As someone involved in art, science and nature, I particularly enjoyed the current show at Lucy Lacoste Gallery, in Concord, Mass. It features the ceramic sculptures of Ashwini Bhat, whose work embodies her experiences as a classical Indian dancer, a painter, a writer, and a gardener. The show, “”What I Touch Touches Me,” is a visual and tactile representation of her California garden as she–and the garden–progressed through the pandemic. The result is a beautiful harvest of earthly and spiritual objects and ideas.

As Bhat explains: The structure of my new body of work is derived from my immersion in my surroundings in a dramatic, highly various, and fragile Northern California landscape. The sculptures are assembled in four segments: Comfort Objects, Animated Objects, Intimate Earth Objects, and Assemblage Objects.

Animated Object #4, below, brings to mind (for me) a leaf in the wind, a deeply colored Indian veil or scarf, and the graceful hand of dancer. ,

Comfort Objects evolved— during a pandemic in which touch has become unsafe— from Bhat’s examination of the shapes and forms of seed-pods “as symbols of mysterious, life-birthing potentialities.”

“Animated Objects are studies in gesture, movement, and the feelings evoked by[her} memories of objects that have deep personal associations for her.”

“Intimate Earth Objects” reference elements of earth and body. T” hese biomorphic forms enact the co-existence and mutuality of the human and non-human. And they also focus on the sorts of objects that are historically or culturally associated with rituals and sacrality. “

“Assemblage Objects juxtapose colors and consortiums of form that reference particular landscapes in which Bhat has spent time, she writes.

“All four segments are linked by allusions to primordial symbols or patterns such as the Mandala, Spiral, Serpent, the Ouroboros, and the Fibonacci sequence. 

“But the meanings of these sculptures are fluid, not rigid,” Bhat explains. The objects might easily cross over and fit into other groupings. And this boundary-less-ness allows them to acquire multiple connotations. There is an open interplay of elements and a possibility of infinitely reassembling alliances. ” Bhat’s aim is”to suggest ways of looking that promote raveled and linked engagements that define the relation between all animate and inanimate matter.”

Also included in the show are several of Bhat’s watercolors….

and a piece from a previous exhibit, “Empowering Voices.”

–Anita M. Harris

Lucy Lacoste Gallery, is located 25 Main Street, Concord, MA The show will be up until June 5.

Anita Harris is a writer, photographer and communications consultant based in Cambridge, MA.
New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge.

Now that Massachusetts has made it into phase 3 of the covid reopening, I’m pleased that our new cases are remaining low and that, perhaps in light of what’s happening elsewhere in the country, more folks seem to be wearing masks, outdoors.

I’m also pleased that, of late, no one has cursed me out (and vice versa) and that those who do call me names now use positive terms. Yesterday, someone actually called out “genius” and the day before, “creative! ” Sometimes, I hear people chuckling as they pass by.

That’s been true for a few weeks, now–ever since the Christmas Tree Shop reopened and I was able to buy a pool noodle which I sport to maintain social distance of almost six feet when running on Fresh Pond or the Charles.

It wasn’t really my idea (a friend told me he’d seen people doing that in New York’s Central Park) but, hey, I’m willing to take credit if this becomes a Cambridge fashion trend. (And I hope it does).

I’d also like to thank some folks and organizations for helping me through the pandemic—in what has not been an easy time:

Ranger Jean, of Fresh Pond, who listened and commiserated when I told her about the maskless covidiot who called me a motherFxxxr when I told him masks were required; she told me not to interact, that people should feel happy on Fresh Pond.

Heidi M. of Evolve Fitness of Cambridge and Framingham, whose Zoom Zumba class, smile and joy lifted my spirits on Saturday mornings before the covid reopening.

Jennifer Miles, whose City of Cambridge online yoga classes continue to provide me with peace, calm and a regular schedule. https://www.facebook.com/huronvillageyoga

Heather Cox Richardson, whose biweekly lectures on political history have taught me ever-so- much about the situations we are facing today .

-The good-natured helpful people at Trader Joe’s and CVS, and the nice older Star Market checkout clerk (I don’t know his name) who offered that he went to Boston College, not BU; and the Starbucks barista who wished me a good day as I walked out the door with my half -caf .

