Lung Cancer Diagnosis on Virtual Histologically Stained Tissue Using Weakly Supervised Learning.

Lung adenocarcinoma (LUAD) is the most common primary lung cancer and accounts for 40% of all lung cancer cases. The current gold standard for lung cancer analysis is based on the pathologists' interpretation of hematoxylin and eosin (H&E)-stained tissue slices viewed under a brightfield microscope or a digital slide scanner. Computational pathology using deep learning has been proposed to detect lung cancer on histology images. However, the histological staining workflow to acquire the H&E-stained images and the subsequent cancer diagnosis procedures are labor-intensive and time-consuming with tedious sample preparation steps and repetitive manual interpretation, respectively. In this work, we propose a weakly supervised learning method for LUAD classification on label-free tissue slices with virtual histological staining. The autofluorescence images of label-free tissue with histopathological information can be converted into virtual H&E-stained images by a weakly supervised deep generative model. For the downstream LUAD classification task, we trained the attention-based multiple-instance learning model with different settings on the open-source LUAD H&E-stained whole-slide images (WSIs) dataset from the Cancer Genome Atlas (TCGA). The model was validated on the 150 H&E-stained WSIs collected from patients in Queen Mary Hospital and Prince of Wales Hospital with an average area under the curve (AUC) of 0.961. The model also achieved an average AUC of 0.973 on 58 virtual H&E-stained WSIs, comparable to the results on 58 standard H&E-stained WSIs with an average AUC of 0.977. The attention heatmaps of virtual H&E-stained WSIs and ground-truth H&E-stained WSIs can indicate tumor regions of LUAD tissue slices. In conclusion, the proposed diagnostic workflow on virtual H&E-stained WSIs of label-free tissue is a rapid, cost effective, and interpretable approach to assist clinicians in postoperative pathological examinations. The method could serve as a blueprint for other label-free imaging modalities and disease contexts.

O-GlcNAcylation stabilizes the autophagy-initiating kinase ULK1 by inhibiting chaperone-mediated autophagy upon HPV infection.

Human papillomaviruses (HPVs) cause a subset of head and neck squamous cell carcinomas (HNSCCs). Previously, we demonstrated that HPV16 oncogene E6 or E6/E7 transduction increases the abundance of O-linked ß-N-acetylglucosamine (O-GlcNAc) transferase (OGT), but OGT substrates affected by this increase are unclear. Here, we focus on the effects of O-GlcNAcylation on HPV-positive HNSCCs. We found that upon HPV infection, Unc-51-like kinase 1 (ULK1), an autophagy-initiating kinase, is hyper-O-GlcNAcylated, stabilized, and linked with autophagy elevation. Through mass spectrometry, we identified that ULK1 is O-GlcNAcylated at Ser409, which is distinct from the previously reported Thr635/Thr754 sites. It has been demonstrated that PKCα mediates phosphorylation of ULK1 at Ser423, which attenuates its stability by shunting ULK1 to the chaperone-mediated autophagy (CMA) pathway. Using biochemical assays, we demonstrate that ULK1 Ser409Ser410 O-GlcNAcylation antagonizes its phosphorylation at Ser423. Moreover, mutations of Ser409A and its neighboring site Ser410A (2A) render ULK1 less stable by promoting interaction with the CMA chaperone HSC70 (heat shock cognate 70 kDa protein). Furthermore, ULK1-2A mutants attenuate the association of ULK1 with STX17, which is vital for the fusion between autophagosomes and lysosomes. Analysis of The Cancer Genome Atlas (TCGA) database reveals that ULK1 is upregulated in HPV-positive HNSCCs, and its level positively correlates with HNSCC patient survival. Overall, our work demonstrates that O-GlcNAcylation of ULK1 is altered in response to environmental changes. O-GlcNAcylation of ULK1 at Ser409 and perhaps Ser410 stabilizes ULK1, which might underlie the molecular mechanism of HPV-positive HNSCC patient survival.

Signal Enhancement of Cadmium in Lettuce Using Laser-Induced Breakdown Spectroscopy Combined with Pyrolysis Process.

