Off-Normal Polarized Single-Photon Emission with Anisotropic Holography Metasurfaces.

Solid-state quantum emitters (QEs) with arbitrary direction emission and well-defined polarization are critical for scalable single-photon sources and quantum information processing. However, the design strategy for on-chip generation of off-normal photon emission with high-purity polarization characteristics has so far remained elusive. Here, we introduce the anisotropic holography metasurfaces for efficiently manipulating the emission direction and polarization of QE.

PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models.

The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare.

Metabolomic and Proteomic Profiling of Athletes Performing Physical Activity under Hypoxic Conditions.

Proteomic and metabolomic research enables quantitation of the molecular profile of athletes. Multiomic profiling was conducted using plasma samples collected from 18 male athletes performing aerobic activity (running) at high altitude. Metabolomic profiling detected changes in the levels of 4-hydroxyproline, methionine, oxaloacetate, and tyrosine during the recovery period.

Analysis of Structural Changes in the Protein near the Phosphorylation Site.

Modification of the protein after synthesis (PTM) often affects protein function as supported by numerous studies. However, there is no consensus about the degree of structural protein changes after modification. For phosphorylation of serine, threonine, and tyrosine, which is a common PTM in the biology of living organisms, we consider topical issues related to changes in the geometric parameters of a protein (Rg, RMSD, C displacement, SASA).

Multiple channelling single-photon emission with scattering holography designed metasurfaces.

Channelling single-photon emission in multiple well-defined directions and simultaneously controlling its polarization characteristics is highly desirable for numerous quantum technology applications. We show that this can be achieved by using quantum emitters (QEs) nonradiatively coupled to surface plasmon polaritons (SPPs), which are scattered into outgoing free-propagating waves by appropriately designed metasurfaces. The QE-coupled metasurface design is based on the scattering holography approach with radially diverging SPPs as reference waves.

Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications.

Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications.

Sub-to-super-Poissonian photon statistics in cathodoluminescence of color center ensembles in isolated diamond crystals.

Impurity-vacancy centers in diamond offer a new class of robust photon sources with versatile quantum properties. While individual color centers commonly act as single-photon sources, their ensembles have been theoretically predicted to have tunable photon-emission statistics. Importantly, the particular type of excitation affects the emission properties of a color center ensemble within a diamond crystal.

PSSNet-An Accurate Super-Secondary Structure for Protein Segmentation.

A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation.

Molecular Dynamics Study of Citrullinated Proteins Associated with the Development of Rheumatoid Arthritis.

Biological activity regulation by protein post-translational modification (PTM) is critical for cell function, development, differentiation, and survival. Dysregulation of PTM proteins is present in various pathological conditions, including rheumatoid arthritis (RA). RA is a systemic autoimmune disease that primarily affects joints, and there are three main types of protein PTMs associated with the development of this disease, namely, glycosylation, citrullination, and carbamylation.

Molecular Modeling Insights into Upadacitinib Selectivity upon Binding to JAK Protein Family.

Rheumatoid arthritis (RA) is a chronic disease characterized by bone joint damage and incapacitation. The mechanism underlying RA pathogenesis is autoimmunity in the connective tissue. Cytokines play an important role in the human immune system for signal transduction and in the development of inflammatory responses.

Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification.

Mass spectrometric profiling provides information on the protein and metabolic composition of biological samples. However, the weak efficiency of computational algorithms in correlating tandem spectra to molecular components (proteins and metabolites) dramatically limits the use of "omics" profiling for the classification of nosologies. The development of machine learning methods for the intelligent analysis of raw mass spectrometric (HPLC-MS/MS) measurements without involving the stages of preprocessing and data identification seems promising.

Current Approaches in Supersecondary Structures Investigation.

Proteins expressed during the cell cycle determine cell function, topology, and responses to environmental influences. The development and improvement of experimental methods in the field of structural biology provide valuable information about the structure and functions of individual proteins. This work is devoted to the study of supersecondary structures of proteins and determination of their structural motifs, description of experimental methods for their detection, databases, and repositories for storage, as well as methods of molecular dynamics research.

Changes in Protein Structural Motifs upon Post-Translational Modification in Kidney Cancer.

Post-translational modification (PTM) leads to conformational changes in protein structure, modulates the biological function of proteins, and, consequently, changes the signature of metabolic transformations and the immune response in the body. Common PTMs are reversible and serve as a mechanism for modulating metabolic trans-formations in cells. It is likely that dysregulation of post-translational cellular signaling leads to abnormal proliferation and oncogenesis.

Proteomic and molecular dynamic investigations of PTM-induced structural fluctuations in breast and ovarian cancer.

Post-translational processing leads to conformational changes in protein structure that modulate molecular functions and change the signature of metabolic transformations and immune responses. Some post-translational modifications (PTMs), such as phosphorylation and acetylation, are strongly related to oncogenic processes and malignancy. This study investigated a PTM pattern in patients with gender-specific ovarian or breast cancer.

Convolutional neural network in proteomics and metabolomics for determination of comorbidity between cancer and schizophrenia.

The association between cancer risk and schizophrenia is widely debated. Despite many epidemiological studies, there is still no strong evidence regarding the molecular basis for the comorbidity between these two pathological conditions. The vast majority of assays have been performed using clinical records of schizophrenic patients or those undergoing cancer treatment and monitored for sufficient time to find shared features between the considered conditions.

Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer.

New advances in protein post-translational modifications (PTMs) have revealed a complex layer of regulatory mechanisms through which PTMs control cell signaling and metabolic pathways, contributing to the diverse metabolic phenotypes found in cancer. Using conformational templates and the three-dimensional (3D) environment investigation of proteins in patients with colorectal cancer, it was demonstrated that most PTMs (phosphorylation, acetylation, and ubiquitination) are localized in the supersecondary structures (helical pairs). We showed that such helical pairs are represented on the outer surface of protein molecules and characterized by a largely accessible area for the surrounding solvent.

On-chip excitation of single germanium vacancies in nanodiamonds embedded in plasmonic waveguides.

Monolithic integration of quantum emitters in nanoscale plasmonic circuitry requires low-loss plasmonic configurations capable of confining light well below the diffraction limit. We demonstrated on-chip remote excitation of nanodiamond-embedded single quantum emitters by plasmonic modes of dielectric ridges atop colloidal silver crystals. The nanodiamonds were produced to incorporate single germanium-vacancy (GeV) centres, providing bright, spectrally narrow and stable single-photon sources suitable for highly integrated circuits.