MaskOCR: Text Recognition with Masked Encoder-Decoder Pretraining

Text images contain both visual and linguistic information. However, existing pre-training techniques for text recognition mainly focus on either visual representation learning or linguistic knowledge learning. In this paper, we propose a novel approach MaskOCR to unify vision and language pre-training in the classical encoder-decoder recognition framework. We adopt the masked image modeling approach to pre-train the feature encoder using a large set of unlabeled real text images, which allows us to learn strong visual representations. In contrast to introducing linguistic knowledge with an additional language model, we directly pre-train the sequence decoder. Specifically, we transform text data into synthesized text images to unify the data modalities of vision and language, and enhance the language modeling capability of the sequence decoder using a proposed masked image-language modeling scheme. Significantly, the encoder is frozen during the pre-training phase of the sequence decoder. Experimental results demonstrate that our proposed method achieves superior performance on benchmark datasets, including Chinese and English text images

Maleic anhydride-modified chicken ovalbumin as an effective and inexpensive anti-HIV microbicide candidate for prevention of HIV sexual transmission

<p>Abstract</p> <p>Background</p> <p>Previous studies have shown that 3-hydroxyphthalic anhydride (HP)-modified bovine milk protein, β-lactoglobulin (β-LG), is a promising microbicide candidate. However, concerns regarding the potential risk of prion contamination in bovine products and carcinogenic potential of phthalate derivatives were raised. Here we sought to replace bovine protein with an animal protein of non-bovine origin and substitute HP with another anhydride for the development of anti-HIV microbicide for preventing HIV sexual transmission.</p> <p>Results</p> <p>Maleic anhydride (ML), succinic anhydride (SU) and HP at different conditions and variable pH values were used for modification of proteins. All the anhydrate-modified globulin-like proteins showed potent anti-HIV activity, which is correlated with the percentage of modified lysine and arginine residues in the modified protein. We selected maleic anhydride-modified ovalbumin (ML-OVA) for further study because OVA is easier to obtain than β-LG, and ML is safer than HP. Furthermore, ML-OVA exhibited broad antiviral activities against HIV-1, HIV-2, SHIV and SIV. This modified protein has no or low <it>in vitro </it>cytotoxicity to human T cells and vaginal epithelial cells. It is resistant to trypsin hydrolysis, possibly because the lysine and arginine residues in OVA are modified by ML. Mechanism studies suggest that ML-OVA inhibits HIV-1 entry by targeting gp120 on HIV-1 virions and also the CD4 receptor on the host cells.</p> <p>Conclusion</p> <p>ML-OVA is a potent HIV fusion/entry inhibitor with the potential to be developed as an effective, safe and inexpensive anti-HIV microbicide.</p

Amino-functionalized macroporous silica for efficient tryptic digestion in acidic solutions

Amino-functionalized macroporous silica foam (NH2-MOSF) has been developed as a host reactor to realize highly efficient proteolysis in acidic solutions where normal tryptic reactions cannot occur. The digestion protocol consists simply of adding the functionalized NH2-MOSF into the protein and trypsin solutions without altering the bulk pH or preloading the enzymes on the materials. With this protocol, digestion of sample fractions from LC can be efficiently realized in the acidic solutions directly. Digestion of a protein fraction extracted from rat liver tissue after LC separation was performed to illustrate this principle, where 103 proteins were successfully identified at pH 3 after 1.5 h of tryptic digestion

Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry

A versatile microreactor protocol based on microfluidic droplets has been developed for on-line protein digestion. Proteins separated by liquid chromatography are fractionated in water-in-oil droplets and digested in sequence. The microfluidic reactor acts also as an electrospray ionization emitter for mass spectrometry analysis of the peptides produced in the individual droplets. Each droplet is an enzymatic micro-reaction unit with efficient proteolysis due to rapid mixing, enhanced mass transfer and automated handling. This droplet approach eliminates sample loss, cross-contamination, non-specific absorption and memory effect. A protein mixture was successfully identified using the droplet-based micro-reactor as interface between reverse phase liquid chromatography and mass spectrometry

