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Updated on 9/16/2026
Philanthropy funding basic biomedical scientists
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HHMI moves science forward by supporting basic biomedical scientists and science educators. It operates as an independent philanthropy, investing in people rather than specific projects, to enable transformative impact. The organization provides resources, collaboration opportunities, and an adaptable, results-driven environment so researchers and educators can work at their highest level. Its goal is to accelerate scientific progress by enabling researchers and teachers to push boundaries in laboratories and classrooms. Compared with others in philanthropy, HHMI emphasizes long-term, people-centered support, cross-disciplinary collaboration, and flexible structures rather than one-off grants or narrowly defined programs.
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1953
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5 amazing visuals show how the male fruit fly's brain map is advancing neuroscience. Sep 03, 2026 A years-long project by HHMI Janelia, Google Research, and collaborators has built the first complete brain map for a male fruit fly, a key model organism in science. Michał Januszewski Research Scientist, Google Research Viren Jain Research Scientist, Google Research Listen to article 4:57 minutes For the first time, scientists have mapped every single neural connection in the brain and central nervous system of an adult male fruit fly. In this years-long project by HHMI Janelia Research Campus, Google Research, and collaborators from the scientific community, this map of the male fruit fly brain includes a record-breaking more than 166,000 neurons. It's a big step in advancing neuroscience experiments on this key model organism. AI is making it possible for scientists and researchers to exponentially scale projects in the field of connectomics, which precisely reconstruct the connections between brain cells. This new complete brain map, a first for a male fruit fly, builds on the earlier release of a complete female fruit fly brain map, and promises to be a foundational resource for neuroscience for years to come. Today, Blog is sharing five images from the project. 1. A record-breaking map: charting more neurons than ever before. This image shows selected neurons in the male fruit fly's brain and ventral nerve cord, which is analogous to a spinal cord. Like humans, flies do most of their sensing using organs located on their heads, including two huge compound eyes and a retractable proboscis that extends to detect smell and ingest liquid food. Neurons in these sensing organs detect external information and pass the signal through pathways that eventually reach the motor neurons that control movement. 2. Brain + nerve cord: Connecting sensing to actions using AI. When seen from above, the fruit fly's massive eyes and central brain stand out. They connect via a thick cord of nerves to the body, where motor neurons control behavior. This map was created by taking thin sections of a fruit fly brain and body, imaging each slice, and then using computers and AI to combine millions of 2D images to create 3D neural shapes. Knowing the structure of the brain allows neuroscientists to understand the mechanisms behind brain function. 3. Inside the black box: Visualizing almost 11,700 types of neurons. (Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Video by Philip Hubbard.) This video shows some of the 11,691 types of neuron cells in the male fruit fly's central nervous system, which includes the brain and ventral nerve cord. Neurons can be categorized by size, shape, function, gene expression, or other factors. This visualization begins with neurons at the core of the brain and body. It then gradually moves to outer layers and, finally, to neurons at the extremities. Computing and AI helped human experts classify more than 166,000 neurons. 4. Vive la différence: Brain differences between male and female fruit flies. (Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Female data acquired by the FlyWire project. Video by Philip Hubbard and Isabella Beckett.) While most neurons in male and fruit females are the same, or isomorphic, a minority are sex-specific. A third category of neurons are "dimorphic," existing in both males and females but connecting to different neighboring neurons. These neighbors may be isomorphic, the same in both male and female, or sex-specific, or even dimorphic themselves. This video shows one example, for the neural type AOTU012 (blue) that plays a role in processing sensory and taste inputs. While paired AOTU012 neurons exist in both male (left) and female (right) fruit fly brains, the AOTU012 connect to both similar (green) and different (red, orange and yellow) neurons in male and female fruit flies. 