Resolution 20 - (Rev. Geneva, 2022) - Procedures for allocation and management of international telecommunication numbering, naming, addressing and identification resources

Resolution 61 - (Rev. Geneva, 2022) - Countering and combating misappropriation and misuse of international telecommunication numbering resources

Resolution 69 - (Rev. Hammamet, 2016) - Non-discriminatory access and use of Internet resources

Resolution 85 - (Hammamet, 2016) - Strengthening and diversifying the resources of the ITU Telecommunication Standardization Sector

ITU-T E.164 numbering resources for trials

Guidelines for ITU-T action on reported misuse of ITU-T E.164 number resources

It’s time for our monthly roundup! In this edition, we’ve gathered some exciting new resources for web developers, with a focus on the PHP ecosystem. PHP has experienced a bit of a renaissance lately, especially with Laravel’s influence on the JavaScript ecosystem, and with the upcoming release of PHP 8.4 around the end of this…

The post Fresh Resources for Web Designers and Developers (October 2024) appeared first on Hongkiat.

The Owens Corning booth at IRE highlights roofing products that fuse high-performance with beauty and style.

Find some of our favorite resources for the April 8, 2024, solar eclipse, including apps, video explainers, children's activities, and books.

The post Eclipse Apps, Books, Videos: Resources for the 2024 Total Solar Eclipse appeared first on Sky & Telescope.

Location: Engineering Library- TJ163.2.N49 2016

Location: Electronic Resource- 

I don't realize it until I'm standing at the base of the steps of the United Brethren Church in Elberton, but I've made the hourlong drive from Spokane to the Whitman County ghost town on a Sunday…

Crammed in a narrow canyon of North Idaho's Silver Valley, in perhaps one of the most inconvenient but also beautiful places for a hub of human habitation, are the rusted remains of a once-lively mountain mine town…

Hatching a plan for an 8-10ish week, self-contained, van-based cross-country solo journey in 2024 while maintaining a work schedule that absolutely requires me to be connected and on video for scheduled calls every workday. Now in the brainstorming and resource-gathering stages and open to creative ideas and tools. The short version:
Because I'm a worker bee and cannot take all of this time off, I feel like anything like this needs to be fairly well structured, with a good idea of where I plan to land most of the time. This is a really non-specific post, and I welcome all thoughts around apps (e.g., Google Maps with pins, VanAlert, iOverlander, Facebook groups) or other online resources or advice, that will help me plan and execute this.

In brief, the 39yo vanagon has a 100ah LiPo aux battery, a WeBoost cel booster, a fridge, propane heat, a kill switch and good mountain tires. She has a new-ish engine and my dearly departed husband was building her out for work-travel. I'm already set up to plug in and work comfortably from the back seat for a couple of days at a time.

The nitty gritty...
About trip planning:
-starting in the PNW and hoping to route thru New England and California;
-no specific time frame in mind, though I would like to avoid intense heat (no a/c) and extended days below freezing... off the cuff and since summers in the PNW are beautiful, it might be great to stay here and enjoy it while working out kinks with the van, and leave mid August. Loosely aim for a New England fall, down to the Carolinas, return (also loosely) via TN, KY, NM, AZ, and then San Diego and north;
-I'd like to largely avoid interstates, driving in the dark and more than 300-mile days;
-I plan to develop a rough itinerary around the results of outreach to my friend network via social media to ask who would like a visit. Something like: "hey friends, I'm exploring the idea of a big road trip in 2024 and want to know if you'd like a visitor." I would include some language around the fact that I have to work, and probe for what kind of visit they would like, if they could accommodate me and the van, if I could stay/play/work in their house, and if not do they have flat and safe off-street parking, access to an outlet, etc. Your ideas welcome around the framing of that post;
-for the parts of the trip that don't involve friends, I will seek out safe and beautiful camping destinations, stealth camping as needed, forest/BLM land, options that wrap in nature and beauty and hiking and making new friends, iOverlander solutions, driveway camping invitations (I know of just a couple van and women's networks that encourage this), etc;
-I really have zero interest in camping at Walmarts, Cracker Barrels, casinos, truck stops, etc., but I know it's a thing and I will if that's my best and safest option in the moment;
-I have an iPhone and general comfort with tech... is my best bet to create a Google map with pins, or is there something better? Any additional considerations if I would like to wrap in social media to share about my trip?
-I'd kind of love to learn more about driveway camping networks, where people add themselves to a map and welcome travelers to a safe camping spot and a friendly connection. I like meeting people who like meeting people;
-I am aware of networks like trustedhousesitters.com and would be open to engagements like that as I move about.

