This article has been withdrawn by the authors. This article did not comply with the editorial guidelines of MCP. Specifically, single peptide based protein identifications of 9-19% were included in the analysis and discussed in the results and conclusions. We wish to withdraw this article and resubmit a clarified, corrected manuscript for review.

Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function.  Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature.  Quite often, however, the assumption behind proteomics that post-translational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation.  Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system.  To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established.  But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes.  The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities.  In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem.

Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine have not been previously investigated in detail. We analysed the glyco/proteome of sparkling wines using protein- and glycopeptide-centric approaches. We developed an automated workflow that created ion libraries to analyse Sequential Window Acquisition of all THeoretical mass spectra (SWATH) Data Independent Acquisition (DIA) mass spectrometry data based on glycopeptides identified by Byonic. We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeast strains used in the Liqueur de Tirage for secondary fermentation. We found that aging a cuvée on lees for 24 months compared to 8 months led to a dramatic decrease in overall protein abundance and an enrichment in large glycans at specific sites in some proteins. Secondary fermentation of a Riesling wine with Saccharomyces cerevisiae yeast strain Siha4 produced more yeast proteins and glycoproteins than with S. cerevisiae yeast strain DV10. The abundance and glycosylation profiles of grape glycoproteins were also different between grape varieties. This work represents the first in-depth study into protein- and peptide-specific glycosylation in sparkling wines and describes a quantitative glycoproteomic SWATH/DIA workflow that is broadly applicable to other sample types.

The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characteristic, individual-specific protein levels and by variant peptides reporting on coding single nucleotide polymorphisms. Furthermore, it is in the nature of blood plasma proteomics profiling that it broadly reports on the health status of an individual – beyond the disease under investigation. Finally, we show that private and potentially sensitive information, such as ethnicity and pregnancy status, can increasingly be derived from proteomics data. Although this is potentially valuable not only to the individual, but also for biomedical research, it raises ethical questions similar to the incidental findings obtained through other omics technologies. We here introduce the necessity of - and argue for the desirability for - ethical and human rights-related issues to be discussed within the proteomics community. Those thoughts are more fully developed in our accompanying manuscript. Appreciation and discussion of ethical aspects of proteomic research will allow for deeper, better-informed, more diverse, and, most importantly, wiser guidelines for clinical proteomics.

Data independent acquisition (DIA) is now an emerging method in bottom-up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications (PTM), such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O- glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA is briefly introduced. DIA based glycoproteomics is then summarized and described into four aspects based on the actual samples. Lastly, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics.

South Africa’s 2019 Election: Polling Data and Party Prospects 13 March 2019 — 12:30PM TO 1:30PM Anonymous (not verified) 7 March 2019 Chatham House, London

On 8 May 2019, South Africans will vote in their sixth national election. Incumbent President Cyril Ramaphosa is leading his ANC party campaign, which promises inclusive economic growth and social transformation, including through a sustainable land reform programme. However, public frustrations with the party’s record of service delivery and government corruption after 25 years in power could threaten the ANC’s electoral dominance especially in urban areas.

At this meeting, Professor David Everatt, head of the Wits School of Governance and political pollster, will present polling data and discuss the prospects and strategies of the main parties and their leaders ahead of the May election.

Attendance at this event is by invitation only.

Large-scale scientific research labs and academic institutions are utilizing high performance computing to accelerate sequencing, simulations, and analytics for research, learning, and discovery.  File data volumes are growing rapidly, and […]

The post Accelerating Research Innovation with Qumulo’s File Data Platform appeared first on HPCwire.

The data fabric has emerged as an enterprise data management pattern for companies that struggle to provide large teams of users with access to well-managed, integrated, and secured data. Now […]

The post NSF-Funded Data Fabric Takes Flight appeared first on HPCwire.

COLLEGE PARK, Md., Nov. 8, 2024 — IonQ, a leader in the quantum computing industry, has announced a partnership with NKT Photonics, a subsidiary of Hamamatsu Photonics, to procure next-generation laser […]

The post IonQ and NKT Photonics Collaborate on Next-Gen Laser Tech for Quantum Data Centers appeared first on HPCwire.

The movement toward open source AI made progress today when the Open Source Initiative released the first Open Source AI Definition (OSAID). While the OSAID provides one step forward, the […]

The post OSI Open AI Definition Stops Short of Requiring Open Data for LLMs appeared first on HPCwire.

Data centers are experiencing increasing power consumption, space constraints and cooling demands due to the unprecedented computing power required by today’s chips and servers. HVAC cooling systems consume approximately 40% […]

The post How Direct Liquid Cooling Improves Data Center Energy Efficiency appeared first on HPCwire.