-Virginia and Maya (in the photo below)and Sheldon at the newly reopened Henrietta’s Cafe, at the Charles Hotel in Cambridge, whose spirit, joy , encouragement and coffee (!) give me great energy to complete my book-in progress.

And Sarah, for taking the photo of me with the pool noodle, and for adding that cinnamon to my coffee!

–Anita Harris

Anita M. Harris is an author, photographer and communications consultant based in Cambridge, MA.

New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge.

I recently interviewed Bob Langer–MIT biotech guru extraordinaire–on behalf of the EBD Group, which holds international partnering conferences for the life sciences six times a year.  Here’s the opening…and a link to the rest, on the EBD Site. The piece will also  appear in xconomy shortly. Full disclosure…Bob is a personal friend, former classmate, and a member of the Harris Communications Group advisory board…so this should be considered a sponsored post.

–Anita M. Harris

When Bob Langer joined the MIT faculty in 1977 he had a rocky start. Trained as a chemical engineer and working on drug delivery systems, many of his ideas went against conventional wisdom. “I had people write the most insulting things about my knowledge of biology and medicine. Many thought my ideas were crazy. A number of professors wanted me to leave and my first nine grant proposals were turned down.”

Eventually, after numerous academic scientists and companies repeated and used his work Langer was able to get grant funding from the NIH. He also turned to companies for research funding—in return for licensing his patents—which, at that time, also went against the conventional grain.

Today, Langer is one of 13 Institute Professors (being an Institute Professor is MIT’s highest honor) at Massachusetts Institute of Technology. With more than 1,400 articles to his credit, he is the ninth most cited individual in history, according to Google scholar. (Sigmund Freud is first). His 1,300 patents, licensed or sublicensed to more than 350 companies in pharmaceutical, chemical, biotechnology and medical device fields, have led to more than 100 products currently in use or in clinical trials. He has received more than 220 major professional awards including the Queen Elizabeth Prize for Engineering, Priestly Medal, National Medal of Science, National Medal of Technology and Innovation, the Charles Stark Draper Prize (considered the equivalent of the Nobel Prize for engineers), and the Lemelson-MIT prize for being “one of history’s most prolific inventors in medicine.” In June 2018, he was named a US international envoy for science by the US State Department.

Despite his success, Langer remains well aware of his early setbacks, and, as a scientific advisor to some 200 companies over the past 40 years, is highly cognizant of what can go wrong.

“You can have bad animal results, failed trials, or patent problems. I’ve seen partners pull out, companies take bad loans, and the FDA create delays. Stumbling blocks can arise anywhere along the way,” he says.

One of the most difficult problems can occur early on “when a researcher has good findings but is not far enough along for investors or companies to want to spend a lot of money.” In that situation, known as “the valley of death,” Langer says, “the question is how to get enough data so that will change.”

More: 

Anita M. Harris is a writer and communications consultant based in Cambridge, MA.

New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge.

Spent an interesting Wednesday afternoon, last week,  visiting exhibitors at the Bio-IT World Conference & Expo –several of whom won “Best of Show” Awards later that day.

The judges, listed below,  named winners in six categories: Data Integration & Management; Analysis & Data Computing; Genomic Data Services; Data Visualization & Exploration; Storage Infrastructure & Hardware; and the Judges’ Prize.  Attendees also voted on the People’s Choice Award, selecting products that they believed measurably improve workflow or capacity, enabling better research.

One of my favorites was Nanome, which won best in show for Data Visualization and Exploration.
Nanome uses virtual reality to improve the drug discovery process, according to its award application. The company offers applications for experimentation, collaborattion, and learning at the nano-scale– leveraging  VR hardware such as the Oculus Rift and HTC Vive to create immersive virtual workspaces allowing users to visualize, design, and simulate molecules, proteins, and more.

At  Nanom’se i BIO–IT World booth, Marketing Director Jarrell James handed me a pair of VR goggles and two joysticks (?) with which  I could explore within a molecule–by seeming to make components larger, smaller or revolve.