More about the van:
-I have been setting aside a little fund to add things this year like a suitcase solar panel that trickle charges the auxiliary battery. I don't quite know how that all works, but there are lots of resources out there to figure this out;
-Starlink? I can never not be available to connect for a video call on a workday, I pay extra on my cell phone to use it as hotspot, but that relies on excellent cellular connectivity (the WeBoost typically gets me one extra bar, but often that's not enough. I don't really know if it's supposed to do better than that).

About security:
-the van has a kill switch to reduce the chance of vehicle theft, but of course this does nothing to prevent breakins, theft and vandalization. There is a locking strongbox between the seats to hold my electronics and cash, and a hitchsafe to hold extra keys, ID and cash. I'm thinking I should hide an AirTag or have some other kind of tracking mechanism;
-I don't carry a gun and really don't want to. I have bear spray. I have thought that a trip like this might call for a small InReach or some other gps tracking device;
-as much as I would like to explore urban areas, I would be worried about the van. in the absence of a safe place to park, probably I will base the van outside of a city and take public transit in to be a tourist.

About me:
-50s, fairly extroverted, lover of outdoors, adventurous, though still new to widowhood and discovering a new timidity around taking risks without my adventure partner at my side;
-have driven solo across the country three times, but that was more than 25 years ago and all in less than 10 days;
-not self-employed. I work full-time from my laptop, with a balance of heads-down work and regularly scheduled calls. I also have a fair amount of flexibility in scheduling my day. I'm planning to stretch my PTO around 3- and 4-day weekends when friends have time to play or if I am wanting to linger and explore. I can also imagine on occasion driving for a couple of hours between meetings in the day and making up for it after it's dark and I'm parked;
-not a mechanic, though I can change oil, tires and filters, look up YouTube solutions and follow basic directions (like yesterday, changing an o-ring on my power steering pump). I do plan to take measures in the next year to learn more of the basics of mechanical troubleshooting;
-possess general common sense around safety, and want to take precautions. No plans to install an alarm system or a dash cam.

This is an unreasonably long post, I know. But I figured it couldn't hurt. Seeking your favorite resources for such a trip, your best advice, what do I need to know, what should I be thinking of, etc.

Washtenaw County has elected its next Water Resources Commissioner. Evan Pratt decided against running for re-election after serving four terms. Former Saline Mayor and State Representative Gretchen Driskell won the race. She joined WEMU's David Fair to discuss the priorities and challenges of the new job.

Foreign scientists working in small island states need to create better collaborations with local researchers and marine management entities if coral reefs, fish, and other marine resources are to be saved from irreversible degradation, according to a new opinion paper published by researchers from the Caribbean, Canada, the USA, and UK. The opinion, published last […]

As a result of the devastating earthquake in Japan early this morning, National Geographic has received requests for maps that show the impacted region. Below is a complete list of titles that are currently available:

1. Japan and Korea Wall Map

2. World Ocean Floor Wall Map

3. Hawaii State Wall Map

4. Alaska State Wall Map

4. World Classic Pacific Centered

5. Oregon State Wall Map

6. California State Wall Map

7. Washington State Wall Map

As this event further unfolds, we shall update the map resources list accordingly.

Italy offers a broad range of opportunities for healthcare professionals who seek career advancement. Whether you are a nurse, physiotherapist, or lab technician, various resources help you grow and specialize. This guide outlines the top options available, helping you navigate your way to leadership roles or more specialized functions in healthcare. Key Points A master’s ... Read more

The post Top Career Advancement Resources for Healthcare Professionals appeared first on Star Two.

