Entries from July 2022 ↓

• writing one sentence per line | Derek Sivers

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• The key to universal Covid-19 vaccines lies in your bones
• Secret Service’s ‘ludicrous’ deletion of Jan. 6 phone data baffles experts
• Top predators as biodiversity indicators: A meta?analysis
  tl;dr: The existence of top predators is a key sign of a healthy ecosystem.
• Hospices Have Become Big Business for Private Equity Firms, Raising Concerns About End-of-Life Care
  tl;dr: Private equity’s expanding death-grip on U.S. hospices
• K2 Sherpa Train Hauls 145 People To The Summit In One Day
  Has K2 jumped the shark?
• Effects of total knee arthroplasty on skeletal muscle structure and function at the cellular, organellar and molecular levels | Journal of Applied Physiology
  Total knee arthroplasty (TKA) is an important treatment option for knee osteoarthritis (OA) that improves self-reported pain and physical function, but objectively measured physical function typically remains reduced for years after surgery due, in part, to precipitous reductions in lower extremity neuromuscular function early after surgery. The present study examined intrinsic skeletal muscle adaptations during the first 5 weeks post-TKA to identify skeletal muscle attributes that may contribute to functional disability. Patients with advanced stage knee OA were evaluated prior to TKA and 5 weeks after surgery. Biopsies of the vastus lateralis were performed to assess muscle fiber size, contractility, and mitochondrial content, along with assessments of whole muscle size and function. TKA was accompanied by marked reductions in whole muscle size and strength. At the fiber (ie, cellular) level, TKA caused profound muscle atrophy that was ~2-fold higher than that observed at the whole muscle level. TKA markedly reduced muscle fiber force production, contractile velocity, and power production, with force deficits persisting in MHC II fibers after expression relative to fiber size. Molecular level assessments suggest reduced strongly bound myosin-actin cross-bridges and myofilament lattice stiffness as a mechanism underlying reduced force per unit fiber size. Finally, marked reductions in mitochondrial content were apparent and more prominent in the sub-sarcolemmal compartment. Our study represents the most comprehensive evaluation of skeletal muscle cellular level adaptations to TKA and uncovers novel effects of TKA on muscle fiber size and intrinsic contractility early after surgery that may contribute to functional disability.

  tl;dr: Knee replacement is associated with profound muscle atrophy. /cc @hjluks

  Effects of total knee arthroplasty on skeletal muscle structure and function at the cellular, organellar and molecular levels

• How can you put a bash array into a wdl variable? – Bioinformatics Stack Exchange
• How to get a job in climate tech | Sifted

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• Pub/Sub launches direct path to BigQuery for streaming analytics | Google Cloud Blog
• DeepMind has predicted the structure of almost every protein known to science | MIT Technology Review
• Announcing the Shortlist for the Inaugural Ursula K. Le Guin Prize for Fiction – Electric Literature
• Reinfection, severe outcome more common with BA.5 variant; virus spike protein toxic to heart cells — Reuters
  The following is a summary of some recent studies on COVID-19. They include research that warrants further study to corroborate the findings and that has yet to be certified by peer review.
• Isomorphic Labs | Newsroom
  LONDON, May 12, 2022 – Isomorphic Labs, a subsidiary of Alphabet, today announced the first phase of its management team. The company, established in November, was launched from Alphabet’s DeepMind to build on the success of AlphaFold, DeepMind’s work in protein folding that was heralded as the “Breakthrough of the Year” by Science and “Method of the Year” by Nature in 2021. Isomorphic Labs’ mission is to use AI and machine learning methods to accelerate and improve the drug discovery process. The company is a pioneer in the emerging field of “digital biology” and aims to usher in a new era of biomedical breakthroughs in order to find cures for some of humanity’s most devastating diseases.

  The new leaders join founder and acting CEO Demis Hassabis, who is currently serving as CEO of both DeepMind and Isomorphic Labs. Together they comprise a truly multidisciplinary leadership team with expertise in domains across science, engineering, machine learning and business operations that will be needed to achieve the company’s goal of dramatically improving how drugs are discovered and developed. Drug development is currently a lengthy, expensive and high-risk process that is poised to benefit from advances in the application of AI and computational methods. Studies peg the cost of bringing a molecule to market at more than $2.5 billion per drug and timelines approaching a decade; in fact, only about 12 percent of drugs entering clinical trials are ultimately approved by the U.S. Food and Drug Administration (FDA).

