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Ancient Egyptians may have relied on a vertical shaft that could be filled with water, along with a network of water channels and filtration structures, to build the Step Pyramid of Djoser 4500 years ago

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The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic.

The analysis of extractables and leachables and subsequent risk assessment is an important aspect of the determination of biocompatibility for many medical devices. Leachable chemicals have the potential to pose a toxicological risk to patients, and therefore it is required that they be adequately characterized and assessed for potential safety concerns. One important consideration in the assessment of leachables is the choice of a suitable simulating solvent intended to replicate the use condition for the device and its biological environment. This aspect of study design is especially difficult for blood-contacting medical devices due to the complexity of simulating the biological matrix. This publication reports a comparison of the extracting power of different binary solvent mixtures and saline in comparison with whole blood for a bloodline tubing set connected to a hemodialyzer. Ten different known extractables, spanning a range of physicochemical properties and molecular weights, were quantified. The results indicated that for low-molecular-weight analytes, a suitable exaggeration for whole blood can be obtained using a low-concentration ethanol/water mixture (20%), and in general, extracted quantity increases with the concentration of alcohol cosolvent. For polyvinylpyrrolidone, the opposite trend was observed, as solubility of the polymer was found to decrease with increasing alcohol concentration, resulting in lower extracted quantities at high alcohol concentrations. Analysis of ethanol/water concentrations in the extract solutions post extraction indicated no change in solvent composition.

For clean-room technologies such as isolators and restricted access barrier systems (RABS), decontamination using hydrogen peroxide (H₂O₂) is increasingly attractive to fulfill regulatory requirements. Several approaches are currently used, ranging from manual wipe disinfection to vapor phase hydrogen peroxide (VPHP) or automated nebulization sanitization. Although the residual airborne H₂O₂ concentration can be easily monitored, detection of trace H₂O₂ residues in filled products is rather challenging. To simulate the filling process in a specific clean room, technical runs with water for injection (WfI) are popular. Thus, the ability to detect traces of H₂O₂ in water is an important prerequisite to ensure a safe and reliable use of H₂O₂ for isolator or clean room decontamination. The objective of this study was to provide a validated quantitative, fluorometric Amplex UltraRed assay, which satisfies the analytical target profile of quantifying H₂O₂ in WfI at low nanomolar to low micromolar concentrations (ppb range) with high accuracy and high precision. The Amplex UltraRed technology provides a solid basis for this purpose; however, no commercial assay kit that fulfills these requirements is available. Therefore, a customized Amplex UltraRed assay was developed, optimized, and validated. This approach resulted in an assay that is capable of quantifying H₂O₂ in WfI selectively, sensitively, accurately, precisely, and robustly. This assay is used in process development and qualification approaches using WfI in H₂O₂-decontaminated clean rooms and isolators.

When nightmarish sci-fi extraction shooter The Forever Winter launched into early access in September it was somewhat messy. Bugs and maddening enemy spawns diminished the tension of being a fleshy human scavenger in a mech battlefield. But one feature annoyed some players much more - fresh water. See, you need to keep your headquarters stocked with water, as it gets steadily used by your settlement's inhabitants. The catch being that this water diminishes even while you're not playing the game. If it runs out completely, then everything you've collected gets wiped. The developers have listened to complaints about this most Farmville of mechanics, and they've answered in an interesting way. Water thieves! Now, on top of the usual downward trickle, burglars will come to steal your H2O as well.

It's not as bad as it sounds.

Read more

We'll have a review of Planet Coaster 2 soon, but I keep making Brendy do other tasks so he's not had enough time yet to ride the rails. That means it falls to me to at least let you know that Frontier's theme park builder is out now.

Read more

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JUDY WOODRUFF: It’s been almost a month since Hurricane Maria destroyed much of Puerto Rico and killed at least 48 people. The island and its residents are still coming to grips with the scale of the devastation.

William Brangham brings us the latest.

WILLIAM BRANGHAM: Many Puerto Ricans are still in the dark, without electrical power. Hundreds of thousands still have no access to running water, and the rebuilding of the countless damaged homes, roads and facilities is just beginning.

The Associated Press reported yesterday that almost half the sewage treatment plants on the island are still out of service, increasing the risk of contamination and disease.