From the ancient origins of zero to the paradox of motion, NOVA’s teaching resources immerse students in the wonder of math.

Bolster learning for middle and high school students about the myriad ways our weather is changing, how communities are being impacted, and innovative solutions.

Find everything you need for the April 8 total solar eclipse here, including eclipse glasses, event registration links, and educational resources.

Informational text — resources whose purpose is to inform — is essential to daily life and fundamental to literacy. Unfortunately, young children typically have limited exposure to informational text. Two 9-week randomized controlled trials with 263 first-grade children from low-income communities examined whether free educational videos and digital games from the PBS KIDS show “Molly of Denali” supported children’s ability to use informational text to answer real-world questions. Study 1 found significant positive intervention impacts on child outcomes; Study 2 replicated these findings.

Adjudicated rapist and convicted felon Donald Trump chose to politicize the Federal response to Hurricane Helene, demonstrating little concern about the actual devastation.

Responsible leaders who care about the people they govern do not leap into every photo opportunity they can find. — Read the rest

The post Trump lies, sows division, and wastes recovery resources as Americans suffer appeared first on Boing Boing.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a plasma membrane anion channel that plays a key role in controlling transepithelial fluid movement. Excessive activation results in intestinal fluid loss during secretory diarrheas, whereas CFTR mutations underlie cystic fibrosis (CF). Anion permeability depends both on how well CFTR channels work (permeation/gating) and on how many are present at the membrane. Recently, treatments with two drug classes targeting CFTR—one boosting ion-channel function (potentiators) and the other increasing plasma membrane density (correctors)—have provided significant health benefits to CF patients. Here, we present an image-based fluorescence assay that can rapidly and simultaneously estimate both CFTR ion-channel function and the protein's proximity to the membrane. We monitor F508del-CFTR, the most common CF-causing variant, and confirm rescue by low temperature, CFTR-targeting drugs and second-site revertant mutation R1070W. In addition, we characterize a panel of 62 CF-causing mutations. Our measurements correlate well with published data (electrophysiology and biochemistry), further confirming validity of the assay. Finally, we profile effects of acute treatment with approved potentiator drug VX-770 on the rare-mutation panel. Mapping the potentiation profile on CFTR structures raises mechanistic hypotheses on drug action, suggesting that VX-770 might allow an open-channel conformation with an alternative arrangement of domain interfaces. The assay is a valuable tool for investigation of CFTR molecular mechanisms, allowing accurate inferences on gating/permeation. In addition, by providing a two-dimensional characterization of the CFTR protein, it could better inform development of single-drug and precision therapies addressing the root cause of CF disease.

The UK needs to address growth and debt problems if it is to match resources to ambitions on international priorities Expert comment LJefferson 5 November 2024

The budget marks the lowest amount in decades the country has spent on development, and it is struggling to fund other international priorities too.

The UK’s Chancellor Rachel Reeves unveiled her much-anticipated budget last week, the first of the new Labour government. Labour is in a difficult place. There are numerous calls on the public purse and public services are not performing well. Meanwhile, public debt remains close to 100 per cent of GDP, and there has been a long run of sluggish growth.
 
Reeves argues with some justification that the previous government left her a challenging inheritance – gaps in this year’s spending plans, and persistent debt questions left unresolved. More importantly, there are longer-term concerns about the sustainability of UK public spending – the country’s Office for Budget Responsibility has warned public debt could triple by the 2070s due to an ageing population, the climate crisis, and security risks. The focus has understandably been on kitchen table questions about tax rises and funding public services.
 
But this picture also has longstanding implications for international policy – on whether the UK can afford to invest in its foreign policy. The Chancellor did announce an increase of £2.9bn for defence. But the question of whether the UK can get on a sustainable path to spending 2.5 per cent of GDP on defence is still being worked through in the ongoing Strategic Review, and remains challenging despite increasingly urgent warnings from parliamentary committees about the UK’s defence readiness.