A more sophisticated user might be able to:

• -Import molecular structures from a local machine or an online database such as RCSB or DrugBank.
• – Manipulate molecular structures by literally grabbing, rotating, or enlarging the area of interest with their hands.
• – Apply different representations to their selection of Atoms, Residues, Chains, or Proteins such as Stick, Wire, Ball & Stick, or Van der Waals.
• – Measure distances and angles between atoms.
• – Mutate amino acids and cycle through rotamer libraries.
• – Design small molecules by building with any element from the periodic table.
• – Minimize manipulated molecules to prevent clashes and provide a local energy minimum conformation.
• – Duplicate or Split any selected area of your structure to modify or export independently.
• – Export your molecular structures to PDB.
• – Join a virtual reality session as a guest with or without virtual reality hardware.

• – Present and collaborate in the same virtual environment with colleagues to demonstrate proposals or compare before and after results.

Nanome plans next to enter the education space. The company’s VR technology wil help high school and college students , likely already proficient in gaming technology,  better understqand biologic processes, James said.

The Hyve 

I also spent some time with the folks at Hyve…whose fake robot ( that is, a “robot inhabited” by a human) did make me  curious about Hyve’s work.

RADAR-base
radar-cns.org

As described in the company’s award submission,  the company’s RADAR-base, developed in the framework of the IMI RADAR-CNS project, is an open source platform designed to securely collect, store and share readings from wearable devices and smartphone sensors to enable remote monitoring. The RADAR-base platform consists of three major categories of components:

• Data ingestion: Recognizing and registering data-sources (including smartphones and wearable devices), collecting the data via a direct Bluetooth connection or through a 3rd party API and streaming in near real time to the server (green box in the figure). Using Apache Kafka, the collected data is streamed to dedicated topics in real-time where the data is optimally schematized using Apache Avro;
• Data storage and management: Consists of two centralized storage systems behind an authorized security layer. A cold-storage based on HDFS that is scalable and fault-tolerant focusing on storing large volumes of high frequency raw-data, and a hot-storage based on MongoDB storing aggregated data to provide a near real-time overview of the raw-data. (blue box in the figure);
• Data sharing: Visualizing aggregated data in a live dashboard and exporting raw data for further analyses in various formats including AVRO, JSON and CSV (yellow box in the figure).

The platform is highly secured by a centralized management system of users and their authorities, participants, allowed devices and their specifications. RADAR-Base platform is distributed as Docker containers with associated scripts and configuration files to enable easy installation.

 In addition, I  visited Sinequa, which took the prize in the Analysis & Data Computing category. 

Sinequa ES v10
sinequa.com

The Sinequa Cognitive Search and Analytics platform handles all structured and unstructured data sources and uses Natural Language Processing (NLP), statistical analysis and Machine Learning (ML) in order to create an enriched “Logical Data Warehouse” (LDW). This LDW is optimized for performance in delivering rapid responses to users’ information needs. Users can ask questions in their native language or ask that relevant information be “pushed” to them in a timely fashion when it emerges.

More than 180 connectors ready for use “out of the box” make the process of connecting multiple data sources fast and seamless. Company and industry-specific dictionaries and ontologies can be easily integrated, putting specific knowledge “under the hood” of the Sinequa platform, making it an intelligent partner for anyone in search of relevant subject information.

Other awards, as descrbed in company literature: :

Genomic Data Services

Diploid
Moon 1.0
diploid.com/moon

Moon is the first software to autonomously diagnose rare diseases from WES/WGS data. By applying AI to the domain of rare disease diagnostics, Moon brings speed and scalability to the genome interpretation process.

The software only requires the patient’s gender, age of onset and his/her symptoms – in addition to the genetic data. Moon then goes from whole genome variant data (VCF) to pinpointing the causal variant in less than 5 minutes.

The software highlights one or a few variants that could explain the patient’s phenotype. For every variant, Moon displays an extensive list of annotations that it mined from the literature, allowing geneticists to easily verify decisions from the AI algorithms. Moon’s speed does not only save a lot of time and money, it also saves lives: Moon has already proven its utility in the NICU at Rady Children’s Hospital (San Diego): https://goo.gl/7TDrQD.

