Browse Articles

Transfer learning in DeepLC improves LC retention time prediction across substantially different modifications and setups

Abstract While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These variations can render retention time prediction models inaccurate and dramatically reduce the value of predictions for identification, validation, and DIA spectral library generation. To date, mitigation of these issues has been attempted through calibration or by training bespoke models for specific experimental setups, with only partial success. We here demonstrate that transfer learning can successfully overcome these limitations by leveraging pre-trained model parameters. Remarkably, this approach can even fit highly performant models to substantially different peptide modifications and LC conditions than those on which the model was originally trained. This impressive adaptability of transfer learning makes it a highly robust solution for accurate peptide retention time prediction across a very wide variety of imaginable proteomics workflows.

A federated deep learning approach for SDN security with quantum optimized feature selection and hybrid MSDC net architecture

XL-MSDigger: a deep learning-based, versatile solution for cross-linking mass spectrometry

Seismic performance of reinforced concrete beam column joints strengthened with ECC shells

Dynamic photochromism in cocrystals and tri-state fluorescence switching in films for multilevel optical encryption

Identifying the shared genes and their related microRNAs, metabolites, and pathways in ischemic stroke and epilepsy

Abstract Background This study aimed to identify shared genes between ischemic stroke (IS) and epilepsy and explore underlying mechanisms. Methods Transcriptomic datasets from the GEO database were analyzed using differential expression and weighted gene co-expression network analysis (WGCNA). Hub-shared genes were identified through protein-protein interaction networks, ROC analysis, and expression validation. Upstream miRNAs were predicted. Additionally, untargeted plasma metabolomics was performed on children with epilepsy and healthy controls, followed by differential metabolite analysis and metabolic pathway construction. Results WGCNA revealed 594 epilepsy-related and 2,623 IS-related DEGs, with 38 shared DEGs identified, including IL10RA, CD2, and C3AR1. These genes showed high diagnostic value, with their AUC value > 0.66 in both training and validation datasets. Additionally, hsa-let-7b-5p was predicted to target C3AR1. Metabolomics identified 139 differential metabolites, and C3AR1 was implicated in synaptic vesicle cycle, taste transduction, and nicotine addiction pathways via acetylcholine. Conclusions The shared genes, especially C3AR1 may be a key regulator in the development IS and epilepsy, showing potential as a biomarker for both diseases. However, its diagnostic efficacy requires further clinical validation. Given the complexity of these diseases, future research may focus on identifying a panel of biomarkers rather than relying on a single gene.

Dynamic chromium dopant promotes interfacial water activation on cobalt spinel oxide for efficient oxygen evolution in acid

Safety and feasibility of liver maximum capacity assessment in patients undergoing transarterial chemoembolisation for hepatocellular carcinoma

Phosphine-mediated hydrogen bond and phosphorescence energy transfer for tunable chiroptical afterglow in stacked polymers

SAT: shift alignment transformer for video denoising without flow estimation

Seq-Scope-eXpanded: spatial omics beyond optical resolution

Development of a controlled ex vivo human skin platform for quantitative evaluation of age-related functional biomarkers following application of topical treatments

Mutant KRAS vaccine with dual checkpoint blockade in resected pancreatic cancer: a phase I trial

Abstract In this phase I study, we test a pooled synthetic long peptide vaccine targeting the six KRAS mutations (G12V, G12A, G12R, G12C, G12D, G13D) with ipilimumab and nivolumab in resected pancreatic adenocarcinoma. Co-primary endpoints include safety and maximal percent change of IFNγ-producing mutant KRAS T cell responses in the blood within 17 weeks. Secondary endpoints include disease-free survival, overall survival, and maximal percent change of IFNγ-producing mutant KRAS T cell responses at any time after vaccination. Vaccine-related adverse events are grade 1-2. 11/12 and 10/12 patients generate a significant increase in average T cell response to 6 mutant KRAS antigens and tumor-specific response, respectively. Immunophenotyping demonstrate Th1 CD4 central memory and effector memory T cells, and CD8 effector memory T cells at a lower frequency. The vaccine also generates cross-reactive T cells that recognize more than one mutant KRAS antigen. These findings support the safety and diverse anti-tumor immunity of mutant KRAS vaccines (NCT04117087).

meso-2,3-dibromosuccinic acid as a temperature-dependent catalyst for the selective synthesis of syn and anti-highly functionalized tetrahydropyridines: experimental and theoretical study

Laser-stimulated 4D printing of magnetostrictive Fe-Co-V

Study on the damage mechanism of deep ingate lining structure disturbed by cyclic blasting

Enabling water-based high-density nanoparticles assembly by using silk fibroin as an adsorbate

Rupture access to hydrous minerals controls aftershocks in subduction zones

Abstract Aftershock productivity varies widely among subduction-zone earthquakes of similar magnitude. We investigate how slab hydration and rupture geometry modulate access to hydrous minerals and the generation of pressurized fluids from co-seismic frictional heating along the interface between subducting slabs and overriding plates. We describe ten large and major earthquakes (Mw > 6.8) that generated thousands of aftershocks (Mw > 4), and eleven nearby earthquakes of similar magnitude that generated few, if any, aftershocks. Kinematic and petrological constraints reveal that earthquakes producing rich aftershock sequences ruptured along slab interfaces containing serpentinized peridotite and hydrated oceanic crust. By contrast, earthquakes with few aftershocks occurred in flat-slab regions where rupture planes were oblique to the hydrated interface (intraslab events). Oblique rupture reduces the volume of volatile-bearing minerals accessed per unit rupture area, diminishing the pressurized fluid production needed to drive aftershock sequences. Globally, we propose that slab geometry and rupture orientation regulate access to fluid-producing hydrated rocks and thereby control aftershock productivity through co-seismically generated pressurized fluids in subduction zones.

A catalogue of early diverged contemporary human genome variation reveals distinct Khoe-San populations

Lifetime MDMA use and associations with meaning in life in the context of childhood trauma

Abstract Recent research has highlighted the potential of 3,4-methylenedioxymethamphetamine (MDMA)-assisted psychotherapy for the treatment of post-traumatic stress disorder and other trauma-related psychiatric conditions. However, less is known about the effects of MDMA use on psychological well-being in populations with trauma histories outside of clinical contexts. In the present study, we assessed associations between naturalistic lifetime MDMA use (i.e., having ever used MDMA) and an overlooked psychological predictor of resilience – meaning in life. Using data from a survey study of a sample of Swedish adults ( n  = 807), multiple linear regression models were fit to assess associations between lifetime MDMA use and meaning in life, as well as interactions with childhood trauma history. Meaning in life was measured using the presence subscale of the 10-item meaning in life questionnaire (MLQ). While lifetime MDMA use was not significantly associated with meaning in life overall (β = 1.80, p  = 0.055), a significant interaction emerged between lifetime MDMA use and childhood trauma on meaning in life (β = 4.06, p  = 0.012). Specifically, MDMA use was associated with higher meaning in life among individuals with a history of childhood trauma. Together, these associations warrant further longitudinal and experimental research to test whether MDMA exposure relates to changes in meaning in life.