September 2019 - Candle-aesp - mailman3.cels.anl.gov

Fwd: Visit to UIC on Oct. 11th...
by Stevens, Rick L. 30 Sep '19

30 Sep '19

Begin forwarded message: From: "Chen, Liaohai Leo" <lhchen(a)uic.edu<mailto:[email protected]>> Subject: Re: Visit to UIC on Oct. 11th... Date: September 30, 2019 at 10:59:03 AM CDT To: "Lutes, Darlyn" <darlyn(a)anl.gov<mailto:[email protected]>> Cc: "Xia, Fangfang" <fangfang(a)anl.gov<mailto:[email protected]>>, "smulligan(a)anl.gov<mailto:[email protected]>" <smulligan(a)anl.gov<mailto:[email protected]>>, "Stevens, Rick L." <stevens(a)anl.gov<mailto:[email protected]>> Hi Darlyn, Here is the flyer for the upcoming visit and workshop. Please spread the word and we look forward more people from Argonne to join us. Two things I would like to mention: 1) we will start at 8:00 am due to the hospital arrangement and 2) working lunch will be provided. Please let me know if you have any questions. Leo From: "Lutes, Darlyn" <darlyn(a)anl.gov<mailto:[email protected]>> Date: Friday, September 13, 2019 at 10:54 AM To: Liaohai Chen <lhchen(a)uic.edu<mailto:[email protected]>> Subject: Fwd: Visit to UIC on Oct. 11th... Good day Leo, I just received confirmation that Rick will be available to attend the Oct. 11th. When you send the details to the group please include RIck and his assistant Silvia on the email. Rick Stevens - stevens(a)anl.gov<mailto:[email protected]> Silvia Mulligan - smulligan(a)anl.gov<mailto:[email protected]> Thank you, Darlyn 630.252.4220 Begin forwarded message: From: "Lutes, Darlyn" <darlyn(a)anl.gov<mailto:[email protected]>> Subject: Visit to UIC on Oct. 11th... Date: September 5, 2019 at 4:24:34 PM CDT To: "Xia, Fangfang" <fangfang(a)anl.gov<mailto:[email protected]>>, "Zhu, Yitan" <yitan.zhu(a)anl.gov<mailto:[email protected]>>, "Ramanathan, Arvind" <ramanathana(a)anl.gov<mailto:[email protected]>>, "Partin, Alexander" <apartin(a)anl.gov<mailto:[email protected]>>, "Getty, Neil James" <ngetty(a)anl.gov<mailto:[email protected]>>, "Hereld, Mark" <hereld(a)anl.gov<mailto:[email protected]>>, "Ferrier, Nicola J." <nferrier(a)anl.gov<mailto:[email protected]>> Cc: "Chen, Liaohai Leo" <lhchen(a)uic.edu<mailto:[email protected]>> Good afternoon, Just a little reminder about the visit to UIC on Oct. 11th. A detailed agenda has not be finalized yet but below is a quick description of the day from Leo. It will be a full day event with a tentative agenda of a) clinical observation of robotic surgery in the operation room and live stream in the conference room in the earlier morning, b) a workshop entitled "Medical Robotics and Digital Medicine”, which will involve presentations and (group) discussions from both sides (and potentially people from Intuitive and other places); and c) hands-on the da Vinci robotic systems in the lab in the afternoon. People will have a direct feeling of operating the robots. The address is: College of Medicine Research Building, Room 1020, 909 S Wolcott Ave Chicago, IL 60612 We look forward to hearing from Leo in the next couple of weeks. Thank you, Darlyn 630.252.4220

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Fwd: Announcing: The Allen Institute Cell Lineage Reconstruction DREAM Challenge
by Stevens, Rick L. 24 Sep '19