5. Fly see, fly do: Connecting stimulus to motion. (Data acquired and analyzed by the FlyEM Project Team at HHMI-Janelia, the Cambridge Connectomics Group, and Google Research. Video by Philip Hubbard and Alexandra Fragniere.) The new brain map of the male fruit fly includes visual-motor pathways. These connect the visual neurons, which help the fly detect its environment, to motor neurons, which help it move in response. This video shows an example of such a pathway, going from the R1-R6 visual neurons (purple) to the DNg13 motor neuron (green). In between are several intermediate steps, including the male-specific LoVP92, named for the so-called "love spot," that plays a role in courtship behavior. Three companion studies also released today apply the new brain map to studying visual systems, taste, and social behavior. Read more about this groundbreaking project, and about its ongoing efforts to map full vertebrate brains, on the Neural Mapping website and in the Google Research Blog post. Posted in:
A connectomics milestone: Mapping the complete male fruit fly brain. September 3, 2026 Michał Januszewski and Viren Jain, Research Scientists, Google Research Research partnered with HHMI Janelia and collaborators to publish a complete map of the male fruit fly's brain and central nervous system, creating the largest brain map to date. Together with ongoing research on other species, such as fish and mice, these wiring maps begin to reveal the mechanics of how all brains work. The common fruit fly, Drosophila melanogaster, has been central to scientific research leading to multiple Nobel Prizes. Fruit flies have been a fundamental model organism in genetics, thanks to their stereotypical behavior and short life cycle, and promise to do the same for neuroscience. While the thoughts of this fruit-loving insect might seem far removed from human cognition, the brains of vastly different species share many similarities. Because mapping the 86 billion neurons in a human brain is not yet possible, scientists are using AI to map the brains of smaller organisms, like fruit flies. This will help Research decipher how animal nervous systems perceive the world, react to stimuli, and how damaged neural pathways might one day be repaired. Now, in a project led by Howard Hughes Medical Institute (HHMI) Janelia Research Campus, its team and collaborators have released a complete wiring diagram of the male fruit fly's brain and central nervous system. Published in Cell, "Sexual dimorphism in the complete connectome of the Drosophila male central nervous system", is the result of a decade-long partnership that advances the field of connectomics using computing and AI to build cellular-scale maps of entire brains. With over 166,000 neurons and 125 million synaptic connections, this is the largest brain map by number of neurons to date, providing a fundamental resource for scientists to use fruit flies as a model organism for studying how the brain works. A small subset of cells in the male fruit fly's brain and central nervous system, as viewed from in front at an angle (left) and from above (right). The male fruit fly connectome also includes the ventral nerve cord, analogous to the spinal cord, and so begins to expand from just the brain into how the brain controls the body. The male fly connectome has been annotated and verified, or proofread, by a team of human experts at HHMI Janelia. It can be viewed, explored and downloaded via Neuroglancer, the open-source tool Research created to enable researchers to visualize huge multidimensional datasets. The new connectome contains neurons from the central brain (green), optic lobes (purple) and ventral (i.e., central) nerve cord (blue). The new connectome enables linking auditory, visual and olfactory inputs to motor outputs for this key model organism. This new brain map complements the female fruit fly brain map and recently released complete female fruit fly brain and nerve cord map. Having both male and female brains and central nervous systems mapped allows the two to be compared in places where neurons differ, and used to study the biological mechanisms for fruit fly courtship and aggression. In parts of the brain that are similar in both sexes, having two complete fruit fly connectomes will allow researchers to begin to see the variability between individuals. An example of a neuron that is different between the male (green) and previously mapped female (magenta) fruit fly brains. The male neuron has two additional projections. AI enables accurate 3D reconstructions to pinpoint these structural differences. Steps toward mapping a full fruit fly brain. Brain mapping, or connectomics, begins with sectioning a brain into millions of thin slices, taking an image of each section, and using computers and AI to stitch the images together. Its researchers build systems that leverage AI to turn flat electron microscope images into 3D reconstructions, using an evolving suite of techniques to generate accurate neural shapes. Its AI connectomics tools include flood-filling networks, which use convolutional neural networks to start at a single pixel and identify all other pixels that are part of the same object. In 2019, its Connectomics team released an initial, fully-automated reconstruction of a female fruit fly brain. By 2020, its team and