The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. Firstly, it can verify the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Secondly, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/.

As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

Protein tyrosine kinases (PTKs) play key roles in cellular signal transduction, cell cycle regulation, cell division, and cell differentiation. Dysregulation of PTK-activated pathways, often by receptor overexpression, gene amplification, or genetic mutation, is a causal factor underlying numerous cancers. In this study, we have developed a parallel reaction monitoring (PRM)-based assay for quantitative profiling of 83 PTKs. The assay detects 308 proteotypic peptides from 54 receptor tyrosine kinases and 29 nonreceptor tyrosine kinases in a single run. Quantitative comparisons were based on the labeled reference peptide method. We implemented the assay in four cell models: 1) a comparison of proliferating versus epidermal growth factor (EGF)-stimulated A431 cells, 2) a comparison of SW480Null (mutant APC) and SW480APC (APC restored) colon tumor cell lines, and 3) a comparison of 10 colorectal cancer cell lines with different genomic abnormalities, and 4) lung cancer cell lines with either susceptibility (11-18) or acquired resistance (11-18R) to the epidermal growth factor receptor tyrosine kinase inhibitor erlotinib. We observed distinct PTK expression changes that were induced by stimuli, genomic features or drug resistance, which were consistent with previous reports. However, most of the measured expression differences were novel observations. For example, acquired resistance to erlotinib in the 11-18 cell model was associated not only with previously reported upregulation of MET, but also with upregulation of FLK2 and downregulation of LYN and PTK7. Immunoblot analyses and shotgun proteomics data were highly consistent with PRM data. Multiplexed PRM assays provide a targeted, systems-level profiling approach to evaluate cancer-related proteotypes and adaptations. Data are available through Proteome eXchange Accession PXD002706.

The increasing consumption of high-fat foods combined with a lack of exercise is a major contributor to the burden of obesity in humans. Aerobic exercise such as running is known to provide metabolic benefits, but how the over-consumption of a high fat diet (HFD) and exercise interact is not well characterized at the molecular level. Here, we examined the plasma proteome in mice for the effects of aerobic exercise as both a treatment and as a preventative regime for animals on either HFD or a healthy control diet. This analysis detected large changes in the plasma proteome induced by the HFD, such as increased abundance of SERPINA7, ALDOB, and down-regulation of SERPINA1E, CFD (adipsin). Some of these changes were significantly reverted using exercise as a preventative measure, but not as a treatment regime. To determine if either the intensity, or duration, of exercise influenced the outcome, we compared high-intensity interval training (HIIT) and endurance running. Endurance running slightly out-performed HIIT exercise, but overall, both provided similar reversion in abundance of plasma proteins modulated by the high-fat diet including SERPINA7, APOE, SERPINA1E, and CFD. Finally, we compared the changes induced by over-consumption of HFD to previous data from mice fed an isocaloric high saturated fat (SFA) or polyunsaturated fat (PUFA) diet. This identified several common changes including increased APOC2 and APOE, but also highlighted changes specific for either over-consumption of HFD (ALDOB, SERPINA7, CFD), SFA-based diets (SERPINA1E), or PUFA-based diets (Haptoglobin - Hp). Together, these data highlight the importance of early intervention with exercise to revert HFD-induced phenotypes and suggest some of the molecular mechanisms leading to the changes in the plasma proteome generated by high fat diet consumption. Web-based interactive visualizations are provided for this dataset (larancelab.com/hfd-exercise), which give insight into diet and exercise phenotypic interactions on the plasma proteome.

We developed a simple and rapid method to enrich protein N-terminal peptides, in which the protease TrypN is first employed to generate protein N-terminal peptides without Lys or Arg and internal peptides with two positive charges at their N-termini, and then the N-terminal peptides with or without N-acetylation are separated from the internal peptides by strong cation exchange chromatography according to a retention model based on the charge/orientation of peptides. This approach was applied to 20 μg of human HEK293T cell lysate proteins to profile the N-terminal proteome. On average, 1,550 acetylated and 200 unmodified protein N-terminal peptides were successfully identified in a single LC/MS/MS run with less than 3% contamination with internal peptides, even when we accepted only canonical protein N-termini registered in the Swiss-Prot database. Since this method involves only two steps, protein digestion and chromatographic separation, without the need for tedious chemical reactions, it should be useful for comprehensive profiling of protein N-termini, including proteoforms with neo-N-termini.