24 Sep '19

Begin forwarded message: From: DREAM Challenges <contact(a)dreamchallenges.org<mailto:[email protected]>> Subject: Announcing: The Allen Institute Cell Lineage Reconstruction DREAM Challenge Date: September 23, 2019 at 12:14:15 PM CDT To: <stevens(a)ci.uchicago.edu<mailto:[email protected]>> Reply-To: DREAM Challenges <contact(a)dreamchallenges.org<mailto:[email protected]>> [https://gallery.mailchimp.com/b146de537186191a9d2110f3a/images/965497f8-218…] [Share]<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> Share<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> [Tweet]<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> Tweet<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> [Forward]<http://us7.forward-to-friend.com/forward?u=b146de537186191a9d2110f3a&id=8c3…> Forward<http://us7.forward-to-friend.com/forward?u=b146de537186191a9d2110f3a&id=8c3…> Sept. 23, 2019 – To advance our understanding of development and disease in multicellular organisms, The Allen Institute has partnered with DREAM Challenges to mobilize a larger community for evaluating new optimal tree-building methods. Top performers in this Challenge will be announced at Hindsight 2020 - The Allen Institute Developmental Recording Symposium<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…>, taking place on March 3-5, 2020, in Seattle, Washington. Challenge Overview CRISPR-based molecular tools allow the reconstruction of cell lineages based on the phylogenetical analysis of DNA mutations induced by CRISPR during development. This enables cell lineage reconstruction for complex model organisms at single-cell resolution. The Allen Institute Cell Lineage Reconstruction Challenge will provide an unprecedented opportunity to rigorously examine the performance and robustness of lineage reconstruction algorithms across datasets, number of cells, and sizes of lineage trees. This DREAM Challenge comprises three sub-challenges to reconstruct cell lineage trees using 1) experimental molecular data from lineages of less than 100 cells and a video-microscopy reconstructed tree as ground truth; 2) data from an in silico-generated tree of 1,000 cells; and 3) data from an in silico-generated tree of 10,000 cells. Data and scientific guidance for this challenge are being provided by IBM, University College London, Weizmann Institute, Caltech, and University of Washington. Timeline Registration Opens: September, 2019 Launch: Mid-October, 2019 Final Submissions: January, 2020 Winners Announced: March, 2020 Learn More<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> [Website]<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> [Twitter]<https://sagebionetworks.us7.list-manage.com/track/click?u=b146de537186191a9…> Copyright © 2019 Sage Bionetworks, All rights reserved. Your participation in Sage Bionetworks/DREAM competitions has placed you on this email list. Our mailing address is: Sage Bionetworks 2901 3rd Ave. #330 Seattle, WA 98121 Add us to your address book<https://sagebionetworks.us7.list-manage.com/vcard?u=b146de537186191a9d2110f…> Want to change how you receive these emails? You can update your preferences<https://sagebionetworks.us7.list-manage.com/profile?u=b146de537186191a9d211…> or unsubscribe from this list<https://sagebionetworks.us7.list-manage.com/unsubscribe?u=b146de537186191a9…>.

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Fwd: You are Invited to an Interactive Virtual MicroLab on Cancer Challenges and Advanced Computing: September 25, 3:00 - 4:30 PM ET
by Stevens, Rick L. 11 Sep '19