collaborators released a human-verified map of half a female fruit fly brain with 25,000 neurons and 21 million connections, a record at the time. Meanwhile, the team was already working on the full, verified brain map for a male fruit fly, which is now complete. These methods continue to improve. A recent effort incorporated synthetic neurons into the training data, successfully improving the speed and accuracy of its state-of-the-art reconstruction system, PATHFINDER. Research is also helping to develop new techniques for labeling and annotating specific types of neurons. Currently, mapping the fruit fly brain requires years of human effort just to verify and annotate the neural shapes. By reducing this need for manual error correction, research groups can tackle even larger brain mapping projects within reasonable budgets and timelines. Looking ahead: Mapping entire fish brains. The field of connectomics is already advancing into vertebrates: organisms with a spinal cord. These are anatomically, evolutionarily and functionally more similar to humans. In a study led by Columbia University and published this week in Nature, its team helped map a portion of the elephantnose fish's hindbrain that is used in signal processing. This paper, "Connectome analysis of a cerebellum-like circuit for sensory prediction", shows for the first time how the connectome, a static resource, can be combined with other information to study neural plasticity and learning, producing the most complete mechanistic model of learning in a vertebrate brain to date. Larval zebrafish are one of the few vertebrates whose brains are small enough to be mapped from end to end using current techniques. Zebrafish also have the advantage of being transparent in their larval stage, allowing measurements of neural activity during experiments, as captured in the ZAPBench dataset. Its upcoming paper with Harvard, "A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain", is the first whole-brain dataset for a vertebrate that includes the neural structure and molecular type spanning an entire vertebrate brain. Its team also released a preliminary version of a dataset that combines neural activity and structure in the same larval zebrafish brain, as an open resource to the research community. An image from the Fish Fire&Wire dataset, which combines whole-brain electrical activity and neural structure for the same larval zebrafish specimen. Conclusion. The male fruit fly connectome is a foundational resource that will support a new era for experimental neuroscience, with future applications in biology, pharmacy and medicine. Three companion papers released today show how the male fruit fly connectome has already been used for research on the neuroscience of visual systems, taste and social behavior. Methods developed here will also help advance other projects, such as the upcoming fully proofread map of the zebrafish brain, and mapping a portion of the mouse brain. While modeling the 86 billion neurons in the human brain remains out of reach, Research is moving toward revealing how brains function and understanding the processes underlying mental ailments, such as Alzheimer's, depression or schizophrenia. Someday, Research hope these efforts lead to new ways to treat cognitive ailments, improve brain health, and support brain repair. Acknowledgments. Research thank its academic collaborators at HHMI Janelia and elsewhere, and acknowledge core contributions from the Connectomics Team at Google. Research is grateful to Hannah Hickey and Elise Kleeman for their help. Thanks to Lizzie Dorfman, Michael Brenner, John Platt, and Yossi Matias for their support, coordination and leadership.
Anthropic wants Claude operating real lab gear. Plus: Welcome, humans. Okay, so here's some dumb fun for your Sunday viewing pleasure: somebody turned the internet's favorite classic memes into one continuous stroll down "Meme Street": Now for something actually cool: someone built penombra, a handwriting notebook where you write with a stylus and Claude writes back on the page. It can read PDFs and ebooks, respond to what you annotate, explain passages, and quiz you. It runs on Android tablets with a stylus, and the creator is taking early-tester signups here. Pretty good timing: MIT says today's AI can now credibly complete most undergraduate assignments, which is either the end of homework or a strong argument for turning Claude into your tutor's tablet. Basically, it's Tom Riddle's diary, except it quizzes you on organic chemistry instead of unleashing a basilisk on your friend's sister. Here's what happened in AI today: * | Anthropic taught agents to operate real lab hardware * | Claude beat 28 humans at alignment research * | Z.ai's GLM-5.3 found 2,436 open-source bugs * | South Korea picked free AI for 52M people * | Make Claude cite every spreadsheet number Anthropic gave AI agents a common language for machines. AI agents to date have mostly lived inside browsers, terminals, and spreadsheets. Anthropic now wants the same kind of agent to walk into a lab and know how to use the machines. Here's what