A nanoporous reactor for efficient proteolysis

A nanoreactor based on mesoporous silicates is described for efficient tryptic digestion of proteins within the mesochannels. Cyano-functionalized mesoporous silicate (CNS), with an average pore diameter of 18 nm, is a good support for trypsin, with rapid in situ digestion of the model proteins, cytochrome c and myoglobin. The generated peptides were analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Proteolysis by trypsin-CNS is much more efficient than in-solution digestion, which can be attributed to nanoscopic confinement and concentration enrichment of the substrate within the mesopores. Proteins at concentrations of 2 ng μL−1 were successfully identified after digestion for 20 min. A biological complex sample extracted from the cytoplasm of human liver tissue was digested by using the CNS-based reactor. Coupled with reverse-phase HPLC and MALDI-TOF MS/MS, 165 proteins were identified after standard protein data searching. This nanoreactor combines the advantages of short digestion time with retention of enzymatic activity, providing a promising way to advance the development of proteomics

Plate for matrix-assisted laser desorption ionization mass spectrometry for, e.g. analyzing peptide, has substrate that is covered with light sensitive matrix with light absorber, charge carrier, probe molecule and photo-sensitizer

NOVELTY - The plate has electrically conductive substrate (1) that is covered with light sensitive matrix (2). The matrix comprises light absorber, charge carrier, probe molecule and photo-sensitizer (3) arranged to oxidize probe molecule by irradiation of light from light source (4). The absorber and carrier comprise crystalline acid. The matrix comprises hybrid organic-inorganic gel, and xerogel. USE - Plate for matrix-assisted laser desorption ionization (MALDI) mass spectrometry for analyzing biomolecules such as peptide by structurally determining oxidation products of probe molecules (claimed) and the products of successive reactions involving the oxidation products of the probe molecules, and for screening and evaluation of anti-oxidants and drugs, and studying metabolic pathway in biological processes. ADVANTAGE - The structural determination of oxidation product of probe molecule can be enabled. DETAILED DESCRIPTION - An INDEPENDENT CLAIM is included for method for preparing plate. DESCRIPTION OF DRAWING(S) - The drawing shows the schematic view of photo-reactive MALDI plate. Substrate (1) Light sensitive matrix (2) Photo-sensitizer (3) Light source (4) Portion of matrix (5

TiO2-modified macroporous silica foams for advanced enrichment of multi-phosphorylated peptides

Novel TiO2-modified macroporous materials (Ti-MOSF, see figure) have been synthesized with high surface area, large pore volume, and functional surfaces that are rich in coordinatively unsaturated TiIV species, which can be applied in the specific extraction of phosphopeptides and which show a preferential capture of multi-phosphorylated peptides with low detection limits and high selectivity

Plate for matrix-assisted laser desorption ionization mass spectrometry, comprises electroconductive substrate covered with sintered nanoparticles, deposited as array of spots, for supporting ionization of sorbed sample molecules