11 Sep '19

Begin forwarded message: From: "Borkon, Lynn (NIH/NCI) [C]" <lynn.borkon(a)nih.gov<mailto:[email protected]>> Subject: You are Invited to an Interactive Virtual MicroLab on Cancer Challenges and Advanced Computing: September 25, 3:00 - 4:30 PM ET Date: September 11, 2019 at 12:06:25 PDT To: "Brettin, Thomas S." <brettin(a)anl.gov<mailto:[email protected]>>, "Dietrich, Emily M." <edietrich(a)anl.gov<mailto:[email protected]>>, "Stevens, Rick L." <stevens(a)anl.gov<mailto:[email protected]>> Cc: "Kimbrough, Miles (NIH/NCI) [C]" <miles.kimbrough(a)nih.gov<mailto:[email protected]>>, "Stahlberg, Eric (NIH/NCI) [C]" <eric.stahlberg(a)nih.gov<mailto:[email protected]>> Dear Rick, Tom, and Emily – Hope all is well with you! Today I am writing about our upcoming interactive virtual MicroLab on September 25, 3:00 – 4:30 pm ET – and to ask if you might consider passing along this information to students or colleagues who may be interested. At the first MicroLab in June, over 200 people participated from 50 organizations and we hope you can join us on September 25<https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6>! The focus will be developing use cases based on various personae created by some of the team leads, derived from the original 4 cancer challenge areas identified at the Scoping Meeting. If you could help spread the word among your computational colleagues, that would be wonderful! A cover note appears below, and a flyer and single power-point slide are attached in hopes of making it easier for you to share. Thank you very much and best wishes from the Team! Lynn L. Borkon [C] HPC Collaborations Development Biomedical Informatics and Data Science Directorate Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. Post Office Box B Frederick, Maryland 21702 Phone: 240.276.7129 (office) 703.725.8182 (mobile) Email: Lynn.Borkon(a)nih.gov<mailto:[email protected]> Dear Colleagues, You may be interested in participating in an interactive virtual MicroLab<https://ncihub.org/groups/cicc/sept25thmicrolab> on Cancer Challenges and Advanced Computing to be held on September 25th, 3:00 – 4:30 PM ET (see flyer, attached). NO TRAVEL REQUIRED. This virtual event is sponsored by the Envisioning Computational Innovations for Cancer Challenges (ECICC) Community, comprised of clinicians, cancer researchers, and data and computational scientists who are dedicated to accelerating computational oncology and developing research collaborations across cancer and computational sciences. Please register<https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6> for the MicroLab on September 25th and help shape future research in computational oncology! Origin * The ECICC community arose from a collaborative program between the National Cancer Institute (NCI) and the Department of Energy (DOE), Joint Design of Advanced Computational Solutions for Cancer (JDACS4C)<https://cbiit.cancer.gov/ncip/hpc/jdacs4c>, to simultaneously accelerate advances in precision oncology and computing. We are holding a series of dynamic, interactive events all of which are free of charge. Recap of Events * March 2019: a two-day, multi-disciplinary Scoping Meeting<https://ncihub.org/groups/cicc/pastmeetings/ecicc> held at the Department of Energy’s Lawrence Livermore National Laboratory<https://www.llnl.gov/>, Livermore Valley Open Campus<https://lvoc.org/> resulted in identification of four cancer challenge areas: 1) Generating Large-Scale Synthetic Data to Protect Personally Identifiable Information, 2) Using Machine Learning for Iterative Hypothesis Generation, 3) Creating a Cancer Patient “Digital Twin” to Optimize Personalized Treatment Decision-Making, and 4) Developing Adaptive Cancer Treatments Targeting Unique Tumor Characteristics & Trajectories. * June 2019: the first interactive virtual MicroLab<https://ncihub.org/groups/cicc/pastmeetings/june_11th_microlab> on Cancer Challenges and Advanced Computing was held with over 200 participants from 50 organizations! Virtual breakout groups discussed key issues and potential next steps related to the 4 cancer challenge areas from the Scoping Meeting. * September 25, 2019: the 2nd interactive virtual MicroLab<https://ncihub.org/groups/cicc/sept25thmicrolab> will be held September 25, 2019, 3:00 – 4:30 pm ET (see attached flyer for details).Building on the breakout discussions from the first MicroLab, participants will develop use cases based on the persona of their choice and will identify critical next steps to shape future research! * Read more about it<https://ncihub.org/groups/cicc/sept25thmicrolab> and * Register<https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6> Please join us<https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6> and forward the attached flyer to any colleagues who may be interested in participating. The web link to the flyer is:https://ncihub.org/groups/cicc/sept25thmicrolab. [cid:[email protected]] Please forward this invitation to colleagues who may be interested! Join the Online Community! For more information about the ECICC Community<https://ncihub.org/groups/cicc/> visit: https://nciphub.org/groups/cicc <https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6> [cid:[email protected]] <https://zoom.us/meeting/register/6a3f0fbc5020ec08c5b9141539e44ee6> Questions? Contact ECICCcommunity(a)nih.gov<mailto:[email protected]> Thank you for adding your voice to the discussions!