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed paraffin-embedded samples, detects extreme underalkylation of cysteine in some datasets, discovers an artefactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multi-center proteomics profiling study.

Advanced technologies in the face of war 24 October 2022 — 1:00PM TO 2:00PM Anonymous (not verified) 5 October 2022 Online

How is NATO strengthening its technological edge?

Russia’s invasion of Ukraine has brought with it a heavy focus on technology and weaponry, particularly as casualties mount and large numbers of equipment are lost on both sides. The conflict has highlighted how states and their militaries seek technological superiority and how access to advanced capabilities can help shape the course of the war.

Aiming to sharpen the Alliance’s technological edge, NATO is working to support the development of emerging and potentially disruptive technologies such as artificial intelligence (AI), autonomous systems, biotechnologies and quantum technologies that are seen as presenting both risks and opportunities for the Alliance.

As part of this work, NATO’s newly formed Defence Innovation Accelerator for the North Atlantic (DIANA), hosted by both the UK and Estonia, brings together academia, industry and government to support the development of critical technologies to deter and defend against existing and future threats.

Key questions to be considered by the panel include:

• How will the technologies that form the focus of DIANA’s efforts strengthen the Alliance and prepare it to better deal with threats to peace and security across the region?

• How will these technologies be applied and used in war?

• To what extent can a war be won by technology?

• Is Ukraine, and other future conflict zones, in danger of becoming a testing ground for emerging technologies?

• What has the war in Ukraine taught NATO about modern warfare and how should the Alliance respond to this?

• After the commotion of AUKUS, how will the Alliance manage the sharing of technologies and IP among member states?

As with all members events, questions from the audience drive the conversation.

Read the transcript. 

Disruptive technologies by nation states and malign cyber actors – the US response 16 February 2023 — 1:00PM TO 2:00PM Anonymous (not verified) 2 February 2023 Chatham House and Online

Lisa Monaco, the US deputy attorney general, discusses how autocratic governments and malign cyber actors use disruptive technologies to project power and engage in illicit activity.

Weaponizing data, ransomware attacks and other illicit cyber activity represent significant threats to national security. 

Governments and malicious cyber actors around the world exploit disruptive technology to engage in criminal activity, track citizens and coerce other countries thereby weakening the rules-based order and fundamental principles of democracy. 

Lisa Monaco discusses how the world is at an inflection point when it comes to meeting this challenge and describes how the US and partner nations are responding to protect their citizens and the broader international community.

Key questions to discuss include:

• What steps does the US government need to take to properly address this threat?
• How are countries coordinating policies to confront the problem?
• To what extent does this challenge go beyond US-China competition?

As with all member events, questions from the audience drive the conversation.

Read the transcript.

Africa and Europe: Cooperation on digital transitions and new technologies 26 May 2022 — 8:00AM TO 12:30PM Anonymous (not verified) 12 May 2022 Online

The 11th Africa Day International Conference takes place under the auspices of the president of the Republic of Slovenia, HE Mr Borut Pahor, and within the framework of the Bled Strategic Forum.

Slovenia’s annual high-level Africa event seeks to improve policy outcomes for citizens in Europe and Africa as a result of a mutual understanding and strengthened cooperation between the two regions.

The event is co-hosted by the Ministry of Foreign Affairs of the Republic of Slovenia, the Chatham House Africa Programme and the European Commission.

Expert discussions at this year’s edition will examine collaborative links between Africa and Europe in promoting responsible innovation and governance of emerging technologies, as well as the role of technology in shaping creative and cultural economies.

The conference will be broadcast live on this website, on the Slovenian Ministry of Foreign Affairs website and on the Africa Programme Facebook page.

