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Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

This article presents an overview of the development of two basic software libraries for image manipulation and data visualization in cryo-EM: emcore and emvis.




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Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.




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A new ZnII metallocryptand with unprecedented diflexure helix induced by V-shaped di­imidazole building blocks

A new ZnII metallocryptand is presented, with an unprecedented diflexure helix.




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Smithsonian researchers help block ship-borne bioinvaders with new screening strategy

To help regulators and engineers develop and test such treatment systems, and ultimately enforce these standards, a team of researchers developed a statistical model to see how to count small, scarce organisms in large volumes of water accurately.

The post Smithsonian researchers help block ship-borne bioinvaders with new screening strategy appeared first on Smithsonian Insider.




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Astronomers find two white-dwarf stars locked in death spiral

"I nearly fell out of my chair at the telescope when I saw one star change its speed by a staggering 750 miles per second in just a few minutes," said Smithsonian astronomer Warren Brown, lead author of the paper reporting the find.

The post Astronomers find two white-dwarf stars locked in death spiral appeared first on Smithsonian Insider.




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Unlocking the mysteries of Jefferson’s bible with high-tech analysis and microscopic testing

The Life and Morals of Jesus of Nazareth, more commonly known as the Jefferson bible, is a volume created by Thomas Jefferson containing passages he […]

The post Unlocking the mysteries of Jefferson’s bible with high-tech analysis and microscopic testing appeared first on Smithsonian Insider.




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Chandra X-ray Observatory clocks stellar wind at 20 million mph

The fastest wind ever discovered blowing off a disk around a stellar-mass black hole has been observed by a team of astronomers using NASA’s Chandra X-ray Observatory.

The post Chandra X-ray Observatory clocks stellar wind at 20 million mph appeared first on Smithsonian Insider.



  • Science & Nature
  • Space
  • astronomy
  • astrophysics
  • Center for Astrophysics | Harvard & Smithsonian
  • Chandra X-Ray Observatory
  • Smithsonian Astrophysical Observatory

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Dust trap around distant star may unlock mystery as to how planets form

Based on a treasure trove of recent discoveries, astronomers now know that planets are remarkably plentiful in our galaxy and may be common throughout the […]

The post Dust trap around distant star may unlock mystery as to how planets form appeared first on Smithsonian Insider.





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Scientists shine light on world’s least-studied bat: Mortlock Islands flying fox

The Mortlock Islands flying fox, a large, breadfruit-eating bat native to a few remote and tiny Pacific islands, has long been regarded as one of […]

The post Scientists shine light on world’s least-studied bat: Mortlock Islands flying fox appeared first on Smithsonian Insider.




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New project to unlock migration mysteries from air

Unlocking the mysteries of animal migration through precise, near real-time tracking can solve major conservation challenges and transform wildlife science worldwide. For the past year, […]

The post New project to unlock migration mysteries from air appeared first on Smithsonian Insider.




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Nest discovery turns back the clock to days of Daniel Boone and Colonial America

Paddling the remote oxbow lakes and bayous of the White River National Wildlife Refuge in Arkansas, the team of scientists was seeking proof of a […]

The post Nest discovery turns back the clock to days of Daniel Boone and Colonial America appeared first on Smithsonian Insider.





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Eight New Planets Found in “Goldilocks” Zone

Astronomers announced today that they have found eight new planets in the “Goldilocks” zone of their stars, orbiting at a distance where liquid water can […]

The post Eight New Planets Found in “Goldilocks” Zone appeared first on Smithsonian Insider.





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Locked and loaded: unique trigger design fires this ant’s snapping jaws

In conflicts between predators and prey, speed is a decided advantage, and evolution has given the trap-jaw ant a distinct advantage with spring-loaded jaws that […]

The post Locked and loaded: unique trigger design fires this ant’s snapping jaws appeared first on Smithsonian Insider.





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Simulink - Incorrect Code Generation: In a model containing blocks from the SoC Blockset and asynchronous sample time, the sorted order might be incorrect

Simulink might produce an incorrect sorted order for a model that meets all of the following conditions:

  • The model contains blocks from the SoC Blockset
  • The Signal logging option is selected in the model configuration set
  • Signals using asynchronous sample time are configured for logging
As a result, Simulink might produce incorrect results in Normal, Accelerator, and Rapid Accelerator simulation modes as well as in generated code.
This bug exists in the following release(s):
R2020a

Interested in Upgrading?