Unfortunately, about 50% of rare disease patients remain undiagnosed, even after whole genome sequencing and expert interpretation. Most hospitals don’t have the resources to keep analyzing negative cases even though new correlations between genes and disorders are published every day. Moon changes all this: as the software autonomously mines the literature and analyses samples, it can reanalyze older, negative cases in the background. Only when new information that might lead to a diagnosis becomes available, the assigned geneticist is notified. That way, hospitals can frequently reanalyze thousands of cases with minimal labor, providing a perspective to undiagnosed patients.

Storage Infrastructure & Hardware

PetaGene
PetaSuite Cloud Edition – Version 1.2
petagene.com

Launching at Bio-IT World 2018, PetaSuite Cloud Edition (CE) combines two innovations: (i) the ability for a user’s software tools and pipelines to seamlessly integrate with a wide variety of cloud platforms without modification, and (ii) significantly improved, high-performance, scalable PetaSuite genomic compression technology. 

For example, users can now directly run, without modification, their custom BWA-mem, GATK, Python, Java, shell scripts, and other POSIX-based software/pipelines streaming directly to/from AWS, Google Cloud, Azure, and private cloud storage, as though they were local filestores. PetaSuite CE supports each platform’s object encryption during transfer and at rest. User applications can connect to multiple cloud platforms, buckets and regions as desired, transparently, and on demand, in user-mode, without needing to modify their pipelines, setup mounts, or have administrator privileges.

Whether running on bare-metal, in VMs, or within Docker containers, for public, private or hybrid cloud, PetaSuite CE enables organizations to unlock the power of distributed object storage seamlessly from their POSIX-compliant tools and pipelines.

PetaSuite CE is built from the ground-up for the extremely high performance streaming and random-access workloads demanded by genomics applications. The integrated, transparent PetaGene compression has been significantly improved to deliver even faster compression and greater reductions of up to 6x of both BAM and FASTQ.GZ files, enabling large costs savings in cloud storage and data transfer times. Moreover, PetaGene compression can also preserve the MD5 checksum of the original BAM or FASTQ.GZ file and not just the internal raw SAM/FASTQ data.

The Judges’ Prize went to 

 Linguamatics and its iScite 2.0 (iscite.com) provide a Software-as-a-Service search application that puts the power of text analytics directly into scientists’ hands, according to the company writeup.

Using Linguamatics’ Award-winning Natural Language Processing
Researchers can extract and analyze relevant data to rapidly answer business-critical questions. iScite utilizes Linguamatics’ award-winning Natural Language  L(NLP) based blend of analytical methods. By understanding the semantics and structure of text, iScite handles the variety of ways people express the same information, ensuring searches are comprehensive and accurate.

Easy to use on any device
iScite’s intuitive HTML interface includes a simple search box and auto-complete suggestions. The innovative answer-routing engine lets users answer simple or complex questions using puzzle-piece building blocks – simplifying access to powerful queries that extract concepts, relationships, numerical data such as drug dosages, mutations and more.

Get answers to questions, not just documents
Data sources include Linguamatics’ cloud-hosted content. MEDLINE, Clinical Trials.gov, FDA Drug Labels, PubMed Central, and Patent Abstracts are annotated with curated terminologies for diseases, drugs, genes and organizations. Scientists can answer questions such as:

• What genes are involved in breast cancer?
• What protocol designs have been used for immuno-oncology trials?
• What are the adverse events for kinase inhibitors?

Actionable results
Results are presented in structured form, with bar chart facets for dynamic, visual results-filtering, a document viewer that highlights key terms and relationships, and relevant link-outs. Users can curate, save, and export their results.

iScite allows users across drug discovery and development to cut through the vast information landscape and discover the most valuable insights.

The People’s Choice award went to 

OnRamp BioInformatics, Inc. and itsROSALIND™ platform:  the first-ever genomics analysis platform specifically designed for life science researchers to  analyze and interpret datasets, while freeing up more time for bioinformaticians.

Named in honor of pioneering researcher Rosalind Franklin, who made a major contribution to the discovery of the double-helix structure of DNA with her famous photograph 51, OnRamp’s ROSALIND platform aims to simplify the practice of genomic data interpretation. According to the company’s writeup,  ROSALIND puts the researcher into the driver’s seat of data analysis and democratizes bioinformatics by broadly expanding access to genomic and proteomic technologies for cancer research, precision medicine and sustainable agriculture.