Noritaka Hoshi, Senior Manager, AI Platform Division, talks about the impetus for and challenges within the development of SX-Aurora TSUBASA or a massive SIMD, created to handle enormous computing and […]

The post Advance Science, Technology and Sophistication with SX-Aurora TSUBASA or Vector Processor or Vector Engine (VE) appeared first on HPCwire.

How can manufacturers apply lessons learned from the dawn of the “Exascale Era” to Computer-Aided Engineering to achieve results like never before? Join Addison Snell, CEO, Intersect360 Research, Bill Mannel, VP, High Performance […]

The post Leveraging Exascale Era Technology for Advanced Computer-Aided Engineering appeared first on HPCwire.

WASHINGTON, Oct. 30, 2024 — The U.S. Department of the Treasury (Treasury) today issued a final rule (Final Rule) to implement Executive Order 14105 of August 9, 2023, “Addressing United […]

The post US Treasury Issues Final Rule Addressing Investments in Certain National Security Technologies and Products appeared first on HPCwire.

Tessa E.S. Charlesworth
Sep 11, 2019; 39:7228-7243
Viewpoints

February’s international symposium, entitled “The role of agricultural biotechnologies in sustainable food systems and nutrition”, will explore how the application of science and technology, and particularly agricultural biotechnologies, can benefit [...]

Who’s afraid of the dark? Our Ask Smithsonian host Eric Schulze is here to explain the illuminating science behind night vision.

Amid rapid global advances and deployment of artificial intelligence technologies, the federal government has invested millions to combine the minds of three existing institutes into one that can keep an eye on potential dangers ahead.

Engineers Use CAD To Adapt Standard Parts, Assemblies To Fit In Custom Body Design from 1950s

World's #1 mainstream analysis software adds 100-plus new features that put powerful design validation in easy-to-use packages

SolidWorks software donation supports fusion of science, technology, engineering, and math (STEM) in education

Innovation introduces expert intelligence into 3D CAD software

Cutting days and weeks from design cycle gives Syncroness more time to focus on designing lightweight, high performance products

Breakthrough technology puts expert design techniques in every user's hands

Schools combine SOLIDWORKS 3D CAD software with 3D scanning and printing to enrich student learning

Canadian aluminum die casting company cuts development time in half, reduces errors with 3D CAD and product data management software

Cyclone Clean Air Engine burns cleaner, more efficiently to power cars, ships, etc.

U.K. company cut weeks out of design time, eliminated prototyping, and increased innovation with SOLIDWORKS and CircuitWorks

Company can design a silo in half an hour and deliver it earlier while helping improve the quality of Mexico's food, plastics, and construction practices

Nearly 100,000 visitors experimented with forward-looking tools and services in first year

Off-Campus, Around-the-Clock Access and Integrated Simulation are Big Advantages for Students

Equipment Designed and Modified With SolidWorks Software Located Miners and Helped Drill Escape Shaft Weeks Sooner Than Predicted

When it comes to reaching the least-reached, OM workers are using new technology to make ministry more effective—one byte at a time.

While laptops and videos can make the classroom fun and interactive, how much does technology really improve achievement?

Integrating technology requires a significant investment of time and money, but the resources are well-spent if the focus is improving instruction, writes educational consultant Matthew Lynch.

Teaching and Learning with Technology (TLT), part of Penn State University Libraries, has announced the Teaching and Learning Technologies Faculty Advisory Committee for the 2024-25 academic year. The committee is pivotal in guiding TLT on integrating technology within teaching and learning at Penn State.

The Richard King Mellon Foundation recently awarded $392,000 to Penn State to build a strong science- and technology-focused workforce in the state’s Mon Valley region through collaboration and virtual, augmented and mixed reality trainings and tools.

Penn State’s Teaching and Learning with Technology (TLT), part of Penn State University Libraries, has welcomed five University instructors across three campuses into its Faculty Fellows cohort for 2024-26 and started collaborating on a new collection of projects. Faculty chosen for the Faculty Fellows program team up with TLT on innovative technology projects, with past endeavors spanning a broad spectrum from learning spaces to virtual reality/immersive experiences to data-empowered learning.