happened: * Anthropic and HHMI Janelia opened a research preview of the Model Hardware Standard (MHS), a shared interface for programmable lab and factory equipment. * Each device gets a standard driver with simple read/write commands plus plain-language tags describing what it does and its safety limits. * Early partners used MHS at Genentech, Carnegie Mellon, and QuEra; QuEra's agent-built script recovered a quantum laser's lock in 695 of 700 trials. Why this matters: Today, every microscope, plate reader, or robot arm tends to need its own custom AI software integration. MHS gives agents one interface for discovering equipment, sequencing work across devices, and turning successful procedures into scripts. The payoff is less integration glue to connect agent software with physical hardware. Anthropic says setups that usually take weeks or months can fall to hours or minutes, making round-the-clock automated experiments much easier to build. This is a fast takeoff scenario y'all. Check yourself: This is still a limited research preview, not an autonomous scientist in a box. Anthropic says Claude still needs expert oversight for physical reasoning, and MHS currently requires hardware with a programmable interface. But if the standard catches on, the next major agent platform may be the layer connecting models to the physical world. Researchers and manufacturers can apply for access here. FROM OUR PARTNERS Your prospects won't sign without proof of security. A proof of compliance request stalls deals and pulls engineers into audit prep. Vanta gets you compliant fast (SOC 2, ISO 27001, HIPAA+) and keeps you that way. Trusted by 16,000+ companies like Ramp, Harvey, and Writer. AI skill of the day: Make Claude show every number it touched. AI can sound confident about a workbook while quietly skipping the cells you care about. Claude for Excel can cite exact cells and highlight edits, so make it prove coverage before changing anything. * Ask for a coverage ledger: every sheet or range reviewed, skipped, or ambiguous. * Require cell-level citations for each conclusion and a log of every formula or value it proposes changing. * End with unresolved assumptions and a no-edit review pass; approve changes only after checking the cited cells. Review this workbook without editing it. List every sheet or range you inspected, cite the cells behind each conclusion, flag anything you could not verify, and show every formula or value you would change before I approve edits. Have a specific skill you want to learn? Request it here. Around the horn. * OpenAI is ending Cursor's direct model access on Nov. 12 as a reaction to SpaceX's acquisition of it, citing "trust" concerns and prior Musk-company contract breaches. Cursor users can still bring their own OpenAI API keys. * Researchers at Google and Purdue introduced SKILL.state, which keeps an agent's current structured state instead of replaying its full history; on a 100-step Gemini 3 Flash benchmark, it cut token use about 94% (65K vs. 1.06M) while accuracy rose from 0.91 to 0.94. * Pollen Robotics' Microduck (above) can train behaviors in simulation and transfer them to a real 25 cm biped. * Anthropic let Claude spend 48 hours and one GPU fixing 10 alignment failures (alignmnet = AI's "rules" for good behavior), beating 28 human researchers at the job; that said, a monitor did catch the AI test-gaming in 2.4% of roughly 1,600 runs. AI still gonna AI. * South Korea selected SK Telecom, Kakao, and KT for free domestic AI access for roughly 52 million residents, backed initially by 512 Nvidia B200 GPUs. * The EU AI Act entered its first transparency-enforcement phase, giving regulators access to company information and models while stricter high-risk-system rules arrive later. * Gemini Co-Scientist moved into real labs, helping guide materials, biology, and medical-reasoning experiments, including a technique that beat six frontier models in blinded physician review. Want absolutely EVERYTHING that happened in AI this week? Click here! Treats to try. * *Generate Music, Speech, and Sound Effects for creative projects, plus Firefly AI Assistant and leading models like Gemini, Runway, and Kling. Try today! * LLM Cliché Highlighter scans pasted text or a URL for common AI-writing tells and explains the pattern it matched. * Gemini Notebook Expert Intelligence turns eligible Google Play Books you own into sources you can question, quiz yourself on, or turn into audio overviews. * LightReel indexes roughly 10,000 new TikToks a day so marketers can search winning hooks, formats, and creative patterns instead of doomscrolling manually. * Hao AI Lab open-sourced FastH3 v1, a four-step MiniMax H3 distill that ran up to 14x faster on one Blackwell GPU, though its team says motion and fine detail still trail base H3. Try the checkpoint. * Z.ai open-sourced GLM-5.3 after post-training sharply improved coding and cyber performance; it says the model found 2,436 bugs across 269 open-source projects. Download the weights or run it on Tinker. * Tencent open-sourced Hy4 preview, a 770B-parameter model that activates 49B parameters per