The availability of highly accurate protein structure predictions from AlphaFold2 (AF2) and similar tools has hugely expanded the applicability of molecular replacement (MR) for crystal structure solution. Many structures can be solved routinely using raw models, structures processed to remove unreliable parts or models split into distinct structural units. There is therefore an open question around how many and which cases still require experimental phasing methods such as single-wavelength anomalous diffraction (SAD). Here, this question is addressed using a large set of PDB depositions that were solved by SAD. A large majority (87%) could be solved using unedited or minimally edited AF2 predictions. A further 18 (4%) yield straightforwardly to MR after splitting of the AF2 prediction using Slice'N'Dice, although different splitting methods succeeded on slightly different sets of cases. It is also found that further unique targets can be solved by alternative modelling approaches such as ESMFold (four cases), alternative MR approaches such as ARCIMBOLDO and AMPLE (two cases each), and multimeric model building with AlphaFold-Multimer or UniFold (three cases). Ultimately, only 12 cases, or 3% of the SAD-phased set, did not yield to any form of MR tested here, offering valuable hints as to the number and the characteristics of cases where experimental phasing remains essential for macromolecular structure solution.

The Protein Data Bank (PDB) was established as the first open-access digital data resource in biology and medicine in 1971 with seven X-ray crystal structures of proteins. Today, the PDB houses >210 000 experimentally determined, atomic level, 3D structures of proteins and nucleic acids as well as their complexes with one another and small molecules (e.g. approved drugs, enzyme cofactors). These data provide insights into fundamental biology, biomedicine, bioenergy and biotechnology. They proved particularly important for understanding the SARS-CoV-2 global pandemic. The US-funded Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and other members of the Worldwide Protein Data Bank (wwPDB) partnership jointly manage the PDB archive and support >60 000 `data depositors' (structural biologists) around the world. wwPDB ensures the quality and integrity of the data in the ever-expanding PDB archive and supports global open access without limitations on data usage. The RCSB PDB research-focused web portal at https://www.rcsb.org/ (RCSB.org) supports millions of users worldwide, representing a broad range of expertise and interests. In addition to retrieving 3D structure data, PDB `data consumers' access comparative data and external annotations, such as information about disease-causing point mutations and genetic variations. RCSB.org also provides access to >1 000 000 computed structure models (CSMs) generated using artificial intelligence/machine-learning methods. To avoid doubt, the provenance and reliability of experimentally determined PDB structures and CSMs are identified. Related training materials are available to support users in their RCSB.org explorations.

The complex [Pt(C9H6NO)Cl(C2H4)], (I), was synthesized and structurally characterized by ESI mass spectrometry, IR, NMR spectroscopy, DFT calculations and X-ray diffraction. The results showed that the deprotonated 8-hy­droxy­quinoline (C9H6NO) coordinates with the PtII atom via the N and O atoms while the ethyl­ene coordinates in the η2 manner and in the trans position compared to the coordinating N atom. The crystal packing is characterized by C—H⋯O, C—H⋯π, Cl⋯π and Pt⋯π inter­actions. Complex (I) showed high selective activity against Lu-1 and Hep-G2 cell lines with IC50 values of 0.8 and 0.4 µM, respectively, 54 and 33-fold more active than cisplatin. In particular, complex (I) is about 10 times less toxic to normal cells (HEK-293) than cancer cells Lu-1 and Hep-G2. Furthermore, the reaction of complex (I) with guanine at the N7 position was proposed and investigated using the DFT method. The results indicated that replacement of the ethyl­ene ligand with guanine is thermodynamically more favorable than the Cl ligand and that the reaction occurs via two consecutive steps, namely the replacement of ethyl­ene with H2O and the water with the guanine mol­ecule.

This review focuses on low-dose near-field X-ray speckle phase imaging in the differential mode introducing the existing algorithms with their specifications and comparing their performances under various experimental conditions.

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.