As the two big groups of states craft common-assessment systems, experts warn that the smallest details could undermine their work.

Recently, the Wildlife Technology Program at Penn State DuBois earned reaccreditation with the North American Wildlife Technology Association for five years.

OM workers in Central Asia use technology to develop new discipleship and worship tools for local believers.

Data science continues to be a pivotal force driving innovation across industries. From enhancing customer experiences to optimizing operational efficiencies, the role of data science is expanding, bringing with it new challenges and opportunities. This article explores the emerging trends and technologies that are shaping the future of data science [...]

The future of data science: 7 emerging trends and technologies to watch was published on SAS Voices by Iain Brown

Secretary of Education Mark Holodick is pleased to recognize the following students for their submissions in this year’s Esri’s 2024 ArcGIS webapp competition. Students were challenged to create and share interactive mapping projects using ESRI ArcGIS software. Delaware entrants to this national competition must create a digital Storymap that explores some aspect of life in Delaware.

The Smart Food Program, a first in the nation project, will save food waste and reach families in need by using an AI-driven app to match surplus food to SNAP demands    WILMINGTON, Del. — Delaware will be the first state to pilot an innovative app to help those hardest hit by economic challenges stretch […]

DEPARTMENT OF HEALTH AND SOCIAL SERVICES: Division of Public Health

DEPARTMENT OF EDUCATION: Professional Standards Board

“What’s our plan if we get hit by a big flood?” While this question may be plenty familiar to emergency management professionals, city administrators, legislators, and other leaders in coastal regions that are known for their exposure to potentially disastrous weather events, these days it’s being asked in some unexpected [...]

The post Four technology tips for government leaders preparing for flood disasters appeared first on Government Data Connection.

Read the in depth Review of Wings Techno Audio Video. Know detailed info about Wings Techno configuration, design and performance quality along with pros & cons, Digit rating, verdict based on user opinions/feedback.

Having the right data analytics platform can help law enforcement solve crimes faster.

The post 5 technology considerations for law enforcement appeared first on The Data Roundtable.

Hi,

My query is regarding importing of layout.

After importing, we see that the imported transistor instances and vias are all referring to the library in which they are imported, instead of referring to the technology library.

Please let me know how we can refer them to the technology library.

Will surely provide more details if my query is unclear.

Thanks,

Mallikarjun.

This is the 23rd installment of The Rationalist, my column for the Times of India.

I had a strange dream last night. I dreamt that the government had passed a law that made using laptops illegal. I would have to write this column by hand. I would also have to leave my home in Mumbai to deliver it in person to my editor in Delhi. I woke up trembling and angry – and realised how Indian farmers feel every single day of their lives.

My column today is a tale of two satyagrahas. Both involve farmers, technology and the freedom of choice. One of them began this month – but first, let us go back to the turn of the millennium.

As the 1990s came to an end, cotton farmers across India were in distress. Pests known as bollworms were ravaging crops across the country. Farmers had to use increasing amounts of pesticide to keep them at bay. The costs of the pesticide and the amount of labour involved made it unviable – and often, the crops would fail anyway.

Then, technology came to the rescue. The farmers heard of Bt Cotton, a genetically modified type of cotton that kept these pests away, and was being used around the world. But they were illegal in India, even though no bad effects had ever been recorded. Well, who cares about ‘illegal’ when it is a matter of life and death?

Farmers in Gujarat got hold of Bt Cotton seeds from the black market and planted them. You’ll never guess what happened next. As 2002 began, all cotton crops in Gujarat failed – except the 10,000 hectares that had Bt Cotton. The government did not care about the failed crops. They cared about the ‘illegal’ ones. They ordered all the Bt Cotton crops to be destroyed.