Fast detection of heavy metals in lettuce is significant for food market regulation and the control of heavy metal pollution. Advanced methods like laser-induced breakdown spectroscopy (LIBS) technology have been tried to determine the cadmium (Cd) content. To retard the negative effect of complex matrix composition from samples and improve quantitative performance of LIBS technology, the pyrolysis process combined with LIBS was adopted to determine the cadmium (Cd) content of lettuce. Adaptive iteratively reweighted penalized least squares (airPLS) was used to preprocess the LIBS spectra and solve the baseline drift. For multivariate linear regression based on the three selected Cd emission lines correlation coefficient in the prediction set Rp2 increased from 0.9154 to 0.9969, and the limit of detection (LOD) decreased from 9.1 mg/kg to 0.9 mg/kg after the pyrolysis process. The partial least squares (PLS) regression and support vector regression (SVR) were applied to construct calibration models based on full spectra. In addition, the least absolute shrinkage and selection operator (LASSO) was implemented to choose limited lines to predict the Cd content. The PLS model with the pyrolysis process obtained the best results with Rp2 = 0.9973 and LOD = 0.8 mg/kg. The results indicated that the pyrolysis method could enhance the spectral signal of cadmium and thus significantly improve the analysis results for all the models. It is shown in this experiment that proper sample preprocessing could effectively amplify the Cd signal in LIBS and make LIBS measurement an efficient method to assess Cd contamination in the vegetable industry.

Rapid Determination of Cadmium Contamination in Lettuce Using Laser-Induced Breakdown Spectroscopy.

Quick access to cadmium (Cd) contamination in lettuce is important to supervise the leafy vegetable growth environment and market. This study aims to apply laser-induced breakdown spectroscopy (LIBS) technology for fast determination of Cd content and diagnosis of the Cd contamination degree in lettuce. Emission lines Cd II 214.44 nm, Cd II 226.50 nm, and Cd I 228.80 nm were selected to establish the univariate analysis model. Multivariate analysis including partial least squares (PLS) regression, was used to establish Cd content calibration models, and PLS model based on 22 variables selected by genetic algorithm (GA) obtained the best performance with correlation coefficient in the prediction set Rp² = 0.9716, limit of detection (LOD) = 1.7 mg/kg. K-Nearest Neighbors (KNN) and random forest (RF) were used to analyze Cd contamination degree, and RF model obtained the correct classification rate of 100% in prediction set. The preliminary results indicate LIBS coupled with chemometrics could be used as a fast, efficient and low-cost method to assess Cd contamination in the vegetable industry.

[Reflectance characteristics of rare earth solution with different concentrations].

In the present paper, ten aqueous samples which contain-different concentrations of REE were collected in south Jiangxi province, and the reflectance spectra and the concentrations of REE were measured by analytical spectral devices (ASD) FieldSpec-3 reflectance spectroscopy and inductively coupled plasma mass spectrometry (ICP-MS), respectively. The results show that the spectra presented mix characteristics of pure water and rare earth oxide. In addition, six diagnostic absorption features caused by REE in visible and near-infrared wavelengths were detected. Then, relative absorption depths of the six absorption wavelength were calculated by the ratio spectra of sample spectra and pure water spectra. Finally, concentrations of total REE of ten samples and relative absorption depths of the six absorption wavelength were selected as two factors, and their relationship was perfectly described using linear regression analysis in which correlation coefficient was up to 96%-97%. The study provides a new method for quantitative estimation of different concentrations of dissolved REE in aqueous media, and strengthens theoretical basis for hyperspectral information extraction of REE.

Deep learning-assisted low-cost autofluorescence microscopy for rapid slide-free imaging with virtual histological staining.

Slide-free imaging techniques have shown great promise in improving the histological workflow. For example, computational high-throughput autofluorescence microscopy by pattern illumination (CHAMP) has achieved high resolution with a long depth of field, which, however, requires a costly ultraviolet laser. Here, simply using a low-cost light-emitting diode (LED), we propose a deep learning-assisted framework of enhanced widefield microscopy, termed EW-LED, to generate results similar to CHAMP (the learning target). Comparing EW-LED and CHAMP, EW-LED reduces the cost by 85×, shortening the image acquisition time and computation time by 36× and 17×, respectively. This framework can be applied to other imaging modalities, enhancing widefield images for better virtual histology.

Mechanisms of N, N-dimethylacetamide-facilitated n-hexane removal in a rotating drum biofilter packed with bamboo charcoal-polyurethane composite.

n-Hexane and N, N-dimethylacetamide (DMAC) are two major volatile organic compounds (VOCs) discharged from the pharmaceutical industry. To enhance DMAC-facilitated n-hexane removal, we investigated the simultaneous removal of multiple pollutants in a rotating drum biofilter packed with bamboo charcoal-polyurethane composite. After adding 800 mg·L-1 DMAC, the n-hexane removal efficiency increased from 59.4 % to 83.1 % under the optimized conditions. The maximum elimination capacity of 10.0 g·m-3·h-1n-hexane and 157 g·m-3·h-1 DMAC were obtained. The biomass of bamboo charcoal-polyurethane and the ratio of protein-to-polysaccharide in extracellular polymeric substances were significantly increased compared with the non-DMAC stage, which is attributed to increased carbon utilization. In addition, Na+ K+-ATPase was positively correlated with increasing electron transport system activity, which was 1.98 and 1.36 times greater. Hydrophilic DMAC improved the bioavailability of hydrophobic n-hexane and benefited bacterial metabolism. Co-degradation of n-hexane and DMAC system can be used for other volatile organic pollutants.