The VDURA Data Platform is a next-generation data storage and management solution, purpose-built to meet the rigorous demands of Artificial Intelligence (AI) and High-Performance Computing (HPC). Leveraging a modern, shared-nothing […]

The post The VDURA Data Platform: Elevating Data Storage for AI and HPC appeared first on HPCwire.

SANTA CLARA, Calif. and MUNICH, Nov. 7, 2024 — Cerabyte, a pioneer of ceramic-based data storage solutions, today announced its participation at SuperComputing 2024 (SC24), taking place at the Georgia […]

The post Cerabyte Discusses Use Cases for Its Ceramic Data Storage Solution at SC24 appeared first on HPCwire.

SAN JOSE, Calif., Nov. 12, 2024 — VDURA, a leader in data infrastructure for AI and HPC, today has announced a groundbreaking release of its VDURA Data Platform software, designed to […]

The post VDURA Unveils Next-Gen Data Platform with Enhanced AI and HPC Performance appeared first on HPCwire.

AI may be a priority at American companies, but the difficulty in managing data and obtaining high quality data to train AI models is becoming a bigger hurdle to achieving […]

The post AI Has a Data Problem, Appen Report Says appeared first on HPCwire.

Physicists have developed a deep understanding of the fundamental laws of nature through careful observations, experiments, and precise measurements. However, what if artificial intelligence (AI) could uncover governing laws of […]

The post Archetype AI’s Newton Model Masters Physics From Raw Data appeared first on HPCwire.

TOKYO, March 7, 2024 — Fujitsu Limited and Carnegie Mellon University today announced the development of a new technology to visualize traffic situations, including people and vehicles, as part of […]

The post Fujitsu and Carnegie Mellon University Develop AI-powered Social Digital Twin Tech with Traffic Data from Pittsburgh appeared first on HPCwire.

Data isn't just about numbers or trends — it's about capturing the stories that shape our lives, says information designer Giorgia Lupi. Following a long COVID diagnosis, she tracked her symptoms meticulously over four years, the data culminating in a visual "New York Times" narrative that resonated deeply with many others suffering from chronic illness. Lupi invites us to consider data not as a rigid or objective truth, but as a living language used to better understand ourselves, offering a surprising shift in perspective — depending on where you look.

Is it possible to meet the world's seemingly infinite demand for data storage while also caring for the natural environment? Biomedical researcher Keolu Fox and professional surfer and scientist Cliff Kapono believe that Indigenous knowledge combined with the science of genetics may offer such a solution: using the DNA of plant cells (like those found in sugar cane) as mini data warehouses. Learn more about the incredible potential of this technology — and how it could help foster ecosystem resilience in a high-tech world.

The Maryland State Department of Education "inappropriately stored" personal information of 1.4 million students and more than 230,000 teachers, leaving them vulnerable to potential bad actors, according to an audit published earlier this month.

Nebraska's education department released an interactive instructional materials map last week, showing what curricula districts have adopted for English-language arts, math, and K-8 science.

The  Food and Agriculture Organization of the United Nations (FAO) is happy to announce significant updates and upgrades to the FAO CONNECT CRM Database section [...]

By analyzing an old lidar survey, researchers found evidence of more than 6,500 ancient structures in a previously unexplored area of Campeche

MatWeb's new export engine pipes data from its 47,000 material information sheetsdirectly into SolidWorks and COSMOSWorks

The 2020-21 academic year remains in a state of limbo because of COVID-19, but states are moving forward with guidelines for local districts to use as they make decisions about when instruction—in-person, online, or a combination of both—will begin.

Since June 2020 Education Week has tracked if & when the over 200 schools named after men with ties to the Confederacy changed their names.

Two Penn State Great Valley graduate students are collaborating with faculty — who received a University Presidential Public Impact Research Award — to conduct a research project that will use artificial intelligence and machine learning to analyze demographic data to help predict and prevent opioid deaths. 

A team from Penn State Harrisburg spent a week at a NASA facility over the summer, building a scientific experiment and sending it to space through the RockOn! program.

The availability of an artificial intelligence system's training data can promote transparency and accountability of that system, according to Penn State researchers.

The Penn State Institute for Computational and Data Sciences announced two new co-hires: Dana Calacci, assistant professor in the College of Information Sciences and Technology, and Enrico Casella, assistant professor of data science for animal systems in the College of Agricultural Sciences. 

