikimediaCommons)

4 June 2015. Innovation Economy Corporation is going public by skipping the usual route of hiring an investment bank, and instead will use crowdfunding to attract investors to its initial public offering of stock. The Riverside, California enterprise, that goes by the trade name ieCrowd, licenses life science and health-related technologies from university research labs for commercialization, and expects to raise some $20 million through this process.

ieCrowd, founded in 2010, helps labs at universities and research institutes bring discoveries to market. The company licenses technologies from institutions, forms spin-off enterprises as a subsidiaries, and provides initial funding and business infrastructure — e.g., facilities and management — to get new businesses off the ground. While the company says it operates nationwide, its first crop of spin-off enterprises are all from California.

In its IPO, ieCrowd plans to offer 3,125,000 units at a price of $6.40 per unit. Each unit has 1 share of common stock and a warrant to purchase a half-share of common stock at $8.00 per entire share within 36 months. A warrant enables the holder to buy additional shares, but is not obligated to do so. The IPO runs through 15 July 2015, after which time, ieCrowd’s shares will trade on the NASDAQ exchange under ticker symbol MYIE.

Under the conventional IPO process, a company going public hires an investment bank to underwrite the stock offering, either marketing all of the initial shares or forming a syndicate of investment banks to offer shares to their investor clients. In this case, ieCrowd is bypassing investment banks with crowdfunding to attract its IPO investors. The company is using the BANQ crowdfunding investment platform from TriPoint Global Equities.

One of the first companies supported by ieCrowd is Olfactor Laboratories, reported on by Science & Enterprise in July 2013. Olfactor Laboratories makes the Kite, a small (1.5 inch square) patch worn on clothing that repels mosquitoes for 48 hours. The Kite is based on research by entomologist Anandasankar Ray at University of California in Riverside on compounds to inhibit the receptor in mosquitoes and other insects to track carbon dioxide exhaled by humans.

Another ieCrowd client profiled in Science & Enterprise (in April 2012) is Nuuma, a spin-off also from University of California in Riverside commercializing research by engineering professor Nosang Myung. Nuuma, first named Nano Engineered Applications, is developing miniaturized sensor chips to detect gases in concentrations as low as parts per billion. The chips are designed with carbon nanotubes to be embedded in other devices, with the goal of simultaneously detecting multiple gaseous substances.

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Trial Shows Immunotherapy Reduces Rheumatoid Arthritis

X-ray f hands with rheumatoid arthritis

(National Institutes of Health)

4 June 2015. A clinical trial of an immune system therapy shows one treatment reduces levels of harmful immune activity and joint inflammation in people with rheumatoid arthritis. The early-stage trial led by researchers at University of Queensland in Brisbane, Australia is reported yesterday in the journal Science Translational Medicine.

Rheumatoid arthritis is an autoimmune disease, where the immune system is tricked into attacking healthy cells, that leads to inflammation of joints (wrists, fingers, feet, and ankles) and surrounding tissue, affecting some 450,000 people in the Australia, according to the university. In the U.S., rheumatoid arthritis is estimated to affect 1.3 million people, making it the most prevalent autoimmune disease. While the rate of occurrence is declining, the disorder occurs in twice as many women as men.

Queensland rheumatology professor Ranjeny Thomas and colleagues aim to treat the disruptions in the immune system causing the joint pain and other symptoms, rather than relieving the symptoms like most current treatments. The therapy they call Rheumavax increases tolerance in people with rheumatoid arthritis for naturally-occurring chemicals in the body known as citrullinated peptides that can activate the immune system to counter the actions causing the pain and inflammation. Most people with rheumatoid arthritis have antibodies that block citrullinated peptides from working.

To encourage the immune system to tolerate citrullinated peptides, the research team — that includes members from Singapore, the Netherlands, and elsewhere in Australia — uses cells from the immune system called dendritic cells that regulate immune tolerance. The researchers first extract dendritic cells from the blood of people with rheumatoid arthritis, culture the cells with citrullinated peptides, then inject the cultured dendritic cells back into the patients.

The team tested Rheumavax in an exploratory clinical trial with individuals having rheumatoid arthritis, and who also have antibodies that block citrullinated peptides from working. Of the 34 participants, 18 received one treatment of Rheumavax in either high or low dosages, while 16 were left untreated for comparison. An earlier safety trial found the treatments caused mild side effects with a short duration. The researchers report the same mild and temporary reactions among patients receiving Rheumavax in the new trial.