I’m joined now by David Begnaud. He’s a correspondent from CBS News who’s been doing some very strong reporting there from since when the storm hit, and is just back from his latest trip to the island.

David, welcome to the NewsHour.

I wonder. We saw many of your reports and others of people still three weeks out from the storm who are still drinking from streams and creeks. You heard — I mentioned this AP report about fears of contamination.

Can you just tell us what is going on there? How are people getting water now?

DAVID BEGNAUD, CBS News: Well, let me tell you this.

The governor of Puerto Rico said this morning that he’s aware of those reports and that they’re looking into it. What’s concerning, William, is that three weeks after the storm and at least a week after the allegations first surfaced that people might be trying to drink from toxic wells at what’s known as Superfund sites, the governor of Puerto Rico is still saying, we’re looking into it and telling people to stay out of rivers where sewage may be spilling into the river.

And, he said, we want them to stay away from the coastal areas.

How are people doing? They’re still desperate to get water. No one seems to be able to figure out how to get enough water to every single person on that island who needs it. And as long as people need water, it’s still an emergency phase.

Nearly four weeks later, no one seems to be able to move from the emergency to the recovery.

WILLIAM BRANGHAM: So, people who are — we see them drinking out of these PVC pipes that they have kind of rigged and sort of poked into the side of a creek.

People are just drinking that water straight, without purification, without boiling it; is that right?

DAVID BEGNAUD: Absolutely.

Look, they have got the PVC pipes tapped into the mountains so that it’s coming out of the stream that way. And they literally are — I saw a woman walk up to a potable water tank that the military had brought in, and she had a Clorox bottle.

And I said, “Ma’am, you’re putting drinkable water in a Clorox bottle?”

And she said, “It’s all I have got.”

Now, that was a good scenario. The other scenarios are people right now who are drinking from streams and creeks and rivers who have no water filters, who have nothing, right? They’re just taking this water.

Now, listen, the government got a million water-purifying tablets within the last week. It took almost three weeks to get those. Now there’s a large push to bring in water filters.

I have got to tell you, most of the water filters I’m seeing brought in are coming from the private sector, and civilian samaritans who are getting 1,000 or more from the mainland and flying them over to Puerto Rico and personally hand-delivering them.

WILLIAM BRANGHAM: That’s really incredible.

Medical facilities were another big — just a huge devastation on the island. I know you have been doing a lot of reporting on the USS Comfort.

DAVID BEGNAUD: Yes.

WILLIAM BRANGHAM: This is the huge Naval hospital that is now just offshore Puerto Rico.

But I understand it hasn’t been fully utilized. Can you tell us what your reporting has found there?

DAVID BEGNAUD: The two men running the ship told us that nearly 87 percent of the ship is empty. Sounds alarming, right? They have 200 beds, and 87 percent are empty.

Now, here’s what they said: We stand ready for whatever the government wants to do. We are waiting to be told by the government.

So, I went to the governor, and said exactly what’s happening. And he said: “Look, I’m not satisfied with what the protocol was from the beginning.”

He said, initially, they were prioritizing only the most critically ill patients go to the Comfort. And he said there was a layered process that was complicating things.

So, the governor, Ricardo Rossello, said: “I started to take out some of those layers, and I, said, listen, take people on the ship who may not be critically ill, but need good medical care and can’t get it at the hospital, where the lights are flickering and the A.C. is not running.”

That’s what the governor said.

Within a matter of hours, I got a tweet from a third-year medical student who said: “Let me tell you what a nightmare it has been to reach the Comfort.”

He said: “We have got a pediatric patient who desperately needs to get off this island, either to a hospital on the mainland or to the Comfort.”

And he said: “I went through Google and the local newspaper to find the number. I couldn’t find it.”

Now, here is how things work. Within about 30 minutes of that tweet going out and that medical student’s story being posted, the governor’s spokesperson responded with numbers that should be able to help.

The bottom line here, William, is that asking relentless questions and the good work of journalism is what’s making a difference there. It’s no one person. There’s no heroic work that’s being done by any journalist, other than people who are going back to the same officials and asking some of the same questions, relentlessly seeking the right answer that will make a difference.