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Fwd: BIOLIFE4D Becomes First U.S. Company to Successfully Demonstrate Ability to 3D Bioprint a Mini Human Heart
by Stevens, Rick L. 10 Sep '19

10 Sep '19

Begin forwarded message: From: "Stevens, Rick L." <stevens(a)anl.gov<mailto:[email protected]>> Subject: BIOLIFE4D Becomes First U.S. Company to Successfully Demonstrate Ability to 3D Bioprint a Mini Human Heart Date: September 10, 2019 at 05:59:01 CDT To: "Kearns, Paul K." <pkearns(a)anl.gov<mailto:[email protected]>> Cc: "Stevens, Rick L." <stevens(a)anl.gov<mailto:[email protected]>> Another possible invitee to the salon. https://www.globenewswire.com/news-release/2019/09/09/1912675/0/en/BIOLIFE4… BIOLIFE4D Becomes First U.S. Company to Successfully Demonstrate Ability to 3D Bioprint a Mini Human Heart Pioneering biotech company reaches significant milestone, using proprietary bioink to successfully 3D bioprint a mini-heart with full structure of a whole heart, including chambers and ventricles BIOLIFE4DSeptember 09, 2019 08:00 ET CHICAGO, Sept. 09, 2019 (GLOBE NEWSWIRE) -- BIOLIFE4D<https://www.globenewswire.com/Tracker?data=7wDxG3vUyDT6BFHHQ-S6k18NF_G9VLAe…>, a biotech pioneer leveraging advances in tissue engineering to 3D print human organs viable for transplant, today announced it has successfully demonstrated its ability to 3D bioprint a mini human heart, a significant step toward its goal of producing a full-sized human heart viable for transplant. The scientific milestone was accomplished at the Company’s research facility at JLABS in Houston, and led by Dr. Ravi Birla, the Company’s Chief Science Officer. The successfully printed mini heart has the full structure of a full-sized heart, with four internal chambers. The mini heart is replicating partial functional metrics compared to a full-sized heart – as close as anyone has gotten to producing a fully functional heart through 3D bioprinting. “We are extremely proud of what we have accomplished, from the ability to 3D bioprint human cardiac tissue last summer to a mini heart with full structure now. These milestones are a testament to the hard work of our team and the proprietary process we have developed that enables this type of scientific achievement,” said Dr. Ravi Birla, Chief Science Officer, BIOLIFE4D. “We believe we are at the forefront of whole heart bioengineering, a field that has matured quickly over the last year, and well positioned to continue our rapid scientific advancement. Today is an exciting day, but we continue forward earnestly toward the end goal of 3D bioprinting whole human hearts.” The Company developed a proprietary bioink using a very specific composition of different extracellular matrix compounds that closely replicate the properties of the mammalian heart. Further, it has developed a novel and unique bioprinting algorithm, consisting of printing parameters optimized for the whole heart. Coupling its proprietary bioink with patient-derived cardiomyocytes and its enabling bioprinting technology, BIOLIFE4D is able to bioprint a heart that, while smaller in size, replicates many of the features of a human heart. With this platform technology in place, BIOLIFE4D is now well-positioned to build upon this platform and work towards the development of a full-scale human heart. The successful demonstration of a mini heart is the latest in a string of scientific milestones from BIOLIFE4D as it seeks to produce the world’s first 3D bioprinted human heart viable for transplant. Earlier in 2019, the Company successfully 3D bioprinted various individual heart components, including valves, ventricles, blood vessels, and in June of 2018 it successfully 3D bioprinted human cardiac tissue<https://www.globenewswire.com/Tracker?data=y7WTKaT-fUdDb7784urXX5E3-60_yZb-…> (a cardiac patch) – all ahead of development times published in scientific literature. BIOLIFE4D’s innovative 3D bioprinting process provides the ability to reprogram a patient’s own (white) blood cells to iPS cells, and then to differentiate those iPS cells into different types of cardiac cells needed to 3D bioprint individual cardia components and ultimately, a human heart viable for transplant. This means BIOLIFE4D can successfully 3D bioprint using cardiac cells derived from their own iPS cells to create living, viable constructs. That ability is crucial as the Company seeks to disrupt how heart disease and other cardiac impairments are treated, particularly by improving the transplant process by eliminating the need for donor organs. Heart disease is the number one killer of men and women in the United States each year, yet countless individuals who need transplants are left waiting as there are not enough donors to meet demand. “This is an incredibly