After 1 month, participants receiving Rheumavax showed more therapeutic immune system action and fewer rheumatoid arthritis symptoms than people in the untreated group. Individuals treated with Rheumavax had sharply reduced levels of harmful autoimmune T-cells and more helpful regulatory T-cells than the untreated group, as well as reduced levels of proteins encouraging joint inflammation. People receiving Rheumavax also reported less severe joint inflammation and lower disease activity scores, using a standard clinical measure.

Thomas and colleagues from Queensland’s Diamantina Institute founded the company Dendright Pty in 2005 to commercialize their research on autoimmune disorders, where Thomas serves as the company’s chief technologist. Dendright is a subsidiary of Uniquest, Queensland’s technology transfer and commercialization office. In 2013 extended a collaboration with Janssen Biotech, a Johnson & Johnson company, to develop Rheumavax through early-stage clinical trials. Janssen Biotech is funding Dendright’s early-stage trials in return for an option to license the technology, which would make Dendright eligible for development and sales milestone payments, as well as royalties on sales.

Thomas says Rheumavax still needs to be formulated into a more feasible therapeutic vaccine, rather than the multi-stage process used in the clinical trial. “At this stage, the technique would not be ideal for widespread treatment or prevention of rheumatoid arthritis because it’s costly and time-consuming,” Thomas notes in a university statement. “However, the promising results of this trial lay the foundations for the development of a more cost-effective, clinically-practical vaccine technology that could deliver similar outcomes for patients.”

Thomas tells more about Rheumavax in the following video.

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Disclosure: The author owns shares in Johnson & Johnson.

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Antibiotic Developer Adds $9.2 Million in Early Funds

Bacteria growing in petri dishes

(Centers for Disease Control and Prevention)

3 June 2015. Auspherix Limited, a start-up developer of new antibiotic drugs, raised £6 million ($US 9.2 million) in early-stage venture financing. Funding for the two year-old enterprise, located in a pharmaceutical and biotechnology incubator at Stevenage, U.K., was led by technology commercialization company Imperial Innovations plc, with earlier investor Australia’s Medical Research Commercialisation Fund.

Auspherix is a spin-off company from University of Technology Sydney in Australia, founded in 2013 by Ian Charles and Dagmar Alber to commercialize their research at the university’s ithree institute — for infection, immunity, innovation. Both Charles and Alber relocated to the U.K. — Charles as director of Institute of Food Research and Alber on the staff at Institute of Child Health at University College London — thus the move of Auspherix to the U.K.

The company is developing what it calls a new class of antibiotics with a novel chemical structure, designed to counter the increasing problem of multi-drug resistant bacteria. Among the drugs in discovery, says Auspherix, are compounds that are active against carbapenem-resistant strains of gram-negative bacteria, with infections often contracted in health care facilities, and multi-resistant forms of gram-positive bacteria. “Gram” refers to a classification for bacteria where the microbes either retain (gram-positive) or shed (gram-negative) a test stain on their protective cell coatings.

The company says it plans to apply the new funds to its drug discovery program, including recruitment of scientific and management staff. Identification of final drug candidates is expected in the next two years. While in Australia, Auspherix secured $AU 2 million ($US 1.6 million) in seed and first venture round financing from Medical Research Commercialisation Fund. The new funding is also considered part of the company’s first venture round.

Imperial Innovations, leading the new financing, is the technology transfer office of Imperial College London, but it invests as well in spin-off enterprises from universities of Cambridge and Oxford. The organization also serves as the technology transfer office for several National Health Service trusts in the U.K. In addition to direct investments, Imperial Innovations says it helps form spin-off companies from partner institutions, provides facilities for early-stage operations, and helps recruit management teams and board members.

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GE, Institute to Design Digital Manufacturing Platform

Industrial robots on factory floor

(General Electric Co.)

3 June 2015. Digital Manufacturing and Design Innovation Institute in Chicago is developing a technology platform to make it easier for manufacturing companies to share technical data with their customers and suppliers, adapting concepts proposed by General Electric, which was chosen to lead the project. The platform, known as digital manufacturing commons, is expected to be an open-source asset for manufacturing supply chains.

Digital Manufacturing and Design Innovation Institute is a consortium of some 70 manufacturing companies, universities, not-for-profit research labs, and government agencies that encourages development of smarter and more efficient manufacturing, particularly with tools that link together different parts of the often fragmented manufacturing ecosystem. The institute aims to bridge the gap needed to connect basic research on manufacturing conducted in academic labs and funded mainly by government with commercialization of research discoveries by industry.