  “We’re thrilled to announce the formation of our extraordinary multidisciplinary leadership team that will allow us to deliver on our ambition to reimagine the entire drug discovery process from first principles, with an AI-first approach,” said Hassabis. “The phenomenal success of AlphaFold demonstrated the huge impact that AI methods can potentially have on biology, and we plan to build powerful new predictive and generative models of biological phenomena to anticipate how drugs will perform and design novel molecules.”

• Unlocking the nuclear pore complex — Unfolded
• alphafold/README.md at main · deepmind/alphafold
• Google AI Blog: High Fidelity Image Generation Using Diffusion Models
• The Irish Lesson | Fintan O’Toole
  “A policy that depends for its success on female impoverishment and powerlessness is not easy to sustain in an open society.” The ruinous Irish experience with banning abortion. @fotoole https://www.nybooks.com/articles/2022/08/18/the-irish-lesson-fintan-otoole/
• jump-cellpainting/2021_Chandrasekaran_submitted

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• DeepMind AI Lab Releases 200 Million 3D Images of Proteins | Time
• What does poison hemlock look like? How to spot one of America's deadliest plants — USA TODAY
  Be ready to identify poison hemlock, one of North America’s "deadliest" plants, which boasts beautiful white flowers and grows throughout the U.S.
• New SARS-CoV-2 Variant BA.2.75 Evades All Approved Monoclonal Antibody Therapies
• Boosters targeting omicron may be available earlier than expected : Shots – Health News : NPR
• The 20 Best Netflix Shows of All Time — Ranked

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• A VFX Artist Explains What It’s Like Working for Marvel
• Public Neurodiversity Support Center
  Don’t worry, we’re here to help!
• fsspec: Filesystem interfaces for Python — fsspec 2022.5.0+15.g42f82a9.dirty documentation
• Ring Vaccination Beat Smallpox. Could It Work for Monkeypox?
  The strategy prioritizes inoculating an infected person’s closest contacts, but it can’t succeed without good contact tracing and enough vaccines.

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• Abortion Is About Freedom, Not Just Privacy
  The right to abortion is an affirmation that women and girls have the right to control their own destiny.
• How it Spreads | Monkeypox | Poxvirus | CDC
• Doing Absolutely Nothing Has Mental Health Benefits | Psychology Today
• Joni Mitchell sings, steals show with surprise Newport Folk Festival concert : NPR
• To Live in the Ending | Journal
  1. The first time The first time I saw the world end I was eight years old. It began peacefully enough. I sat in a well-padded chair in the dark with the rest of my second grade class, all of us tilted back, faces turned up to the white dome of the ceiling. We watched it shade into blue dusk, the stars and the planets…Continue reading ?
• Joni Mitchell “Summertime “Live at Newport Folk Festival, Sunday, July 24, 2022
  Joni Mitchell â??Summertime â??Live at Newport Folk Festival, Sunday, July 24, 2022
• Mystery Fanfare: MACAVITY AWARD NOMINATIONS 2022
• How a Mormon Housewife Turned a Fake Diary Into an Enormous Best-Seller
  Beatrice Sparks always insisted that there was a real teen-ager behind “Go Ask Alice,” but would never say who it was.
• GoogleCloudPlatform/vertex-ai-alphafold-inference-pipeline: This repository compiles prescriptive guidance and code samples demonstrating how to operationalize AlphaFold batch inference using Vertex AI Pipelines.