For a reliable characterization of materials and systems featuring multiple structural levels, a broad length scale from a few ångström to hundreds of nanometres must be analyzed and an extended Q range must be covered in X-ray and neutron scattering experiments. For certain samples or effects, it is advantageous to perform such characterization with a single instrument. Neutrons offer the unique advantage of contrast variation and matching by D-labeling, which is of great value in the characterization of natural or synthetic polymers. Some time-of-flight small-angle neutron scattering (TOF-SANS) instruments at neutron spallation sources can cover an extended Q range by using a broad wavelength band and a multitude of detectors. The detectors are arranged to cover a wide range of scattering angles with a resolution that allows both large-scale morphology and crystalline structure to be resolved simultaneously. However, for such analyses, the SANS instruments at steady-state sources operating in conventional monochromatic pinhole mode rely on additional wide-angle neutron scattering (WANS) detectors. The resolution must be tuned via a system of choppers and a TOF data acquisition option to reliably measure the atomic to mesoscale structures. The KWS-2 SANS diffractometer at Jülich Centre for Neutron Science allows the exploration of a wide Q range using conventional pinhole and lens focusing modes and an adjustable resolution Δλ/λ between 2 and 20%. This is achieved through the use of a versatile mechanical velocity selector combined with a variable slit opening and rotation frequency chopper. The installation of WANS detectors planned on the instrument required a detailed analysis of the quality of the data measured over a wide angular range with variable resolution. This article presents an assessment of the WANS performance by comparison with a McStas [Willendrup, Farhi & Lefmann (2004). Physica B, 350, E735–E737] simulation of ideal experimental conditions at the instrument.

High-pressure crystallographic data can be measured using a diamond anvil cell (DAC), which allows the sample to be viewed only along a cell vector which runs perpendicular to the diamond anvils. Although centring a sample perpendicular to this direction is straightforward, methods for centring along this direction often rely on sample focusing, measurements of the direct beam or short data collections followed by refinement of the crystal offsets. These methods may be inaccurate, difficult to apply or slow. Described here is a method based on precise measurement of the offset in this direction using a confocal optical device, whereby the cell centre is located at the mid-point of two measurements of the distance between a light source and the external faces of the diamond anvils viewed along the forward and reverse directions of the cell vector. It is shown that the method enables a DAC to be centred to within a few micrometres reproducibly and quickly.

Soft X-ray spectroscopy is an important technique for measuring the fundamental properties of materials. However, for measurements of samples in the sub-millimetre range, many experimental setups show limitations. Position drifts on the order of hundreds of micrometres during thermal stabilization of the system can last for hours of expensive beam time. To compensate for drifts, sample tracking and feedback systems must be used. However, in complex sample environments where sample access is very limited, many existing solutions cannot be applied. In this work, we apply a robust computer vision algorithm to automatically track and readjust the sample position in the dozens of micrometres range. Our approach is applied in a complex sample environment, where the sample is in an ultra-high vacuum chamber, surrounded by cooled thermal shields to reach sample temperatures down to 2.5 K and in the center of a superconducting split coil. Our implementation allows sample-position tracking and adjustment in the vertical direction since this is the dimension where drifts occur during sample temperature change in our setup. The approach can be easily extended to 2D. The algorithm enables a factor of ten improvement in the overlap of a series of X-ray absorption spectra in a sample with a vertical size down to 70 µm. This solution can be used in a variety of experimental stations, where optical access is available and sample access by other means is reduced.

Manufacturers are poised to tackle the various challenges of the chips category.

Looking through the mind of an unconventional genius, the user delves into the fascinating hidden worlds of numbers, connective logic, belief, and possibility

Experiment will conclude whether or not activated charcoal can adsorb bacteria in microgravity

Working at the interface of the most advanced AI and Human Intelligence, NGO is building a worldwide 'Hero's Journey' to address planetary challenges

The online application ChatGPT and its integration into Microsoft search engines have put generative artificial intelligence technology in the hands of millions of people. Early adopters are using them in their daily jobs, and preliminary academic studies show big boosts in productivity. Managers can’t sit on the sidelines, says Ethan Mollick, an associate professor of management at The Wharton School of the University of Pennsylvania. He argues that companies urgently need to experiment with ChatGPT and eventually develop policies for it. He explains the breakthrough, some promising uses, open questions, and what the technology could mean for workers, companies, and the broader economy. Mollick wrote the HBR article "ChatGPT Is a Tipping Point for AI."

Google's new Learn About tool offers an interactive approach to learning about topics, including heady questions like whether money buys happiness.

A glitchy theme, built with Blockbase.