The budget also marks one of the lowest amounts in recent years the UK will spend on development overseas, despite setting an ambition to reset relations with the Global South and recover the UK’s role as a leader in international development.
  
The UK needs to either match resources to ambition, spend much more efficiently, or, in the case of the aid budget, it could seek to focus on priorities that are less dependent on spending. But even this will still require consistent resources, alongside significant diplomatic attention, intellectual leadership, and focus.

Longer-term, the UK may need to consider larger questions: addressing broader problems with its lack of growth and productivity will be critical to fund an expansive international role.

With this budget, UK aid spent overseas is at a historic low

In 2020 the UK government cut its goal for spending on international development to 0.5 per cent of Gross National Income (GNI), ending a longstanding policy of spending 0.7 per cent. Labour have echoed this, promising to only return to previous levels when fiscal circumstances allow.
 
But this masks a bigger issue. Since 2022, significant amounts of the UK’s aid budget have been spent on accommodation for asylum seekers in the UK. This is within the rules governing aid, but reduces the amount spent on reducing poverty overseas. In 2023 this spending was 28 per cent of the £15.4bn aid budget. In 2016, it was 3.2 per cent. 

Previous Chancellor Jeremy Hunt quietly allowed a top-up of aid spending over the last two fiscal years to offset how much is being spent at home on asylum seeker accommodation. That provided an additional £2.5 billion for 2022–23 and 2023–24.

But Rachel Reeves declined to provide extra funding this time, meaning the amount being spent overseas is likely the lowest its been since 2007 – an effective cut – under a Labour government.

The Minister for Development, Anneliese Dodds, speaking at Chatham House last month, said the government is working on clearing the backlog of asylum claims, which should free up more to spend overseas.

But beyond this there has been little clarity on plans to address the issue. And costs for asylum seeker accommodation have increased significantly – the UK appears to spend much more than comparator countries per head, according to the Center for Global Development, raising questions about how this spending is managed.

Development is not just about money – but money is important

The UK debate about development has often focused on the 0.7 per cent figure, which can distract from larger questions about what development policy is intended to achieve. As many experts have argued, development aid is about more than spending, and the wider, complex process by which the UK contributes to broad-based growth and stability for poorer countries is not about hitting a specific number.
 
There are things the UK can do that aren’t about spending more directly. This might include focusing on priorities like reforming multilateral development banks so they provide more low-cost public finance, and more flexible and agile loans to poorer countries – a priority echoed by Dodds. It might also incorporate focusing more broadly on helping developing countries attract more investment to bolster growth. 

There is also the issue of developing country debt, much of which is held by the private sector. Dodds previously said, when she was shadow chancellor, she might consider changing the law to address this issue. However,  she declined to recommit to this when questioned at Chatham House. 

None of this can be done unilaterally – on debt, for example, the UK has spearheaded some creative policies. Its UK Export Finance body developed climate-resilient debt clauses – agreements that countries can pause debt repayments in the event of a climate shock – but the UK holds limited amounts of developing country debt. Impact will only come by galvanizing and coordinating others to adopt similar approaches.

Chatham House appoints Tim Benton as Research Director for Energy, Environment and Resources News Release sysadmin 30 May 2019

Chatham House is pleased to announce that Professor Tim Benton has been appointed as research director of the Energy, Environment and Resources Department.

Time: 10:00 AM, Location: E1.012 (Hearing Room)

TNF is a highly pro-inflammatory cytokine that contributes not only to the regulation of immune responses but also to the development of severe inflammatory diseases. TNF is synthesized as a transmembrane protein, which is further matured via proteolytic cleavage by metalloproteases such as ADAM17, a process known as shedding. At present, TNF is mainly detected by measuring the precursor or the mature cytokine of bulk cell populations by techniques such as ELISA or immunoblotting. However, these methods do not provide information on the exact timing and extent of TNF cleavage at single-cell resolution and they do not allow the live visualization of shedding events. Here, we generated C-tag TNF as a genetically encoded reporter to study TNF shedding at the single-cell level. The functionality of the C-tag TNF reporter is based on the exposure of a cryptic epitope on the C terminus of the transmembrane portion of pro-TNF on cleavage. In both denatured and nondenatured samples, this epitope can be detected by a nanobody in a highly sensitive and specific manner only upon TNF shedding. As such, C-tag TNF can successfully be used for the detection of TNF cleavage in flow cytometry and live-cell imaging applications. We furthermore demonstrate its applicability in a forward genetic screen geared toward the identification of genetic regulators of TNF maturation. In summary, the C-tag TNF reporter can be employed to gain novel insights into the complex regulation of ADAM-dependent TNF shedding.