WILLIAM BRANGHAM: One of the other pieces of reporting that you did that was very early in the story was this backlog of supplies trapped in container ships on the ports in Puerto Rico.

I understand some of that — some of those supplies are now moving. Can you tell us, are they getting to where they need to be throughout the island?

DAVID BEGNAUD: So, the shipping containers you’re talking about, about 3,000 sitting in the Port of San Juan, have been moved out, not all of them, but a majority of them.

And they were intended for grocery stores around the island. Right? So, those were private companies that had brought in these shipping containers, paid for the supplies, but couldn’t move them because their truck drivers were either at home, because the home had been destroyed, or the road was impassable.

More and more supplies are getting out. But let me tell you, the grocery stores around the island, they have a lot of nonperishables, Pringles, candy, cookies, all on the shelf.

But when you go to the meat section, it’s nearly 75 percent empty at the stores we have been to, the produce section 90 percent empty. And finding bottled water there is almost like playing a game.

WILLIAM BRANGHAM: David Begnaud, CBS News, thank you so much for your reporting. Thanks for your time.

DAVID BEGNAUD: You bet.

The post Puerto Ricans still don’t have reliable drinking water, and fears of contamination are rising appeared first on PBS NewsHour.

Researchers recently found a possible reservoir of liquid water more than 11 kilometres below Mars's surface – the latest in a long series of potential water discoveries on the Red Planet, hinting at its temperate past

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The water column is hazy as an unusual remotely operated vehicle glides over the seafloor in search of a delicate tilt meter deployed three years ago off the west side of Vancouver Island. The sensor measures shaking and shifting in continental plates that will eventually unleash another of the region’s 9.0-scale earthquakes (the last was in 1700). Dwindling charge in the instruments’ loggers threatens the continuity of the data.

The 4-metric-ton, C$8-million (US $5.8-million) remotely operated vehicle (ROV) is 50 meters from its target when one of the seismic science platforms appears on its sonar imaging system, the platform’s hard edges crystallizing from the grainy background like a surgical implant jumping out of an ultrasound image. After easing the ROV to the platform, operators 2,575 meters up at the Pacific’s surface instruct its electromechanical arms and pincer hands to deftly unplug a data logger, then plug in a replacement with a fresh battery.

This mission, executed in early October, marked an exciting moment for Josh Tetarenko, director of ROV operations at North Vancouver-based Canpac Marine Services. Tetarenko is the lead designer behind the new science submersible and recently dubbed it Jenny in homage to Forrest Gump, because the fictional character named all of his boats Jenny. Swapping out the data loggers west of Vancouver Island’s Clayoquot Sound was part of a weeklong shakedown to test Jenny’s unique combination of dexterity, visualization chops, power, and pressure resistance.

Jenny is only the third science ROV designed for subsea work to a depth of 6,000 meters.

By all accounts Jenny sailed through. Tetarenko says the worst they saw was a leaky O-ring and the need to add some spring to a few bumpers. “Usually you see more things come up the first time you dive a vehicle to those depths,” says Tetarenko.

Jenny’s successful maiden cruise is just as important for Victoria, B.C.–based Ocean Networks Canada (ONC), which operates the NEPTUNE undersea observatory. The North-East Pacific Time-series Undersea Networked Experiments array boasts thousands of sensors and instruments, including deep-sea video cameras, seismometers, and robotic rovers sprawled across this corner of Pacific. Most of these are connected to shore via an 812-kilometer power and communications cable. Jenny was custom-designed to perform the annual maintenance and equipment swaps that have kept live data streaming from that cabled observatory nearly continuously for the past 15 years, despite trawler strikes, a fault on its backbone cable, and insults from corrosion, crushing pressures, and fouling.

NEPTUNE remains one of the world’s largest installations for oceanographic science despite a proliferation of such cabled observatories since it went live in 2009. ONC’s open data portal has over 37,000 registered users tapping over 1.5 petabytes of ocean data—information that’s growing in importance with the intensification of climate change and the collapse of marine ecosystems.

Over the course of Jenny’s maiden cruise, her operators swapped devices in and out at half a dozen ONC sites, including at several of NEPTUNE’s five nodes and at one of NEPTUNE’s smaller sister observatories closer to Vancouver.