GE says its global research division was chosen by the institute to lead the digital manufacturing commons initiative because of its work in developing a digital ecosystem for its own factories and suppliers. The company is advancing the concept of the brilliant factory that digitizes the extended manufacturing process from design through fulfillment, and can adjust in real time to changing conditions, or even problems that haven’t yet happened.

An essential ingredient of the brilliant factory is the digital thread connecting data about the manufactured product created throughout its lifecycle and across its supply chain. While data are being created at all stages of a manufactured product’s lifetime, the data are not aggregated or connected, thus not providing their full benefit to other stakeholders in the product’s development, manufacture, and distribution.

The digital manufacturing commons aims to create an open-source platform for aggregating manufacturing data into a digital thread. GE says it plans to build on the crowdsourcing cloud-based software designed three years ago with DARPA and MIT for the development of military vehicles and complex design systems. That software, says the company, makes it possible for scientists, engineers, and designers to form teams and share ideas, as well as submit designs to communities of experts for testing and vetting.

Neither GE nor the institute give a target date for completion of the digital manufacturing commons, but a company statement says its goal is to attract 100,000 users from companies, universities, research institutes, and entrepreneurs by 2017.

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Spin-Off Biotech Formed for Autoimmune Disorders

Diabetes items

(Centers for Disease Control and Prevention)

2 June 2015. Drug maker Astellas Pharma Inc. in Tokyo and Anokion SA, a biotechnology company in Lausanne, Switzerland, are forming Kanyos Bio Inc., a  spin-off enterprise to develop therapy candidates for autoimmune diseases. The deal could bring Kanyos Bio, based in Cambridge, Massachusetts, as much as $760 million, as well as an equity investment by Astellas and other investors.

Anokion is itself a spin-off company from the lab of Jeffrey Hubbell at Ecole Polytechnique Fédérale de Lausanne (EPFL) , who studies regenerative medicine. Hubbell, also on the faculty at University of Chicago, co-founded Anokion, and is the founder or co-founder of two other companies, Kuros Biosurgery in Zurich, and Focal Inc. in Lexington, Massachusetts, which was acquired by Genzyme in 2001.

Anokion’s technology designs proteins that enlist the body’s natural powers to regulate immune reactions, to help treatments for allergies and autoimmune disorders do their jobs. Autoimmune disorders are conditions where the immune system is tricked into attacking healthy cells and tissue as if they were foreign invaders, like viruses. Likewise, some biologic therapies for allergies and autoimmune conditions can also be misinterpreted and attacked as invaders rather than welcomed as helpers.

The Anokion technology creates engineered proteins that interact with T-cell lymphocytes, white blood cells in the immune system, as if they came from the same body, thus preventing a damaging overreaction. The proteins act as training agents, encouraging the T-cells to accept the incoming therapeutic molecules as native helpers and not as invaders.

Kanyos Bio will apply the Anokion technology to two specific autoimmune disorders, type 1 diabetes and celiac disease, developing therapy candidates through their preclinical stages. Type 1 diabetes, once known as juvenile diabetes, is usually diagnosed in children and young adults, and affects about 5 percent of people with diabetes. In type 1 diabetes, the body’s immune system erroneously interprets cells producing insulin as foreign, thus attacking the cells. Kanyos plans to develop an engineered protein to train the immune system to accept an individual’s insulin-producing cells, and inhibit only the immune system’s reaction to those cells.

Celiac disease is a genetic autoimmune disorder where ingestion of gluten leads to damage in the small intestine. It is estimated to affect about 1 in 100 people worldwide. Kanyos intends to develop a therapy that inhibits the immune system cells causing damage to the intestine, leaving other immune system actions as is.

The deal calls for Astellas to provide R&D funding and milestone payments to Kanyos, with Astellas holding an option to add a third autoimmune disorder to the Kanyos agenda. Astellas will also have an option to acquire Kanyos after certain, but undisclosed, milestones are achieved. The total value of R&D and milestone payments, and acquisition of Kanyos is valued at $760 million. In addition, Astellas is taking part in a $16 million equity funding round for Kanyos with other Anokion investors.

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Trial to Test Cancer Drugs Matched to Gene Mutations

Genetic testing illustration

(National Institute of General Medical Sciences, NIH)

2 June 2015. A new clinical trial will test 20 cancer drugs and drug combinations targeted to specific genetic mutations, regardless of cancer type. The study, known as NCI-Match is a joint project of National Cancer Institute, an agency of National Institutes of Health, and the Ecog-Acrin Cancer Research Group, and announced yesterday at the annual meeting of American Society of Clinical Oncology. Enrollment in the trial is expected to begin next month.