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• These 10 states are America’s best places to live in 2022
• These 10 states are America's worst places to live in 2022
• Texas is the second-worst state to live in. The state received an 'F' grade for its quality of life.
• Is Abortion Sacred? | The New Yorker
  Abortion is often talked about as a grave act. But bringing a new life into the world can feel like the decision that more clearly risks being a moral mistake.
  By Jia Tolentino
• Paul Newman and Joanne Woodward were movie stars for 50 years. A new doc explains how
  Ethan Hawke, whose docuseries ‘The Last Movie Stars’ explores the pair, says they regularly shifted ‘who’s the rose and who’s the gardener.’
• Mystery shrouds colossal Brink's heist at I-5 truck stop: Who stole millions in gems, gold?
  It took just 27 minutes to steal tens of millions in jewelry and gemstones from a Brink’s trailer in Lebec, Calif.
• Home – Razom
  Razom is building a prosperous Ukraine, one project at a time. Together we are Ukraine.
• Christopher Walken – Lets Misbehave | Pennies From Heaven | Warner Archive
  Pennies From Heaven (1981) #WarnerArchive #WarnerBros #PenniesFromHeavenSteve Martin stars as a womanizing sheet-music salesman in this lip-sync "musical" ba…
• Amanda Shires – 'I'm Your Man' | Amazon Music
  See more from Love Me, Love Me Not: http://amzn.to/2ls3n2C#AmazonMusic #AmandaShires #I’mYourManSUBSCRIBE NOW: http://bit.ly/AZMusicYTAbout Amazon Music:Amaz…
• Amanda Shires – Take It Like A Man (Official Live Session)
  â??Take It Like A Manâ? is the title track on Amanda Shires’ upcoming album which will be released on July 29. Listen here and pre-order the album on vinyl, CD,…

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• Patti Smith Mourns Lou Reed
  “When Lou said goodbye, his dark eyes seemed to contain an infinite and benevolent sadness,” Smith wrote, in memory of the late musician, in 2013.
• National Wastewater Surveillance System
  New public health tool to understand COVID-19 spread in a community.
• COVID Data Tracker
  CDC’s home for COVID-19 data. Visualizations, graphs, and data in one easy-to-use website.
  Wastewater tracking.
• Covid sewage data kept under wraps despite possible public health benefits
  Looking for Covid in wastewater can serve as an early warning system for outbreaks — at least in theory.
• “What Do Women Want?” by Kim Addonizio | Poetry Foundation
• Why do tree-based models still outperform deep learning on tabular data?
  While deep learning has enabled tremendous progress on text and image
  datasets, its superiority on tabular data is not clear. We contribute extensive
  benchmarks of standard and novel deep learning methods as well as tree-based
  models such as XGBoost and Random Forests, across a large number of datasets
  and hyperparameter combinations. We define a standard set of 45 datasets from
  varied domains with clear characteristics of tabular data and a benchmarking
  methodology accounting for both fitting models and finding good
  hyperparameters. Results show that tree-based models remain state-of-the-art on
  medium-sized data ($\sim$10K samples) even without accounting for their
  superior speed. To understand this gap, we conduct an empirical investigation
  into the differing inductive biases of tree-based models and Neural Networks
  (NNs). This leads to a series of challenges which should guide researchers
  aiming to build tabular-specific NNs: 1. be robust to uninformative features,
  2. preserve the orientation of the data, and 3. be able to easily learn
  irregular functions. To stimulate research on tabular architectures, we
  contribute a standard benchmark and raw data for baselines: every point of a 20
  000 compute hours hyperparameter search for each learner.
• Practical Deep Learning for Coders – Practical Deep Learning
  A free course designed for people with some coding experience, who want to learn how to apply deep learning and machine learning to practical problems.
• Introduction to Transformers
• Cambridge lab for clever birds saved from closure by public donations
  The "corvid palace", a renowned UK centre for research on intelligence in crows and their kin that was due to be shut down this month, has been saved by a campaign kick-started by a New Scientist article
• As more bird species go extinct those that are left may be more alike
  A global analysis predicts that as we lose more bird species to extinction, those that remain will be more similar in terms of size, beak shape and other features
• Welcome to nbdev
  nbdev is a library that allows you to develop a python library in Jupyter Notebooks, putting all your code, tests and documentation in one place. That is: you now have a true literate programming environment, as envisioned by Donald Knuth back in 1983!

  nbdev makes debugging and refactoring your code much easier relative to traditional programming environments. Furthermore, using nbdev promotes software engineering best practices because tests and documentation are first class citizens.