Managing natural resources

Research analyzing options for the sustainable management of natural resources and how to use them in a way that enhances the resilience of ecosystems.

Areas of focus include examining what is the future for fossil fuels and other extractive industries (especially coal, oil and natural gas), forest governance in light of continued illegal logging and deforestation, and ocean governance.

Natural resources are vital for the future sustainability of major industries such as agriculture, mining, tourism, fisheries and forestry. Research is carried out in areas such as land use planning, water management, biodiversity conservation, and the scientific and technical understanding of resources governance.

The dimeric ectonucleotidase CD73 catalyzes the hydrolysis of AMP at the cell surface to form adenosine, a potent suppressor of the immune response. Blocking CD73 activity in the tumor microenvironment can have a beneficial effect on tumor eradication and is a promising approach for cancer therapy. Biparatopic antibodies binding different regions of CD73 may be a means to antagonize its enzymatic activity. A panel of biparatopic antibodies representing the pairwise combination of 11 parental monoclonal antibodies against CD73 was generated by Fab-arm exchange. Nine variants vastly exceeded the potency of their parental antibodies with ≥90% inhibition of activity and subnanomolar EC50 values. Pairing the Fabs of parents with nonoverlapping epitopes was both sufficient and necessary whereas monovalent antibodies were poor inhibitors. Some parental antibodies yielded potent biparatopics with multiple partners, one of which (TB19) producing the most potent. The structure of the TB19 Fab with CD73 reveals that it blocks alignment of the N- and C-terminal CD73 domains necessary for catalysis. A separate structure of CD73 with a Fab (TB38) which complements TB19 in a particularly potent biparatopic shows its binding to a nonoverlapping site on the CD73 N-terminal domain. Structural modeling demonstrates a TB19/TB38 biparatopic antibody would be unable to bind the CD73 dimer in a bivalent manner, implicating crosslinking of separate CD73 dimers in its mechanism of action. This ability of a biparatopic antibody to both crosslink CD73 dimers and fix them in an inactive conformation thus represents a highly effective mechanism for the inhibition of CD73 activity.

Protein quality control is maintained by a number of integrated cellular pathways that monitor the folding and functionality of the cellular proteome. Defects in these pathways lead to the accumulation of misfolded or faulty proteins that may become insoluble and aggregate over time. Protein aggregates significantly contribute to the development of a number of human diseases such as amyotrophic lateral sclerosis, Huntington's disease, and Alzheimer's disease. In vitro, imaging-based, cellular studies have defined key biomolecular components that recognize and clear aggregates; however, no unifying method is available to quantify cellular aggregates, limiting our ability to reproducibly and accurately quantify these structures. Here we describe an ImageJ macro called AggreCount to identify and measure protein aggregates in cells. AggreCount is designed to be intuitive, easy to use, and customizable for different types of aggregates observed in cells. Minimal experience in coding is required to utilize the script. Based on a user-defined image, AggreCount will report a number of metrics: (i) total number of cellular aggregates, (ii) percentage of cells with aggregates, (iii) aggregates per cell, (iv) area of aggregates, and (v) localization of aggregates (cytosol, perinuclear, or nuclear). A data table of aggregate information on a per cell basis, as well as a summary table, is provided for further data analysis. We demonstrate the versatility of AggreCount by analyzing a number of different cellular aggregates including aggresomes, stress granules, and inclusion bodies caused by huntingtin polyglutamine expansion.