While many open-source tools remain the lifeline of genomic analysis, a simplified and innovative user experience for the biologist can empower them to run their own analyses, while utilizing these tools without the need for typing any command-line instructions.

ROSALIND is powered in partnership with Google Cloud and features scalable compute power and economical cloud-based storage. ROSALIND is a swarming docker-based genomic analysis solution incorporating the industry’s most trusted open-source tools and algorithms, with an angular front-end and secure RESTful API. ROSALIND is also deployable on-premise.

On Ramp technololgists believe that empowering biologists with “an intuitive and comprehensive platform” to explore their data and collaborate with colleagues and bioinformaticians, they  can help accelerate their industry and the widespread adoption of genomic technologies by dramatically lowering costs, reducing  complexity and, ultimately, focus more on what what to do with results, rather than on how to get to them.

In the words of Allison Profitt, BIO-IT World’s editor,” The awards program recognizes the best of the innovative product solutions for the life sciences industry on display at the conference,

“It’s always a treat to explore what’s new in our industry.

” The innovation on display by Bio-IT World exhibitors never disappoints, and we are excited to shine a spotlight on the best life sciences has to offer.”

Judges
“The Best of Show program relies on a panel of expert judges from academia and industry who screen eligible new products and hear presentations from a list of finalists on site. This year our judges considered 46 new products and viewed presentations on site from 18 finalists.”

The 2018 judging panel included Joe Cerro, BostonCIO; Chris Dwan, Bridgeplate; Richard Holland, New Forest Ventures; Eleanor Howe, Diamond Age Data Science; Phillips Kuhl, Cambridge Healthtech Institute; Steve Marshall, Marshall Data Solutions; Michael Miller, Genentech; Art Morales, Analgesic Solutions; Nanguneri Nirmala, Tufts University School of Medicine; Alexander Sherman, Massachusetts General Hospital; Subi Subramanian, Vertex Pharmaceuticals; Bill Van Etten, BioTeam; and Proffitt.

–Anita M. Harris
Anita Harris is a science writer based in Cambridge, MA. 
New Cambridge Observer is a publication of the Harris Commmunications Group, also in Cambridge, ma.  

Had a great time at this year’s women’s march…Much good cheer; great signage, and a wide range of participants. At about 2 pm, half-way through, a police officer told me that the crowd estimate was 4000…but he believed the number of participants was twice that, and I’d guess even a few more. (Given that there were only about 10 porta-potties, I’d also guess that was many more than the organizers expected). The sound system left something to be desired (from my perch on a monument, I could see the speaker but not hear an understandable word) but I much enjoyed the creativity of the signage and enthusiasm of the attendees.

–Anita Harris
Anita M. Harris is a writer and communications consultant based in Cambridge, MA. She is the author of Broken Patterns, Professional Women and the Quest for a New Feminine Identity  

and Ithaca Diaries, Coming of Age in the 1960s. 

New Cambridge Observer is a publication of the Harris Communications Group, a pr and content marketing firm  in Cambridge.

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I found Ani Kasten’s latest ceramics exhibit, which opened yesterday at the Lacoste Gallery in Concord, MA, inspirational.  The work, comprised mainly of vessels of irregular shapes and sizes,  is  delicate, with seams sometimes held together with thin wires, and replete with beautiful, unexpected embellishments, cracks. colors and patterns that make the viewer stop to contemplate.

Entitled From the Ruins, the show focuses on vessels and sculptures that are “deconstructed…  ‘barely holding together’, ‘coming apart at the seams’, and searching for a cohesive beauty in their tenuous state of existence,”  according to the exhibit writeup.

I mentioned to Kasten that her work “spoke” to me, especially because too many of my close friends and family members have passed away, recently, and that I’m working on writing and photography projects that I hope will help bring shape, beauty, meaning and new life to past experiences.  Kasten responded that she, too, has gone through several major losses, which in part, inspired her current work.

Ani Kasten

 “Investigating the materiality of the clay is the foundation and focal point for all of my sculptural vessels. I create wheel-thrown and hand-built forms in families, and these sculptural groupings explore the meeting point between natural and man-made worlds. The vessels take their influence from plants, water, rocks and clay, as well as from architecture, industry and machinery.