NCI-Match, short for Molecular Analysis for Therapy Choice, seeks to determine if tumors with specific genetic mutations can be treated with drugs developed to address those abnormalities, independent of the type of cancer affecting the individual. The intermediate-stage trial plans to pair each cancer patient enrolled with one or more of 10 drugs to begin, eventually expanding to 20 different therapies.

The trial is open to adults with solid tumors or lymphomas that advanced even if treated with standard therapies, or if no standard treatments are available. Beginning in July, NCI-Match plans to screen some 3,000 prospects with the goal of enrolling 1,000 participants, including at least one-quarter of the individuals having a rare form of cancer. Enrollment will be conducted through National Clinical Trials Network at 2,400 sites in the U.S.

Patients will first have biopsies to remove tissue from their tumors for DNA sequencing to identify genetic variations that may be encouraging growth of their tumors. The DNA analysis will use a test developed at the NCI Molecular Characterization Laboratory that hunts for 143 genes associated with cancer that can be targeted in the trial. All of testing will be done at the Acog-Acrin Biorepository and Pathology Facility at the University of Texas MD Anderson Cancer Center in Houston.

If eligible for participation, individuals will be treated with drugs matching the abnormalities the treatments are designed to address. About 35 participants will be assigned to each treatment. All of the drugs tested in the trial are either already approved or under review by FDA, and contributed by their manufacturers.

MCI-Match’s main measure of efficacy is overall response rate, determined by predefined tumor shrinkage in a specified period of time, aiming for response rates of 16 to 25 percent. The study is also measuring progression-free survival for 6 months, where the objective is 35%.

Ecog-Acrin Cancer Research Group is an organization that designs and conducts biomarker-driven cancer research with adults who have or are at risk of developing cancer. The group formed from a merger of Eastern Cooperative Oncology Group (Ecog) and the American College of Radiology Imaging Network (Acrin), and is part of National Clinical Trials Network.

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Mini Gamma Camera Developed, Spin-Off Company Formed

Mini gamma ray camera

Mini gamma ray camera (University of Leicester)

1 June 2015. Physicists and medical researchers at two universities in the U.K. designed a hand-held camera that performs gamma ray imaging, normally requiring a powerful room-sized device for diagnosing tumors and other medical functions. The team from Universities of Leicester and Nottingham also formed a spin-off company, Gamma Technologies Ltd., to take the device to market.

The researchers designed the mini gamma ray camera as an alternative to current full-size systems requiring an entire and dedicated room to operate. Unlike X-rays that provide images of the body’s anatomy and structure, gamma ray cameras track bodily processes and functions. Gamma ray cameras record high resolution images from radioactive tracers injected in the body that illuminate in response to gamma rays emitted by the camera.

The new device is designed to provide the functions of gamma ray cameras, but at the patient’s bed side, as well as in intensive care and surgical units. Because of its small size and dual gamma- and optical-imaging capabilities, the developers believe the new device can improve the diagnosis of tumors, identification of lymph node problems, and imaging of disorders in smaller organs, such as tear duct blockages. The developers say the device could also visualize delivery of drugs in the patient.

The Leicester part of the team is led by physicist John Lees, with funding from the Science and Technology Facilities Council, a science funding agency in the U.K. The council offers the Challenge Led Applied Systems Programme or Clasp that supports commercialization of its discoveries, and funded the mini gamma camera project. The Nottingham group is led by medical school physicist Alan Perkins.

Lees, Perkins, and others formed Gamma Technologies Ltd. to commercialize their patented invention. Perkins is the company’s interim CEO and clinical director, while Lees is the technical director. The company says it already raised more than £250,000 ($US 381,000) in early venture funds.

Gamma Technologies, located in University of Leicester’s Space Research Centre, says the mini gamma ray camera is is still a prototype, but is being tested with healthy volunteers at the Queens Medical Centre in Nottingham.

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Antibody Improves Lung Cancer Survival Time in Trial

Chemotherapy vials

(National Cancer Institute)

1 June 2015. A late-stage clinical trial shows an engineered antibody that harnesses the immune system increases the survival time of people with a common form of lung cancer compared to standard chemotherapy. The study of the drug nivolumab, marketed as Opdivo by Bristol-Myers Squibb, was reported yesterday at the annual meeting of American Society of Clinical Oncology and in the New England Journal of Medicine.