In a world that often emphasizes grand gestures and monumental achievements, it’s easy to overlook the profound impact of small actions. Yet, it’s these minuscule steps that are the true catalysts for change and progress in our lives. “Tiny Experiments.” I keep these words on a Post-It note on my monitor, a daily reminder that the key to unlocking my potential and propelling myself towards my desired future lies in the willingness to take small, manageable actions. Now, you might be skeptical. What can you really accomplish in just a few minutes? The answer is—a lot more than you think. Examples of Tiny Experiments Here are some of the tiny experiments I’ve integrated into my routine: A Ten-Minute Run: It’s short, yes, but it boosts my energy and clears my mind, making me more productive. One Strategic Email: Something as simple as sending an email can advance my projects, like moving forward with an upcoming TV series. Fifty Pushups: This quick burst of physical activity increases my physical stamina and mental toughness. Ten-Minute Meditation: Helps me center my thoughts and combat the stresses of daily life. A Five-Minute Call: Reconnecting with a friend or family member, like my mom, nurtures...

The post Tiny Experiments: How Little Moments Influence Your Life first appeared on Chase Jarvis.

The post Tiny Experiments: How Little Moments Influence Your Life appeared first on Chase Jarvis.

Video effects have revolutionized how we experience visual forms of entertainment. They're used in almost every type of show, commercial, or film available ...

Targeting is an important but challenging process in the design and delivery of social and humanitarian assistance programs. Community-based targeting (CBT) approaches are often preferred for their local information advantages, especially when data-driven methods are not feasible. However, how different variants of CBT approaches fare under various constraints and environments remains unclear. For example, it […] Source: IFPRI Ethiopia: Ethiopia Strategy Support Program

Agricultural production remains the main source of livelihood for rural communities in Sub-Saharan Africa, providing employment to more than 60 percent of the population and contributing about 30 percent of gross domestic product. With likely long-term changes in rainfall patterns and shifting temperature zones, climate change is expected to significantly affect agricultural production, which could be detrimental to the region’s food security and economic growth.

How much does take-up timing for agricultural inputs depend on price? Evidence from an experiment in Nigeria

Insights into buying behavior.

The post How much does take-up timing for agricultural inputs depend on price? Evidence from an experiment in Nigeria appeared first on IFPRI.

There's this fundamental question in economics that has proven really hard to answer: What's a good way to help people out of poverty? The old-school way was to fund programs that would support very particular things, like buying cows for a village, giving people business training, or building schools.

But over the past few decades, there has been a new idea: Could you help people who don't have money by ... just giving them money? We covered this question in a segment of This American Life that originally ran in 2013. Economists who studied the question found that giving people cash had positive effects on recipients' economic and psychological well-being. Maybe they bought a cow that could earn them money each week. Maybe they could replace their grass roofs with metal roofs that didn't need fixing every so often.

The success of just giving people in poverty cash has spawned a whole set of new questions that economists are now trying to answer. Like, if we do just give money, what's the best way to do that? Do you just give it all at once? Or do you dole it out over time? And it turns out... a huge new study on giving cash was just released and it's got a lot of answers.

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Experiment launched aboard SpaceX CSR‑9 mission to International Space Station should deliver answersToronto, ON – U of T Engineering researchers are launching an experiment that aims to solve the longstanding myster of how water behaves in space. Their experiment will launch at 12:45 am on Monday, July 18 aboard SpaceX CRS‑9 from Cape Canaveral, Florida, headed […]

Design of Experiments (DOE) helps improve products and processes more efficiently, providing a comprehensive understanding of influences on the end result.

AGU is an organization committed to a culture of Experiment / Learn / Adapt. In response to voter input over many elections, the Leadership Development / Governance Committee chose to test ranked choice voting in 4 elections – International Secretary, Board Director, Council Students and Council Early Career Scientists. In case you’re not familiar, this is an increasingly popular electoral system that allows voters to rank candidates by preference, meaning …

The post Experiment. Learn. Adapt.: Ranked Choice Voting in the 2024 AGU Elections appeared first on AGU Blogosphere.

Verification experiments related to increase of efficiency of air-conditioning and control technologies at a data centre

Experimental studies on plates and ducts installed at equipment inlets and outlets

HSTP-VID-WPOM - Working practices using objective metrics for evaluation of video coding efficiency experiments

Status of Radiocommunications between Amateur Stations of different Countries (In accordance with optional provision No. 25.1 of the Radio Regulations) and Form of Call Signs assigned by each Administration to its Amateur and Experimental Stations

La Justicia abrió la causa por la muerte de al menos 10 de los 50 animales que fueron introducidos en el parque natural por un proyecto piloto de Conselleria para prevenir incendios Leer

Microsoft brings two new opt-in trial features to some users of its Copilot AI-assistant.