token and supports a 1-million-token context window. Download or run it here. Sunday special. Top 5 Stories of the Week * Hackers used Cursor to compromise seven real companies. * NVIDIA reportedly moved to buy Hugging Face for about $13B. * OpenAI's Jalapeño chip posted faster, more efficient inference results. * Anthropic's IPO could become one of tech's biggest raises. * AWS and NVIDIA planned 2 million more GPUs. Top 5 Tools of the Week * Construct turns repeatable work into scheduled agent workflows. * BrowserOS Neo gives Claude, Codex, and Cursor a local browser. * Atlaso shares one persistent memory across your AI tools. * Xirp gives coding agents your company's real system context. * Mem Agent tracks unfinished work and follows up automatically. New from the neuron: AI explained. New episode: Why AI agent security gets "almost infinite" once agents can act. Alice CEO and co-founder Noam Schwartz joins Corey and Grant to explain why model safety is only one layer, why prompt injection may never disappear, and why real agent security also has to cover tools, data, permissions, and policies. A chatbot can say the wrong thing. An agent can delete files, move money, change a database, or even influence another agent. It's about to get weird y'all. A cat's commentary. good problems only | / | That's all for now. If you want to get featured above, fill out the poll below and tell us how we did today! | What'd you think of today's email? | | * | Like a hit of catnip * | Good, not great * | It sucked | | Login or Subscribe to participate in polls. P.S: Love the newsletter, but only want to get it once per week? Don't unsubscribe - update your preferences here.
She studies cell lineage in the eye. Now she's leaving research lineage of her own. Award-winning biologist Connie Cepko, who advanced work on vision-threatening disease, passes the torch to scientific successors. Sy Boles Harvard Staff Writer Connie Cepko is not tired. She's not burnt out. And she's certainly no less fascinated by the complicated and beautiful human eye than she was when she started researching it some four decades ago. When Cepko, the Bullard Professor of Genetics and Neuroscience at Harvard Medical School, retires on July 31, it will be on principle: It's time, she says, to pass the torch of scientific discovery to a new generation. "I still love what I do," she said. "But it's time to step aside and make resources available for the up-and-coming junior people who want to do what I do, especially right now with a contraction going on because of the federal government." For decades, Cepko's lab has made major advances toward gene therapies for vision-threatening diseases such as retinitis pigmentosa and age-related macular degeneration (AMD) that affect millions. She has been an investigator with the Howard Hughes Medical Institute since 1994 and has won numerous prestigious awards, including the Bressler Prize in Vision Science and the Friedenwald Award for research in ophthalmology. Cepko didn't start out decades ago with treatments in mind. Her early passion was for understanding the development of the retina. In the 1980s, she used retroviral vectors to tag retinal progenitor cells and the process by which a common set of "mother" cells produced the stunning 120 cell subtypes involved in human vision. Later, researchers in her lab would demonstrate a remarkable oscillating pattern of cellular development, the first and only glimpse into the timeline of cell genesis at that level of precision. It was an unexpected phone call that turned her attention to therapeutics. "After about 20 years of doing developmental biology, I got a call from a guy named Alan Schwartz, who just coincidentally was the president of the U.S. Tennis Association," Cepko said. "His opening line was, 'What are you doing about blindness?' Just out of the blue. I'd never heard of this guy, and I'd never had anyone ask me that." "He asked what I would do if it was my own child. I had to own up to it. I said, 'Well, I'd probably work on it.'" Schwartz's grandson had been born with Leber congenital amaurosis (LCA), a rare genetic retinal disease characterized by the dysfunction of the photoreceptors - the rods and cones that capture light and make vision possible. Children with LCA are born blind or nearly blind. At the time, there was no treatment for LCA. Cepko explained that she was a basic scientist. She did the research that, she hoped, clinical or translational researchers would develop into therapies. Schwartz didn't buy it. "He asked what I would do if it was my own child," Cepko said. "I had to own up to it. I said, 'Well, I'd probably work on it.'" So she did. In the process of tracing retinal cell lineage, her team had identified some of the genes that, when mutated, lead to blindness. Researchers had identified hundreds of disease-related genes associated with blindness. Designing a bespoke therapy for each one - a process that can take years and millions of dollars - seemed impractical. So Cepko and her team decided to pursue a gene-agnostic approach. When a person loses vision, it's usually