Participants in the trial were individuals with squamous cell non–small-cell lung cancer who had not responded to earlier chemotherapy. Worldwide, lung cancer causes some 1.6 million deaths, according to World Health Organization. Non-small cell lung cancer is the most common form of lung cancer, accounting for about 85 percent of all cases. American Cancer Society estimates more than 221,000 new cases of lung cancer will be diagnosed in the U.S. during 2015, affecting somewhat more men than women, leading to 158,000 deaths.

Nivolumab is an antibody that limits a protein called programmed cell death-1 or PD-1 that prevents activation of T-cells in the immune system, which in turn encourages progression of tumors. Bristol-Myers Squibb is testing its nivolumab drug Opdivo as a single therapy or in combination with other drugs against a number of solid tumor cancers in more than 50 clinical studies.

This clinical trial — conducted in the U.S., Europe, and Latin America — tested Opdivo against the chemotherapy drug docetaxel, considered the standard of care for treating non-small-cell lung cancer and other solid tumor cancers. The 272 participants, people who did not respond to earlier chemotherapy treatments, were randomly divided to receive Opdivo infusions every 2 weeks or docetaxel infusions every 3 weeks. The trial looked primarily at overall survival rates and times, but also for response rates to the respective drugs and progression-free survival time, as well as risk of death, measured by a hazard ratio.

The results show after 1 year, individuals receiving Opdivo had a median survival time of 9.2 months and an overall survival rate of 42 percent, compared to 6 months survival time and 24 percent survival rate for docetaxel recipients. Some 20 percent of participants receiving Opdivo responded completely or in part to treatments, compared to 9 percent for those receiving docetaxel. Likewise, Opdivo recipients had a a 41 percent lower risk of death, and somewhat longer median progression-free survival time (3.5 months) compared to docetaxel patients (2.8 months).

Bristol-Myers Squibb also reported on a similar clinical trial where the combination of Opdivo and another of its immunotherapy drugs Yervoy had a longer progression-free survival time than Yervoy alone among people with advanced untreated melanoma. In addition, participants receiving Opdivo alone had a longer progression-free survival time than those receiving Yervoy alone.

The company reported as well that the U.S. Food and Drug Administration accepted its biologics license application — request to review the therapy for marketing approval — for the combination of Opdivo and Yervoy to treat advanced untreated melanoma, and granted an expedited process for the review. That review is expected to be completed by 30 September 2015.

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Health Data, Analytics Firms to Boost Cancer Trial Access

DNA molecules

DNA molecule display (Christian Guthier, Flickr)

29 May 2015. A health data company and genetic analytics firm are beginning a service that they say will make it easier for cancer patients to take part in clinical trials of new drugs. Financial details of the collaboration between Guardian Research Network in Spartanburg, South Carolina and Molecular Health in Cambridge, Massachusetts were not disclosed.

The partnership aims to increase access for people with cancer to genomic profiling of their tumors matched to clinical trials through the combined offerings of the two companies. Molecular Health provides genetic analysis of solid tumors through its TreatmentMAP testing service using high-throughput sequencing that the company says returns a genomic analysis to guide an individual’s treatment decisions. TreatmentMAP uses either Molecular Health’s panel of target genes or conducts a whole-exome sequencing that covers all protein coding genes.

Guardian Research Network is aggregating a database of electronic health records from medical centers nationwide to identify prospects for clinical trials. The company says its database combines detailed medical data including demographics, pathology reports, lab analyses, images, physician notes, and genetic information. Guardian says its goal is to increase clinical trial access to people in their own communities, thus reducing the burdens of travel that limit access to these studies.

Under the agreement, Guardian will adopt Molecular Health’s TreatmentMAP program for genetic analyses, and use InsightMAP services for trial matching, sample stratification, and analytics. InsightMAP enhances TreatmentMAP with modeling of drug mechanisms and toxicity, and integrates customer-specific clinical and molecular data. The company also provides an outcomes analysis service.

Guardian says it can reduce clinical trial recruitment times from years to weeks. Through its database, says the company, it can not only find optimal patients for clinical trials, but also identify trial sites most convenient to patient prospects, reducing their time and financial burdens. Guardian was founded in late 2014, and so far presents no case studies nor customer lists on its Web site.

Molecular Health was founded in 2004 in Germany, and still has its headquarters in Heidelberg. The company has about 100 employees in Germany and the U.S., in Cambridge, Massachusetts and Houston, Texas.

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