It was time for a satyagraha – and not just in Gujarat. The late Sharad Joshi, leader of the Shetkari Sanghatana in Maharashtra, took around 10,000 farmers to Gujarat to stand with their fellows there. They sat in the fields of Bt Cotton and basically said, ‘Over our dead bodies.’ ¬Joshi’s point was simple: all other citizens of India have access to the latest technology from all over. They are all empowered with choice. Why should farmers be held back?

The satyagraha was successful. The ban on Bt Cotton was lifted.

There are three things I would like to point out here. One, the lifting of the ban transformed cotton farming in India. Over 90% of Indian farmers now use Bt Cotton. India has become the world’s largest producer of cotton, moving ahead of China. According to agriculture expert Ashok Gulati, India has gained US$ 67 billion in the years since from higher exports and import savings because of Bt Cotton. Most importantly, cotton farmers’ incomes have doubled.

Two, GMO crops have become standard across the world. Around 190 million hectares of GMO crops have been planted worldwide, and GMO foods are accepted in 67 countries. The humanitarian benefits have been massive: Golden Rice, a variety of rice packed with minerals and vitamins, has prevented blindness in countless new-born kids since it was introduced in the Philippines.

Three, despite the fear-mongering of some NGOs, whose existence depends on alarmism, the science behind GMO is settled. No harmful side effects have been noted in all these years, and millions of lives impacted positively. A couple of years ago, over 100 Nobel Laureates signed a petition asserting that GMO foods were safe, and blasting anti-science NGOs that stood in the way of progress. There is scientific consensus on this.

The science may be settled, but the politics is not. The government still bans some types of GMO seeds, such as Bt Brinjal, which was developed by an Indian company called Mahyco, and used successfully in Bangladesh. More crucially, a variety called HT Bt Cotton, which fights weeds, is also banned. Weeding takes up to 15% of a farmer’s time, and often makes farming unviable. Farmers across the world use this variant – 60% of global cotton crops are HT Bt. Indian farmers are so desperate for it that they choose to break the law and buy expensive seeds from the black market – but the government is cracking down. A farmer in Haryana had his crop destroyed by the government in May.

On June 10 this year, a farmer named Lalit Bahale in the Akola District of Maharashtra kicked off a satyagraha by planting banned seeds of HT Bt Cotton and Bt Brinjal. He was soon joined by thousands of farmers. Far from our urban eyes, a heroic fight has begun. Our farmers, already victimised and oppressed by a predatory government in countless ways, are fighting for their right to take charge of their lives.

As this brave struggle unfolds, I am left with a troubling question: All those satyagrahas of the past by our great freedom fighters, what were they for, if all they got us was independence and not freedom?

The India Uncut Blog © 2010 Amit Varma. All rights reserved.
Follow me on Twitter.

Designing 3D-ICs with integrity involves a commitment to ethical practices, reliability, and sustainability throughout the design and manufacturing process. This includes using environmentally friendly materials, ensuring robust and efficient performance, and incorporating thorough testing and verification. By prioritizing transparency, responsibility, and long-term sustainability, designers can create advanced integrated circuits that meet high standards of quality and social responsibility.

Start Learning Now!

Start with our Designing with Integrity 3D-IC online course, which introduces Integrity 3D-IC, the industry's first comprehensive, high-capacity 3D-IC platform that integrates 3D design planning, implementation, and system analysis in a single, unified environment. You will be guided through the following activities involved in designing a silicon interposer with a digital ASIC and HBM2 interface in a 2.5D configuration.

• You will design the interposer from scratch in the new Integrity System Planner and the Integrity 3D-IC implementation environment.
• You will examine the ASIC and interposer designs using some of the new 3D-IC multi-die design features.
• You will route the interposer using some of the new advanced routing capabilities with NanoRoute

—and this in only two days!

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• Demo: How To Pull The Interposer Design From System Planner Into Integrity 3D-IC Layout? (Video)
• Demo: Routing The Interposer Design Using The Integrity 3D-IC Layout_Part 1 (Video)
• Demo: Routing The Interposer Design Using The Integrity 3D-IC Layout_Part 2 (Video)
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