“They investigate the nature of change, the compiling of memory, and a feeling of profound loss– the recognition of temporal beauty bound inextricably with grief. The pieces are like remnants, a landscape of objects that remain after some kind of significant change, grave markers, or organic matter that has survived a great fire.

According to a gallery publication, Kasten was drawn to the medium of clay as an apprentice to British ceramist Rupert Spira, Then she headed a stoneware making facility in Nepal for four years before returning to the USA to set up ceramic studios in California, Maryland and most recently Minnesota.  She has exhibited her work nationally and internationally with works in the permanent collections of the Racine Art Museum, Wisconsin; the Weisman Art Museum Minneapolis MN; and the Sana’ a Collection, the US Embassy, Sana’ a Yemen.

Fresh Pond, Cambridge
Credit: Anita M. Harris

I often run at Fresh Pond. True,  I have a “running” debate with my exercise app, which sometimes  calls what I do “walking”  but be that as it may… I have struck up a number of very cordial relationships, there, with the dogs and their humans.

Ordinarily,  everyone is quite friendly (though I can get a bit ferocious when a human attached to three dogs on leashes blocks the entire width of running path).

But a  few weeks ago,  I ran into a spate of ungracious humans who yelled at me that I was running on the wrong side of the road, gave me the finger (to be honest, I responded in kind)  and one who even tried to force me off the dirt path. I asked Ranger Jean Rodgers if there are right-of-way rules for the Pond. 

Here’s her response.

Dear Anita,

Thank you for taking the time to write and share your experiences here at Fresh Pond Reservation.  I’m sorry to hear you are having some less than civil interactions with other users.  Soft running surfaces are in short supply here at Fresh Pond.  No one has a right to them to the exclusion of others. As with all public spaces, sharing and civility are required however frustrating.   If most people keep to the right as they are able, travel on the Perimeter Road would have a level of predictability.  

The behavior of others as you have reported it is unacceptable for any reason.  I will post some signs in our information boards, the ranger station and at entrances excerpted from the street code booklet that help visitors know that sharing and civil interactions are  expected.

The City has just issued “Street Code, Rules and Etiquette for Getting There Together” to address the need for safe and civil behavior when people are moving about the City’s Public Spaces.  Shared Path Etiquette is addressed on page 16. I plan to post it around the Reservation.  http://bit.ly/CambridgeStreetCode  

Here’s a summary and some links to our Shared Use Plan that was developed a while ago with the public to encourage civil interactions and use of Fresh Pond Reservation:

https://www.cambridgema.gov/Water/freshpondreservation/aboutfreshpond/shareduse

Shared Use Plan 

As the terminal reservoir in the water system that provides drinking water to the City of Cambridge, Fresh Pond Reservation serves as in important buffer to protect the health and water quality of Fresh Pond.  The Reservation is also an important open space for Cambridge residents and visitors. Due to limited space on paths, trails, and open areas, as well as increasing popularity due to restoration efforts, occasional conflicts among users can arise. To address these conflicts, the City sought to engage the public in order to develop a shared vision for future use and a clear implementable plan between the Summer 2010 and Spring 2011. The result of this process was the Shared Use Plan with the intent to accomplish the following objectives (in no particular order):
*Protect the flora, fauna, and overall ecosystem and water supply, 
*Promote a welcoming and safe place, 
*Provide for a multitude of recreational activities, 
*Promote mutual respect and civility among users, 
*Improve communication among users and with those managing the Reservation, 
*Provide for additional education and opportunities to participate in stewardship, 
*Enhance user safety and enforcement through rules that are easy to understand, posted, and enforceable, 
*Provide for enjoyment by current and future generations. 

Please feel free to put the ranger phone number (617 349-xxxx) in your phone contact list and call me to come out and assist if you if people don’t settle down and share the space with you.   I do my best to answer the phone whether I’m on or off duty.   If someone threatens you or puts a hand on you, call the police for immediate assistance (911 or at their business number 617 349-3300).

We all matter and we all make a difference.

Jean Rogers
Chief Ranger
Fresh Pond Reservation

Anita Harris is a writer and communications consultant based in Cambridge, MA.
New Cambridge Observer is a publication of the Harris Communications Group, also in Cambridge.