Mitochondrial DNA (mtDNA) encodes proteins and RNAs that support the functions of mitochondria and thereby numerous physiological processes. Mutations of mtDNA can cause mitochondrial diseases and are implicated in aging. The mtDNA within cells is organized into nucleoids within the mitochondrial matrix, but how mtDNA nucleoids are formed and regulated within cells remains incompletely resolved. Visualization of mtDNA within cells is a powerful means by which mechanistic insight can be gained. Manipulation of the amount and sequence of mtDNA within cells is important experimentally and for developing therapeutic interventions to treat mitochondrial disease. This review details recent developments and opportunities for improvements in the experimental tools and techniques that can be used to visualize, quantify, and manipulate the properties of mtDNA within cells.

Ion mobility brings an additional dimension of separation to LC–MS, improving identification of peptides and proteins in complex mixtures. A recently introduced timsTOF mass spectrometer (Bruker) couples trapped ion mobility separation to TOF mass analysis. With the parallel accumulation serial fragmentation (PASEF) method, the timsTOF platform achieves promising results, yet analysis of the data generated on this platform represents a major bottleneck. Currently, MaxQuant and PEAKS are most used to analyze these data. However, because of the high complexity of timsTOF PASEF data, both require substantial time to perform even standard tryptic searches. Advanced searches (e.g. with many variable modifications, semi- or non-enzymatic searches, or open searches for post-translational modification discovery) are practically impossible. We have extended our fast peptide identification tool MSFragger to support timsTOF PASEF data, and developed a label-free quantification tool, IonQuant, for fast and accurate 4-D feature extraction and quantification. Using a HeLa data set published by Meier et al. (2018), we demonstrate that MSFragger identifies significantly (~30%) more unique peptides than MaxQuant (1.6.10.43), and performs comparably or better than PEAKS X+ (~10% more peptides). IonQuant outperforms both in terms of number of quantified proteins while maintaining good quantification precision and accuracy. Runtime tests show that MSFragger and IonQuant can fully process a typical two-hour PASEF run in under 70 min on a typical desktop (6 CPU cores, 32 GB RAM), significantly faster than other tools. Finally, through semi-enzymatic searching, we significantly increase the number of identified peptides. Within these semi-tryptic identifications, we report evidence of gas-phase fragmentation before MS/MS analysis.

Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.

In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic proteins and low-abundance proteins, which play critical roles in signaling networks, are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously satisfy the requirements on strong solubilizing ability to membrane proteins and good enzyme compatibility. Thus, it is urgent to screen out ideal extractant from the huge compound libraries in a fast and effective way. Herein, by investigating the interior mechanism of extractants on the membrane proteins solubilization and trypsin compatibility, a molecular dynamics simulation system was established as complement to the experimental procedure to narrow down the scope of candidates for proteomics analysis. The simulation data shows that the van der Waals interaction between cation group of ionic liquid and membrane protein is the dominant factor in determining protein solubilization. In combination with the experimental data, 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) is on the shortlist for the suitable candidates from comprehensive aspects. Inspired by the advantages of C12Im-Cl, an ionic liquid-based filter-aided sample preparation (i-FASP) method was developed. Using this strategy, over 3,300 proteins were confidently identified from 10³ HeLa cells (~100 ng proteins) in a single run, an improvement of 53% over the conventional FASP method. Then the i-FASP method was further successfully applied to the label-free relative quantitation of human liver cancer and para-carcinoma tissues with obviously improved accuracy, reproducibility and coverage than the commonly used urea-based FASP method. The above results demonstrated that the i-FASP method could be performed as a versatile tool for the in-depth coverage proteomic analysis of biological samples.

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.

Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared with other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Because of efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of noncleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a data set from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenPepXL finds from 7% to over 50% more unique residue pairs (URPs) than other tools. On data sets with available high-resolution structures for cross-link validation OpenPepXL reports from 7% to over 40% more structurally validated URPs than other tools. Additionally, we used a synthetic peptide data set that allows objective validation of cross-links without relying on structural information and found that OpenPepXL reports at least 12% more validated URPs than other tools. It has been built as part of the OpenMS suite of tools and supports Windows, macOS, and Linux operating systems. OpenPepXL also supports the MzIdentML 1.2 format for XL-MS identification results. It is freely available under a three-clause BSD license at https://openms.org/openpepxl.