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Simulink - Subsystem Reference block's position changes on loading or during synchronization of contents

In certain scenarios, a Subsystem Reference block changes its position. It can happen during: 

  1. Loading of top model which contains the Subsystem Reference block 
  2. Synchronization of Subsystem Reference block's contents
  3. Converting a subsystem to Subsystem Reference block 
This bug exists in the following release(s):
R2019b

Interested in Upgrading?




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Blockpass, Tozex partner for KYC, AML compliance of crypto trading

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LAUSD teacher negotiations reached gridlock over budget

LAUSD Superintendent Ramon Cortines commented Thursday on teacher contract talks that have been ongoing since July.; Credit: Benjamin Brayfield/KPCC

Annie Gilbertson

A budget deficit is preventing the Los Angeles Unified School District from offering teachers more than a 5 percent raise, Superintendent Ramon Cortines said Friday.

"I want some resolution," Cortines told reporters, but he said the district is now projecting a shortfall of $160 million heading into the next school year.

United Teachers Los Angeles, the union representing 31,000 teachers, declared an impasse Thursday in the contract negotiations. The two sides have been bargaining since July.

The teachers haven't had a pay increase in eight years, and their salaries are below that of neighboring districts. 

"You are not going to recruit and retain the quality teachers you need," UTLA President Alex Caputo-Pearl told KPCC's AirTalk this week. The union is seeking an 8.5 percent raise as well as smaller class sizes, more counselors and nurses, and revised teacher evaluations.

Cortines said the district's pay raise offer of 5 percent, retroactive to July 2014, would help make salaries more competitive. But he said the projected deficit is why LAUSD can't afford more.

Projections for the deficit have changed over the months. Last October, it was $365 million; in January, $88 million; and this month, $160 million. 

Teachers union representatives said California schools are receiving more money this year than any time since the recession. Gov. Jerry Brown's Local Control Funding process, which gives local districts more resources for education, is projected to garner the district $240 million more next school year. 

Cortines said he hopes to reach an agreement and he cautioned against any walkout.

"You talk about a budget deficit? It will exacerbate the budget deficit, because parents have other options," Cortines said. "They can go to other schools, private, parochial schools, they can go to charter schools, etc."

Cortines said a mediator is being called into the talks to help resolve the impasse.

The superintendent also repeated his doubts that the district can currently afford to put a computer in the hands of every district student. The program, a key initiative of his predecessor, John Deasy, used bond funds to pay for iPads and other devices.

Cortines said a statement elaborating on his remarks to reporters that "as we are reviewing our lessons learned, there must be a balanced approach to spending bond dollars to buy technology when there are so many brick and mortar and other critical facility needs that must be met."

This content is from Southern California Public Radio. View the original story at SCPR.org.




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A Domestic Electron Ion Collider Would Unlock Scientific Mysteries of Atomic Nuclei, Maintain U.S. Leadership in Accelerator Science, New Report Says

The science questions that could be answered by an electron ion collider (EIC) – a very large-scale particle accelerator – are significant to advancing our understanding of the atomic nuclei that make up all visible matter in the universe, says a new report by the National Academies of Sciences, Engineering, and Medicine.




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Child Sexual Abuse Reports Are On The Rise Amid Lockdown Orders

; Credit: Fanatic Studio/Gary Waters/Science Photo Library/Getty Images

Anya Kamenetz | NPR

There has been a rise in the number of minors contacting the National Sexual Assault Hotline to report abuse. That's according to RAINN, the Rape, Abuse and Incest National Network, which runs the hotline.

By the end of March, with much of the country under lockdown, there was a 22% increase in monthly calls from people younger than 18, and half of all incoming contacts were from minors. That's a first in RAINN's history, Camille Cooper, the organization's vice president of public policy, tells NPR.

Of those young people who contacted the hotline in March, 67% identified their perpetrator as a family member and 79% said they were currently living with that perpetrator. In 1 out of 5 cases where the minor was living with their abuser, RAINN assisted the minor in immediately contacting police.

"As a result of looking at the information that we had from those sessions, it was clear that the abuse was escalating in both frequency and severity," Cooper says. "So a lot of the kids that were coming to the hotline were feeling pretty vulnerable and traumatized. And it was a direct result of COVID-19, because they were quarantined with their abuser. The abuser was now abusing them on a daily basis."