exciting time for BIOLIFE4D, and we are so proud of Dr. Birla and the team for this tremendous accomplishment,” said Steven Morris, CEO, BIOLIFE4D. “We began this journey with an end goal of developing a technology that has the potential to save lives, and we are a step closer to that today. We will continue our work until we are able to 3D bioprint full-sized hearts for viable for transplant, and change the way heart disease is treated forever.” To see how BIOLIFE4D’s process starts with a patient’s own cells and ends with a functional human heart ready for transplant, please watch this video<https://www.globenewswire.com/Tracker?data=Z8YODWnGvgTxxzZUaHGx9wLVt4JU8H8Z…>. The Company also recently re-opened its Regulation A+ equity crowdfunding campaign. To learn more about BIOLIFE4D and to express interest in investing please https://biolife4d.com/investing-in-biolife/<https://www.globenewswire.com/Tracker?data=oIXlMgwtoYhnaQXuIybLKkM2-X1yFqQO…>. Securities are offered pursuant to a Regulation A+. Investors are encouraged to read the Offering Circular and exhibits and consult with their tax, legal, or financial professional prior to investing. About BIOLIFE4D BIOLIFE4D is a pioneering biotech company laser focused on leveraging advances in life sciences and tissue engineering to 3D bioprint a viable human heart suitable for transplant – lifesaving technology that gives patients the gift of time. With BIOLIFE4D, a patient-specific, fully functioning heart will be created through 3D bioprinting using the patient’s own cells – eliminating the well-known challenges of organ rejection and long donor waiting lists that plague existing organ transplant methods. Financed through equity crowdfunding, BIOLIFE4D is driving a movement to transform the treatment of heart disease, the leading cause of death among both men and women globally. Learn more and invest at biolife4d.com<https://www.globenewswire.com/Tracker?data=bKqFw4fAGVXZcO4TmWpYRyyMWBZCtYVV…>. Connect with us on social media on Twitter<https://www.globenewswire.com/Tracker?data=T9nXpc846uoiM9j6l_Gh7L74mWvJs02w…> (@BIOLIFE4D), Facebook<https://www.globenewswire.com/Tracker?data=dtaJVqB3ib8i-R71qG6-2RFkmxJCWrEs…>, LinkedIn<https://www.globenewswire.com/Tracker?data=fsqF_GZBWFiu7PRtQ28UbOQPYLLSz-a2…>, and Instagram<https://www.globenewswire.com/Tracker?data=jk-vLdX9FsisaIThRwuJnDHUSfDxbceN…>. Forward-Looking Statements We caution you that, whether or not expressly stated, certain statements made in this news release that reflect management's expectations regarding future events and economic performance are forward-looking in nature and, accordingly, are subject to risks and uncertainties. All statements other than statements of historical facts included in this press release are forward-looking statements. In some cases, forward-looking statements can be identified by words such as "believe," "expect," "anticipate," "plan," "potential," "continue" or similar expressions. Such forward-looking statements include risks and uncertainties, and there are important factors that could cause actual results to differ materially from those expressed or implied by such forward-looking statements. Investors should not place any undue reliance on forward-looking statements since they involve known and unknown, uncertainties and other factors which are, in some cases, beyond the Company’s control which could, and likely will, materially affect actual results, levels of activity, performance or achievements. Media Contact Matthew Bretzius FischTank Marketing and PR biolife4d(a)fischtankpr.com<https://www.globenewswire.com/Tracker?data=bKqFw4fAGVXZcO4TmWpYRwQD1gNkhsS5…>

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MLIR -- AI open source compiler infrastructure with google, Cerebras and others...
by Ramanathan, Arvind 10 Sep '19

10 Sep '19

https://www.blog.google/technology/ai/mlir-accelerating-ai-open-source-infr…

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Deep learning enables rapid identification of potent DDR1 kinase inhibitors
by Brettin, Thomas S. 05 Sep '19

05 Sep '19

https://www.nature.com/articles/s41587-019-0224-x Deep learning enables rapid identification of potent DDR1 kinase inhibitors Abstract We have developed a deep generative model, generative tensorial reinforcement learning (GENTRL), for de novo small-molecule design. GENTRL optimizes synthetic feasibility, novelty, and biological activity. We used GENTRL to discover potent inhibitors of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, in 21 days. Four compounds were active in biochemical assays, and two were validated in cell-based assays. One lead candidate was tested and demonstrated favorable pharmacokinetics in mice.

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