Location: Electronic Resource- 

Library - Art Library, Location - OSIZ, Call number - FOLIO NX456.5.N49 E54 2016

Location: Electronic Resource- 

Location: Engineering Library- TS156.B375 2016

Experimental Cinema and Soviet Ideology Versus National Dignity: Two Films by Hamo Bek-Nazaryan

This interview was originally conducted for inclusion in our “experimentation” theme. Mac Smith is a Sound Designer and Supervising Sound Editor at Skywalker Sound, who has been working on films since 1999. Mac has worked on Toy Story 3, Tron: Legacy, Dawn of the Planet of the Apes, Little Evil, and Transpecos, as well as […]

Autoconocimiento: experimentar realmente quienes somos.

Hey awesome blog reader… can you help me with an experiment? Below you’ll find five of my favorite videos from my YouTube channel. A mix that covers photography, travel, post-processing, AI and Machine Elf. I’d love it if you’d pick whichever one appeals most to you and watch a bit. That can be a minute […]

The post Can You Help Me With an Experiment? appeared first on Stuck in Customs.

AI-powered search engine Perplexity says it’ll begin experimenting with ads on its platform starting this week. Ads will appear in the U.S. to start, formatted as “sponsored follow-up questions.” (E.g., “How can I use LinkedIn to enhance my job search?”) Paid media will be positioned to the side…

Abstract: The Lorentz force law is fundamental for electromagnetism. However, it is known long ago that the Lorentz forces between two current elements do not respect the Newton’s third law. This seemingly harmless flaw had never been corrected. In physical sciences a discrepancy often hides in it new understanding or unexpected breakthrough. For solving this...

Can one infinity be bigger than another?

Tandem mass tag (TMT) is a multiplexing technology widely-used in proteomic research. It enables relative quantification of proteins from multiple biological samples in a single MS run with high efficiency and high throughput. However, experiments often require more biological replicates or conditions than can be accommodated by a single run, and involve multiple TMT mixtures and multiple runs. Such larger-scale experiments combine sources of biological and technical variation in patterns that are complex, unique to TMT-based workflows, and challenging for the downstream statistical analysis. These patterns cannot be adequately characterized by statistical methods designed for other technologies, such as label-free proteomics or transcriptomics. This manuscript proposes a general statistical approach for relative protein quantification in MS- based experiments with TMT labeling. It is applicable to experiments with multiple conditions, multiple biological replicate runs and multiple technical replicate runs, and unbalanced designs. It is based on a flexible family of linear mixed-effects models that handle complex patterns of technical artifacts and missing values. The approach is implemented in MSstatsTMT, a freely available open-source R/Bioconductor package compatible with data processing tools such as Proteome Discoverer, MaxQuant, OpenMS, and SpectroMine. Evaluation on a controlled mixture, simulated datasets, and three biological investigations with diverse designs demonstrated that MSstatsTMT balanced the sensitivity and the specificity of detecting differentially abundant proteins, in large-scale experiments with multiple biological mixtures.

In quantitative proteomics work, the differences in expression of many separate proteins are routinely examined to test for significant differences between treatments. This leads to the multiple hypothesis testing problem: when many separate tests are performed many will be significant by chance and be false positive results. Statistical methods such as the false discovery rate (FDR) method that deal with this problem have been disseminated for more than one decade. However a survey of proteomics journals shows that such tests are not widely implemented in one commonly used technique, quantitative proteomics using two-dimensional electrophoresis (2-DE). We outline a selection of multiple hypothesis testing methods, including some that are well known and some lesser known, and present a simple strategy for their use by the experimental scientist in quantitative proteomics work generally. The strategy focuses on the desirability of simultaneous use of several different methods, the choice and emphasis dependent on research priorities and the results in hand. This approach is demonstrated using case scenarios with experimental and simulated model data.

Read more at http://blogs.smithsonianmag.com/science/2010/04/01/a-peep-experiment/ Our Surprising Science blogger tests whether stale peeps or fresh peeps are better for the spring tradition of peep jousting.

A clip from the father of video art's 1969 piece

A new exhibition spotlights the Spanish artist's printmaking talents, which he began honing in his 20s. In the decades that followed, he produced thousands of breathtaking creations

A Two-Day Festival in the historic Arts & Industries Building brings community, artists and scholars together for a “Culture Lab”

Google released a new experimental artificial intelligence (AI) tool on Monday aimed at helping users learn about new topics. Dubbed Learn About, the tool is different from the Mountain View-based tech giant's usual AI offerings, such as Gemini or AI Overviews. The experimental tool shows the information in a visual and interactive style and picks the data from educational sources.