Mutual inhibition mechanism of simultaneous catalytic removal of NOx and toluene on Mn-based catalysts.

NOx and toluene have been identified as the dominant air pollutants in solid wasted combustion, and it is of great importance to remove these two pollutants simultaneously. Here, we found that Mn/CeO2 and Mn/TiO2 exhibited a bifunctional property in both NO reduction and toluene oxidation, and both of which could achieve 80% of conversion rate in NO reduction and toluene oxidation processes. However, the activity of both Mn/CeO2 and Mn/TiO2 decreased in simultaneous removal of NOx and toluene compared with separate NOx reduction and toluene oxidation. This indicates that there is a mutual inhibition between NOx reduction and toluene oxidation in simultaneous removal process over Mn-based catalysts, attributing to the competitive adsorption and utilization of active oxygen. In detail, the adsorption of toluene occupied the Lewis acid sites and restrained the NH3 adsorption. Meanwhile, the competitive utilization of active oxygen by NH3/NOx inhibited toluene oxidation to CO2 by active oxygen species as the reaction between NH3/NOx and active oxygen species would occur more easily.

An in vitro assay for enzymatic studies on human ALG13/14 heterodimeric UDP-N-acetylglucosamine transferase.

The second step of eukaryotic lipid-linked oligosaccharide (LLO) biosynthesis is catalyzed by the conserved ALG13/ALG14 heterodimeric UDP-N-acetylglucosamine transferase (GnTase). In humans, mutations in ALG13 or ALG14 lead to severe neurological disorders with a multisystem phenotype, known as ALG13/14-CDG (congenital disorders of glycosylation). How these mutations relate to disease is unknown because to date, a reliable GnTase assay for studying the ALG13/14 complex is lacking. Here we describe the development of a liquid chromatography/mass spectrometry-based quantitative GnTase assay using chemically synthesized GlcNAc-pyrophosphate-dolichol as the acceptor and purified human ALG13/14 dimeric enzyme. This assay enabled us to demonstrate that in contrast to the literature, only the shorter human ALG13 isoform 2, but not the longer isoform 1 forms a functional complex with ALG14 that participates in LLO synthesis. The longer ALG13 isoform 1 does not form a complex with ALG14 and therefore lacks GnTase activity. Importantly, we further established a quantitative assay for GnTase activities of ALG13- and ALG14-CDG variant alleles, demonstrating that GnTase deficiency is the cause of ALG13/14-CDG phenotypes.

Deep-learning-assisted microscopy with ultraviolet surface excitation for rapid slide-free histological imaging.

Histopathological examination of tissue sections is the gold standard for disease diagnosis. However, the conventional histopathology workflow requires lengthy and laborious sample preparation to obtain thin tissue slices, causing about a one-week delay to generate an accurate diagnostic report. Recently, microscopy with ultraviolet surface excitation (MUSE), a rapid and slide-free imaging technique, has been developed to image fresh and thick tissues with specific molecular contrast. Here, we propose to apply an unsupervised generative adversarial network framework to translate colorful MUSE images into Deep-MUSE images that highly resemble hematoxylin and eosin staining, allowing easy adaptation by pathologists. By eliminating the needs of all sample processing steps (except staining), a MUSE image with subcellular resolution for a typical brain biopsy (5 mm × 5 mm) can be acquired in 5 minutes, which is further translated into a Deep-MUSE image in 40 seconds, simplifying the standard histopathology workflow dramatically and providing histological images intraoperatively.

Recent Progress in Chemo-Enzymatic Methods for the Synthesis of N-Glycans.

Asparagine (N)-linked glycosylation is one of the most common co- and post-translational modifications of both intra- and extracellularly distributing proteins, which directly affects their biological functions, such as protein folding, stability and intercellular traffic. Production of the structural well-defined homogeneous N-glycans contributes to comprehensive investigation of their biological roles and molecular basis. Among the various methods, chemo-enzymatic approach serves as an alternative to chemical synthesis, providing high stereoselectivity and economic efficiency. This review summarizes some recent advances in the chemo-enzymatic methods for the production of N-glycans, including the preparation of substrates and sugar donors, and the progress in the glycosyltransferases characterization which leads to the diversity of N-glycan synthesis. We discuss the bottle-neck and new opportunities in exploiting the chemo-enzymatic synthesis of N-glycans based on our research experiences. In addition, downstream applications of the constructed N-glycans, such as automation devices and homogeneous glycoproteins synthesis are also described.