Inside Jenny

ROV Jenny aboard the Valour, Canpac’s 50-meter offshore workhorse, ahead of October’s NEPTUNE observatory maintenance cruise.Ocean Networks Canada

What makes Jenny so special?

• Jenny is only the third science ROV designed for subsea work to a depth of 6,000 meters.
• Motion sensors actively adjust her 7,000-meter-long umbilical cable to counteract topside wave action that would otherwise yank the ROV around at depth and, in rough seas, could damage or snap the cable.
• Dual high-dexterity manipulator arms are controlled by topside operators via a pair of replica mini-manipulators that mirror the movements.
• Each arm is capable of picking up objects weighing about 275 kilograms, and the ROV itself can transport equipment weighing up to 3,000 kg.
• 11 high-resolution cameras deliver 4K video, supported by 300,000 lumens of lighting that can be tuned to deliver the soft red light needed to observe bioluminescence.
• Dual multibeam sonar systems maximize visibility in turbid water.

Meghan Paulson, ONC’s executive director for observatory operations, says the sonar imaging system will be particularly invaluable during dives to shallower sites where sediments stirred up by waves and weather can cut visibility from meters to centimeters. “It really reduces the risk of running into things accidentally,” says Paulson.

To experience the visibility conditions for yourself, check out recordings of the live video broadcast from the NEPTUNE maintenance cruise. Tetarenko says that next year they hope to broadcast not only the main camera feed but also one of the sonar images.

3D video could be next, according to Canpac ROV pilot and Jenny codesigner, James Barnett. He says they would need to boost the computing power installed topside, to process that “firehose of data,” but insists that real-time 3D is “definitely not impossible.” Tetarenko says the science ROV community is collaborating on software to help make that workable: “3D imagining is kind of the very latest thing that’s being tested on lots of ROV systems right now, but nobody’s really there yet.”

More Than Science

Expansion of the cabled observatory concept is the more certain technological legacy for ONC and NEPTUNE. In fact, the technology has evolved beyond just oceanography applications.

ONC tapped Alcatel Submarine Networks (ASN) to design and build the Neptune backbone and the French firm delivered a system that has reliably delivered multigigabit Ethernet plus 10 kilovolts of direct-current electricity to the deep sea. Today ASN deploys a second-generation subsea power and communications networking solution, developed with the Norwegian international energy company Equinor.

ASN’s “Direct Current/Fiber Optic” or DC/FO system provides the 100-km backbone for the ARCA subsea neutrino observatory near Sicily, in addition to providing control systems for a growing number of offshore oil and gas installations. The latter include projects led by Equinor and BP where DC/FO networks drive the subsea injection of captured carbon dioxide and monitor its storage below the seabed. Future oil and gas projects will increasingly rely on the cables’ power supply to replace the hydraulic lines that have traditionally been used to operate machinery on the seafloor, according to Ronan Michel, ASN’s product line manager for oil and gas solutions.

Michel says DC/FO incorporates important lessons learned from the Neptune installation. And the latter’s existence was a crucial prerequisite. “The DC/FO solution would probably not exist if Neptune Canada would not have been developed,” says Michel. “It probably gave confidence to Equinor that ASN was capable to develop subsea power and coms infrastructure.”

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Around half the people in the French Indian Ocean territory of Mayotte were without potable water Tuesday after a "technical incident" at a treatment plant, a local authority said in a statement. The "event of electrical origin" at the Ouroveni plant overnight from Monday to Tuesday "is leading to water cuts mostly located in the centre and south" of Mayotte's main island Grande Terre, the p

José González is an illustrator, author and animator originally from Buenos Aires now living in English Harbour. González was selected to be one of the Artists in Residence at Business and Arts N.L. (Un)Common Threads Creativity and Innovation Summit happening on Nov. 7. In advance of the summit, González has been busy preparing for his installation, which will feature a large-scale fish tank with animated sea creatures brought to life through projections and augmented reality.

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2020 was a difficult year for dental providers as the COVID-19 pandemic swept across the country. When stay-at-home orders went into effect in the spring, dental offices closed their doors to all but emergency patients.

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Oil and water can be separated efficiently by pumping the mixture through thin channels between two semipermeable membranes