• What is a cell type and how to define it?
• These soaring temperatures have given Britain a taste of the dystopia to come | Sophie Mackintosh
• Big Tech is bracing for a possible recession, spooking other industries — The Washington Post
  Big Tech has soared for the past decade. But hiring freezes, slowing revenue growth and lay-offs show Silicon Valley is preparing for a recession.
• Kris Kristofferson and Rita Coolidge Help me make it through the night live 1972 – YouTube
• The Moose by Elizabeth Bishop | Poetry Foundation
• How To Be Influenced – by Ian Leslie – The Ruffian
  Once you see yourself as merely a junction point for a whole set of influences, from your parents to your teachers to the feeds you follow and the articles and books you read, you can relax about being ‘you’. You can focus, instead, on making your influence-set as unique, layered and rich as possible. Nobody else will be at your junction point.
• Google pauses hiring for two weeks to ‘review our headcount needs’ – The Verge
• Blouses for Women in Cotton, Satin & More | Shop Universal Standard

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• The Unwritten Laws of Physics for Black Women — WIRED
  I never meant to be a trailblazer—I just wanted to be a scientist. But in my field, nearly every Black woman is an anomaly who faces constant scrutiny for her race and gender.
• The Disabled Hiker’s Guide – Disabled Hikers
  The Disabled Hiker’s Guide to Western Washington and Oregon: Outdoor Adventures Accessible by Car, Wheelchair, and Foot is being published by FalconGuides in September 2022!
• Big Tech builds AI with bad data. So scientists sought better data.
• The father of American gynecology fought to criminalize abortion in the 1850s
  Horatio Storer’s legacy remains even after Roe v. Wade
• Inside Trump '25: A radical plan for Trump’s second term
  There is a good chance you have not heard of Schedule F, but it represents one of the biggest threats to democracy if Trump or a Trump-like populist takes power. And there is no plan in place to stop it.
  https://www.axios.com/2022/07/22/trump-2025-radical-plan-second-term
• The Jan. 6 Hearings Did a Great Service, by Making Great TV
  Investigating a threat to democracy was always going to be important. But this time, it also managed to be buzzworthy.
• DIY Collective Embeds Abortion Pill Onto Business Cards, Distributes Them At Hacker Conference
  An anarchist biohacker collective has developed a DIY kit to make and discreetly mail abortion medication at home.
• The Wager by David Grann: 9780385534260
  From the #1 New York Times bestselling author of Killers of the Flower Moon, a page-turning story of shipwreck, survival, and savagery, culminating in a court martial that reveals a shocking truth….
• Meet the covid super-dodgers
• Police chief bragged about shooting Black man 119 times, according to recording
• Opinion | We’re All ‘Experts’ Now. That’s Not a Good Thing.
  Widespread scams and institutional failures force us to rely on only ourselves.
• Bloopers from Mel Brook's "Young Frankenstein" (1974). The scene which required the most takes to be filmed was when Marty Feldman bites Madeline Kahn's animal wrap. Each time he did it, he was left with a piece of fur in his mouth… which caused the oth
• Saying Goodbye to Safety: All-Female Mills College Turns Co-ed
  When Kate Valente packed for college, she did not pack pepper spray. Now, she may
• Could GOP States Really Stop Pregnant People From Traveling to Get Abortions?
• rmcelreath/rethinking: Statistical Rethinking course and book package
  This R package accompanies a course and book on Bayesian data analysis: McElreath 2020. Statistical Rethinking, 2nd edition, CRC Press. If you are using it with the first edition of the book, please see the notes at the bottom of this file.

  It contains tools for conducting both quick quadratic approximation of the posterior distribution as well as Hamiltonian Monte Carlo (through RStan or cmdstanr – mc-stan.org). Many packages do this. The signature difference of this package is that it forces the user to specify the model as a list of explicit distributional assumptions. This is more tedious than typical formula-based tools, but it is also much more flexible and powerful and—most important—useful for teaching and learning. When students have to write out every detail of the model, they actually learn the model.

• Perspective | Four reasons the Jan. 6 hearings have conquered the news cycle
• Raindrop is the best bookmarking app — here’s why you need one – The Verge
• Ted Nguyen on Twitter: "People seem to be confused about what a Hippo violation is https://t.co/NJkA9kjU8y" / Twitter

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• The “Nathan for You” Finale, My New Favorite Love Story | The New Yorker
  Errol Morris
• Donald Trump on 2024: ‘I’ve Already Made That Decision’
• Potential fabrication in research images threatens key theory of Alzheimer’s disease
  A neuroscience sleuth challenges data showing one toxic form of amyloid protein is a cause of brain condition

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