Effect of magnesium particle fraction on osteoinduction of hydroxyapatite sphere-based scaffolds.

Magnesium (Mg) is an emerging degradable metal for orthopaedics and its degradation product, Mg2+, has been reported to positively affect osteogenesis. Porous hydroxyapatite (HA) has been extensively studied for bone regeneration, but its slow degradation is an important factor limiting its uses. Therefore, we studied the combination of Mg and HA to integrate the advantages of the two materials while circumventing their disadvantages, with the aim of determining the optimum Mg/HA ratio. Surface-treated Mg particles (Φ âˆ¼ 1.3 mm) and HA spheres (Φ âˆ¼ 1.4 mm) were mixed at 0, 10, 30, and 50% (v/v). The mixtures were filled in titanium cages to form complexes. In vitro biocompatibility was studied by culturing MC3T3-E1 osteoblasts in extracts prepared from the complexes. In vivo biocompatibility and osteoinduction were evaluated by implantation in canine dorsal muscles. All complexes were not cytotoxic to the osteoblasts, regardless of the Mg proportion. Eight weeks after implantation in muscles, complexes containing 50% Mg showed inflammatory cell infiltration, whereas all other groups showed no evident inflammatory response. Additionally, complexes containing 30% Mg had significantly higher new bone area percentage (BV/TV), trabecular number (Tb.N), and bone growth rate than those containing 0, 10%, or 50% Mg. In comparison, complexes containing 50% Mg had significantly lower BV/TV and Tb.N than all other groups, and also had a significantly lower bone growth rate than those containing 10% or 30% Mg. Sixteen weeks after implantation, the trend in bone formation was similar to that observed at week 8. This shows that metallic Mg affected the osteoinductivity of HA-Mg complexes in a dose-dependent manner. In the present model, 30% Mg induced optimum osteoinduction. More studies are needed to explore the optimum Mg fractions for other implantation sites or forms of use.

Integrated Analysis of Genome-Wide Copy Number Alterations and Gene Expression Profiling of Lung Cancer in Xuanwei, China.

OBJECTIVES: Lung cancer in Xuanwei (LCXW), China, is known throughout the world for its distinctive characteristics, but little is known about its pathogenesis. The purpose of this study was to screen potential novel "driver genes" in LCXW. METHODS: Genome-wide DNA copy number alterations (CNAs) were detected by array-based comparative genomic hybridization and differentially expressed genes (DEGs) by gene expression microarrays in 8 paired LCXW and non-cancerous lung tissues. Candidate driver genes were screened by integrated analysis of CNAs and DEGs. The candidate genes were further validated by real-time quantitative polymerase chain reaction. RESULTS: Large numbers of CNAs and DEGs were detected, respectively. Some of the most frequently occurring CNAs included gains at 5p15.33-p15.32, 5p15.1-p14.3, and 5p14.3-p14.2 and losses at 11q24.3, 21q21.1, 21q22.12-q22.13, and 21q22.2. Integrated analysis of CNAs and DEGs identified 24 candidate genes with frequent copy number gains and concordant upregulation, which were considered potential oncogenes, including CREB3L4, TRIP13, and CCNE2. In addition, the analysis identified 19 candidate genes with a negative association between copy number change and expression change, considered potential tumor suppressor genes, including AHRR, NKD2, and KLF10. One of the most studied oncogenes, MYC, may not play a carcinogenic role in LCXW. CONCLUSIONS: This integrated analysis of CNAs and DEGs identified several potential novel LCXW-related genes, laying an important foundation for further research on the pathogenesis of LCXW and identification of novel biomarkers or therapeutic targets.

Determination of the internal pressure of fluid inclusions by using Raman spectroscopy.

In situ Raman spectroscopic measurements of H2O-NaCl systems with three different salinities (0, 5.0, and 10.0 wt% NaCl) in the region of O-H stretching vibration were obtained at pressures up to 1800 MPa and temperatures from 298 to 453 K, with a hydrothermal diamond-anvil cell. The peak position was determined by fitting the obtained O-H stretching band with one Gaussian component. At a given temperature, the shift of the band decreased systematically with increasing pressure, and the data show a good linear relationship. For systems of different salinity, the slopes of the isotherms seem to be independent of temperature under the conditions investigated. With increasing salinity, the slope of the isotherm gradually increases. The relationships measured for the shift of the O-H stretching band with temperature, salinity, and pressure can be used to determine the internal pressure and isochore of fluid inclusions as well as the formation temperature and pressure of host minerals.