Discovery Health Medical Scheme's (DHMS) 2023 cancer claims payouts were almost 19% higher than the previous year though the scheme says screening rates in South Africa have mostly returned to pre-pandemic levels.

Here are five takeaways on the teaching profession from the newly released 2017-18 National Teacher and Principal Survey.

Scientists from IISc, University of Pennsylvania, and MIT reveal a breakthrough with indium selenide that transforms crystalline structures to glass using significantly less energy. By passing a continuous electric current, the crystalline material experiences a “shock” that converts it to glass. The low energy requirement could help lower power needs for data storage devices, potentially advancing phase-change memory in computers and mobile devices. This research opens a pathway for integrating this memory tech on CMOS platforms.

Insurance Commissioner Trinidad Navarro highlights successes, resilience The Delaware Department of Insurance published today a series of statistics outlining performance and productivity during 2020. These metrics show successes notwithstanding the pandemic and operational changes such as working remotely. These data have been shared visually in the Department of Insurance 2020 Year in Review infographic. “Despite […]

Participating in National Insurer Climate Risk Disclosure Survey Insurance Commissioner Trinidad Navarro has announced Delaware’s participation in the National Association of Insurance Commissioners’ Insurer Climate Risk Disclosure Survey, an effort to assess how the impacts of climate change will reverberate across the insurance industry. From investment practices, to increased claim occurrences impacting companies’ financial sturdiness, […]

Successes in serving residents continue The Delaware Department of Insurance (DOI) today published performance and productivity data for 2021. While the pandemic necessitated continued operational adjustments, staff continued to focus efforts on consumer services and saw great success. The department also released an infographic of key statistics. “Year after year, our DOI team delivers for […]

Consumers continue to benefit from carrier expansion and insurer oversight The Delaware Department of Insurance (DOI) has published its annual performance and productivity data, indicating continued success in serving consumers throughout the state. “In the face of inflation, climate change, the pandemic, and other challenges, our priority remains the same: the residents of our great […]

Insureds, agents, and beneficiaries should watch for notification On June 16, PBI Research Services, a third-party vendor for Genworth Financial, disclosed a data breach that impacted the personal information of an estimated 2.5-2.7 million individuals, including about 8,000 Delaware residents. At this time, the company has indicated that the potentially compromised information may include agents, […]

More than 37,500 Delaware agents, policyholders, beneficiaries impacted Following the receipt of additional data breach reports from insurers, including those related to the breach of the MOVEit file transfer services system used by third-party vendors, the Delaware Department of Insurance is updating this consumer alert and will be updating the online posting as information is […]

Another banner year for consumer protection and insurer competition In 2023, the Delaware Department of Insurance’s 101 team members served Delaware residents and seniors, attracted new companies, oversaw expansions of coverage and enhanced competition, and contributed substantial funds to the state. Today’s data release details how each team contributed to Delaware’s strong insurance environment. “Each […]

Nifty hit a fresh record high on Friday, as faster-than-expected economic growth in the September-quarter added to optimism over the global interest rate outlook.

Attorney General Kathy Jennings announced Wednesday that Delaware has joined a total $39.5 million settlement with Anthem stemming from the massive 2014 data breach that involved the personal information of 78.8 million Americans. Through the settlement, Anthem has reached a resolution with the 43-state multistate coalition and California. The DOJ’s Consumer Protection Unit helped secure […]

Attorney General Kathy Jennings announced Tuesday that Delaware has joined a total $17.5 million settlement against Georgia-based retailer The Home Depot, resolving a multistate investigation of a 2014 data breach which exposed the payment card information of approximately 40 million Home Depot consumers nationwide. Through the settlement The Home Depot has reached a resolution with […]

Attorney General Kathleen Jennings urges all Delaware residents who believe they were impacted by the data breach announced by T-Mobile in August 2021 to take appropriate steps to protect their information from identity theft. On August 17,  T-Mobile reported a massive data breach compromising the sensitive personal information of millions of current, former, and prospective […]

Attorney General Kathleen Jennings announced today that Delaware, along with 39 states, has obtained two multistate settlements with Experian Information Solutions, Inc. (“Experian”) and T-Mobile USA, Inc. (“T-Mobile”) concerning a 2015 data breach experienced by Experian that compromised the personal information of more than 15 million individuals who submitted credit applications with T-Mobile. Under the […]

Attorney General Jennings announced today that Delaware has reached a multistate settlement with software company Blackbaud for its deficient data security practices and response to a 2020 ransomware event that exposed the personal information of millions of consumers across the United States. Under the settlement, Blackbaud has agreed to overhaul its data security and breach […]