Lockdown orders are first and foremost public health and safety measures. But statistically speaking, home is not the safest place for every young person. RAINN reports that about 34% of child sexual abusers are family members. Closing schools and canceling youth activities like sports removes children from the watchful eyes of "mandatory reporters" — those trusted adults, like teachers, nurses and child care providers, who are required by law in most states to report suspicions of child abuse or neglect.

However, Cooper says her organization has confirmed with authorities around the country that the child welfare system is still operating during the pandemic. That is, an official report of current and ongoing abuse will still trigger an investigation, and, if necessary, a child will be removed from the home.

"[Child welfare workers] will be coming to the home in person and proceeding with a formal investigation and a child forensic interview and things like that," she says. If the abuse is farther in the past and the child is not quarantined with the accused, Cooper says, the interview may take place over video chat.

In the meantime, RAINN and other child welfare organizations are lobbying to make it easier for children to report abuse. Cooper says, "One of the solutions we came up with that we are now currently working directly with the leadership in Congress on is to get all of the online learning platforms that children are interacting with to have a reporting function on that platform in plain sight for children."

Copyright 2020 NPR. To see more, visit https://www.npr.org.

This content is from Southern California Public Radio. View the original story at SCPR.org.




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Dr.Web quietly decrypting TorrentLocker for paid customers or distributors




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Sites using Dr.Web's TorrentLocker decryption taking advantage of victims




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Apple: iOS 8 prevents cooperation with police unlocking requests

Apple Senior Vice President of Worldwide Marketing Phil Schiller announces the new iPhone 6 during an Apple special event at the Flint Center for the Performing Arts on September 9, 2014 in Cupertino, California. Apple unveiled the two new iPhones the iPhone 6 and iPhone 6 Plus.; Credit: Justin Sullivan/Getty Images

Apple's latest mobile operating system — iOS 8 — is now available, and with it, a new technical hurdle for law enforcement. The company says it will be technologically impossible to access data on phones and iPads running iOS 8, because it won't allow user passcodes to be bypassed.

Our phones, of course, contain troves of information — contacts, messages, recordings — which can be helpful for investigative or prosecutorial purposes. The Supreme Court earlier this year ruled law enforcement cannot access that kind of data without a warrant. Prosecutors had already feared the warrant hurdle would be too much — Rockland County, N.Y., District Attorney Thomas Zugibe told the Wall Street Journal in June that technology "is making it easier and easier for criminals to do their trade," while the court "is making it harder for law enforcement to do theirs."

Now, even with a warrant, data from Apple devices running iOS 8 will be tough — and, Apple says, impossible — for law enforcement to get its hands on.

As The Washington Post reports, the move "amounts to an engineering solution to a legal quandary: Rather than comply with binding court orders, Apple has reworked its latest encryption in a way that prevents the company — or anyone but the device's owner — from gaining access to the vast troves of user data typically stored on smartphones or tablet computers."

 

Not so fast, writes an iOS forensics expert, Jonathan Zdziarski. Just because Apple will no longer help police doesn't mean police can't find ways to use existing commercial forensics tools to extract the data themselves. Wired Magazine describes how Zdziarski proved his own point:

Zdziarski confirmed with his own forensics software that he was still able to pull from a device running iOS 8 practically all of its third-party application data — that means sensitive content from Twitter, Facebook, Instagram, web browsers, and more — as well as photos and video. The attack he used impersonates a trusted computer to which a user has previously connected the phone; it takes advantage of the same mechanisms that allow users to siphon data off a device with programs like iTunes and iPhoto without entering the gadget's passcode.

"I can do it. I'm sure the guys in suits in the governments can do it," says Zdziarski.

And, Apple will still be able to turn over user data stored outside its phones, for example, on its iCloud service, The Washington Post notes. Users often back up photos, videos, emails and more to iCloud, as the recent nude photo theft reminded us.

Apple, in creating plausible deniability for itself, is also using its strongly worded new privacy stance as a marketing opportunity. It's reinforcing what it says is a commitment to privacy and transparency when it comes to government data requests. Apple says so far this year, it has received fewer than 250 government requests for data, including requests to unlock encrypted iPhones.




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Mukesh Ambani isn't letting a lockdown derail his plans of tech domination

The flurry of transactions show the tycoon's ambitions to pivot Reliance Industries into an Indian technology titan are going into hyperdrive