due to loss of function of the cone photoreceptors, which are essential for high-acuity vision and color perception. But in many conditions, including retinitis pigmentosa, the genetic mutation actually affects the rod photoreceptors, which are responsible for night vision. Therefore, Cepko reasoned, the cones had to be dying from a bystander effect: something in the retinal environment causing them to die independent of a genetic mutation. That meant she could potentially design gene-agnostic therapies to address those environmental conditions in any number of disease indications created by any of the hundreds of genetic mutations. Over time, she identified seven genes that could be inserted into the eye via an AAV vector (essentially, an engineered virus) to combat the oxidative stress, inflammation, and metabolic problems that contribute to cell death in many retinal diseases. It took years to thoroughly test each treatment in multiple models of disease to prove that the treatments really were gene-agnostic. "Connie is especially rigorous and thorough in the way she attacks a research question," said Grant Zimmermann, the managing director of business development at Harvard's Blavatnik Biomedical Accelerator, which has worked with Cepko to catalog about 40 inventions from the lab to select the most promising technologies for commercialization. "If she gets interesting results in one of her models, she'll repeat it using two, three, four different experimental variations before she convinces herself she's got the right answer." The data on her gene-agnostic therapies are promising. But demonstrating safety and efficacy in humans will take years. Cepko plans to stay involved as a consultant to those who are carrying the work forward. And she's keenly following her trainees' work as they move forward in their careers, blazing a path that began before Cepko and will follow after. Science proceeds slowly. The discoveries made by one researcher become the therapies developed by their trainees. The naming of one's mentors is the tracing of one's scientific genealogy. (For what it's worth, Cepko's was Richard Mulligan, Mallinckrodt Professor of Genetics and professor of pediatrics, emeritus, at Harvard Medical School and Phillip Sharp, a Nobel laureate, at MIT.) Cepko is just as proud of those who come after her: Emma West, now the co-founder and CEO of the biotech company Digital Biology, whose gifts with experiment design revealed the oscillating pattern of cell differentiation; Ryan Delgado, who is developing an even clearer window into cell lineage; Xiang Ma, whose work on extracellular vesicles could open up new avenues for delivering treatments. (Besides her scientific lineage, Cepko also notes she has a hugely important personal one, which includes daughters Leah and Ellie and her grandchildren.) "Connie has created a training environment in which people are encouraged to grow not only as scientists, but also as independent thinkers," said Ma, who has worked with Cepko for nearly 12 years. "Connie has been a role model for me in rigorously performing good science while being extremely humble," said Yunlu Sawyer Xue, a former postdoc in the Cepko lab. "She's super smart and has a great taste in research directions. I could see science coming out of her lab directly benefiting visually impaired patients in the next couple of years."
Training the next generation. Even with her many breakthroughs, Cepko is clear about what she is proudest of: "My trainees." She has mentored more than 100 graduate students and postdocs and is quick to credit them for the lab's achievements. Cepko's influence extends well beyond her lab. She helped launch and lead Harvard Medical School's Biological and Biomedical Sciences (BBS) Graduate Program - a role she held for more than a decade. She later co-founded the Leder Medical Sciences Program, now the Leder Human Biology and Translational Medicine, which she continues to co-direct today. Paying it forward. Although Cepko is retiring from Harvard and HHMI in July 2026, she plans to keep pushing the therapies she's helped develop for blindness toward the clinical stage. She also hopes to launch a one-on-one mentorship program pairing 12- and 13-year-old girls with female graduate students and postdocs. The goal is simple: two weeks in a lab over the summer, learning how science works and what a scientific career can look like. She is especially committed to reaching girls at the age when many turn away from STEM. It's no coincidence that she was 12 when a mentor first invited her into a lab - and changed the course of her life. Building tools to answer questions. When existing methods fell short, Cepko often built new ones. In the early 1990s, her lab devised the first barcoded viral libraries to track cell lineages in the brain. By giving cells unique genetic tags, her team could identify which cells descended from the same progenitor - even after they had migrated far apart. The approach opened new ways to study development in complex tissues. Media Contact: Halea Kerr-Layton, Media Relations Manager [email protected]