Trypsin is the protease of choice in bottom-up proteomics. However, its application can be limited by the amino acid composition of target proteins and the pH of the digestion solution. In this study we characterize ProAlanase, a protease from the fungus Aspergillus niger that cleaves primarily on the C-terminal side of proline and alanine residues. ProAlanase achieves high proteolytic activity and specificity when digestion is carried out at acidic pH (1.5) for relatively short (2 h) time periods. To elucidate the potential of ProAlanase in proteomics applications, we conducted a series of investigations comprising comparative multi-enzymatic profiling of a human cell line proteome, histone PTM analysis, ancient bone protein identification, phosphosite mapping and de novo sequencing of a proline-rich protein and disulfide bond mapping in mAb. The results demonstrate that ProAlanase is highly suitable for proteomics analysis of the arginine- and lysine-rich histones, enabling high sequence coverage of multiple histone family members. It also facilitates an efficient digestion of bone collagen thanks to the cleavage at the C terminus of hydroxyproline which is highly prevalent in collagen. This allows to identify complementary proteins in ProAlanase- and trypsin-digested ancient bone samples, as well as to increase sequence coverage of noncollagenous proteins. Moreover, digestion with ProAlanase improves protein sequence coverage and phosphosite localization for the proline-rich protein Notch3 intracellular domain (N3ICD). Furthermore, we achieve a nearly complete coverage of N3ICD protein by de novo sequencing using the combination of ProAlanase and tryptic peptides. Finally, we demonstrate that ProAlanase is efficient in disulfide bond mapping, showing high coverage of disulfide-containing regions in a nonreduced mAb.

Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS²) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS² data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC–MS measurements. Peptide masses are then extracted from MS¹ data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient – less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS¹ peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.

Pathway analyses are key methods to analyze 'omics experiments. Nevertheless, integrating data from different 'omics technologies and different species still requires considerable bioinformatics knowledge.

Here we present the novel ReactomeGSA resource for comparative pathway analyses of multi-omics datasets. ReactomeGSA can be used through Reactome's existing web interface and the novel ReactomeGSA R Bioconductor package with explicit support for scRNA-seq data. Data from different species is automatically mapped to a common pathway space. Public data from ExpressionAtlas and Single Cell ExpressionAtlas can be directly integrated in the analysis. ReactomeGSA greatly reduces the technical barrier for multi-omics, cross-species, comparative pathway analyses.

We used ReactomeGSA to characterize the role of B cells in anti-tumor immunity. We compared B cell rich and poor human cancer samples from five of the Cancer Genome Atlas (TCGA) transcriptomics and two of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteomics studies. B cell-rich lung adenocarcinoma samples lacked the otherwise present activation through NFkappaB. This may be linked to the presence of a specific subset of tumor associated IgG+ plasma cells that lack NFkappaB activation in scRNA-seq data from human melanoma. This showcases how ReactomeGSA can derive novel biomedical insights by integrating large multi-omics datasets.

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.

Governors in several natural resource-dependent states said recently they will have to continue to cut public education funding because prices for oil and coal have not rebounded.

These tools encourage school administrators to gather as much information as possible about the students who will be entering kindergarten and the early-learning offerings in their communities.

Governors in several natural resource-dependent states said recently they will have to continue to cut public education funding because prices for oil and coal have not rebounded.

Resource Mobilization (RM) has replaced the term fundraising as it expanded to account for not only funds but also human resources, goods and services. It is a fundamental component of [...]

Informal Seminar: Human resources policies - Invitation for all Permanent Representatives

 Friday, 12 October 2018 - 15.00 to 17.30 (Green Room)

Ahead of the Food Systems Summit, join the Publications team to find out more about where to find FAO publications, the different formats available, how you can re-use the [...]

Ahead of the Food Systems Summit, join the Publications team to find out more about where to find FAO publications, the different formats available, how you can re-use the [...]