NOVELTY - A plate comprises an electroconductive substrate (1) at least partially covered with sintered nanoparticles (2), deposited as an array of individual spots, for use as a sorbing phase for a sample, and for supporting ionization of sorbed sample molecules covered by or present in an overlayer or matrix. The overlayer or matrix comprises a light absorber and/or a charged carrier acid. USE - Plate is used for matrix-assisted laser desorption ionization mass spectrometry analysis of molecules or reaction products (oxidized or reduced) of molecules, such as oligomers, oligosaccharides and biomolecules e.g. peptides, oligonucleotides (all claimed), proteins, and DNA. Can also be used for tagging reactions, disulfide bridge reductions, and ion source decay reactions. ADVANTAGE - The plate provides a very efficient tool to analyze biomolecules by mass spectrometry and to study the products of photo-induced electron transfer reactions. DETAILED DESCRIPTION - A plate comprises an electroconductive substrate at least partially covered with sintered nanoparticles, deposited as an array of individual spots, for use as a sorbing phase for a sample, and for supporting ionization of sorbed sample molecules covered by or present in an overlayer or matrix. The overlayer or matrix comprises a light absorber and/or a charged carrier acid. The nanoparticles are made of titania, alumina, zinc oxide, silica, ferrous oxide, zirconia, and/or niobium oxide. Or, the nanoparticles are quantum dots, such as cadmium sulfide, cadmium selenide, zinc oxide, or materials which can be photosensitized. The sorbing nanoparticles are derivatized by hydrophobic molecules to specifically bind other hydrophobic molecules, such as peptides. The electroconductive substrate comprises stainless steel, aluminum, nickel, zinc, copper, silicon, tin-indium oxide on glass, or conductive/semi-conductive polymer. INDEPENDENT CLAIMS are included for the following: (1) preparation method of plate; and (2) usage method of plate. DESCRIPTION OF DRAWING(S) - The drawing shows a schematic view of the plate. Electroconductive substrate (1) Sintered nanoparticles (2) Laser (3) Material including molecules from sample (4

Multifunctional Nanoreactor for Comprehensive Characterization of Membrane Proteins Based on Surface Functionalized Mesoporous Foams

An integrated protocol is proposed here for efficient analysis of membrane proteins based on surface functionalized mesoporous graphene foams (MGF). The inherent hydrophobic nature of MGF and surface modification with hydrophilic chitosan (CS) make it highly suitable for the enrichment of hydrophobic membrane proteins from organic solvent, while remaining well-dispersed in aqueous solution for subsequent proteolysis. Therefore, such a multifunctional reactor ensures a facile solvent adjustment route. Furthermore, as a chitosan modified nanoporous reactor, it also provides a biocompatible nanoenvironment that can maintain the stability and activity of enzymes to realize efficient <i>in situ</i> digestion of the enriched membrane proteins. The concept was first proved with a standard hydrophobic membrane protein, bacteriorhodopsin, where a high number of identified peptides and amino acid sequence coverage were achieved even at extremely low protein concentration. The mesoporous reaction system was further applied to the analysis of complex real-case proteome samples, where 931 membrane proteins were identified in triplicate analyses by 2D LC-MS/MS. In contrast, with in-solution proteolysis, only 73 membrane proteins were identified from the same sample by the same 2D LC-MS/MS. The identified membrane proteins by the MGF-CS protocol include many biomarkers of the cell line. These results suggest that the multifunctional MGF-CS protocol is of great value to facilitate the comprehensive characterization of membrane proteins in the proteome research

Polydopamine Grafted Porous Graphene as Biocompatible Nanoreactor for Efficient Identification of Membrane Proteins

Functional nanomaterials, used as nanoreactors, have shown great advantages in a variety of applications in biomedical fields. Herein, we designed a novel nanoreactor system toward the application in membrane proteomics by using polydopamine-coated nanoporous graphene foams (NGFs-PD) prepared by a facile <i>in situ</i> oxidative polymerization. Taking advantage of the unique 3-D structure and surface functionalization, NGFs-PD can quickly adsorb a large amount of hydrophobic membrane proteins dissolved in sodium dodecyl sulfonate (SDS)/methanol and hydrophilic trypsin in aqueous solution, and then confine the proteolysis in the nanoscale domains to fasten the reaction rate. Therefore, the current nanoreactor system combines the multifunctions of highly efficient solubilization, immobilization, and proteolysis of membrane proteins. With the nanoreactor, digestion of standard membrane proteins can be finished in 10 min. 893 membrane proteins were identified from human glioma cells (U251). All these superiorities indicate that the biocompatible NGFs-PD nanoreactor system is of great promise to facilitate high-throughput membrane proteomic analysis