Infrared Spectral Analysis for Prediction of Functional Groups Based on Feature-Aggregated Deep Learning

Infrared (IR) spectroscopy is a powerful and versatile tool for analyzing functional groups in organic compounds. A complex and time-consuming interpretation of massive unknown spectra usually requires knowledge of chemistry and spectroscopy. This paper presents a new deep learning method for transforming IR spectral features into intuitive imagelike feature maps and prediction of major functional groups. We obtained 8272 gas-phase IR spectra from the NIST Chemistry WebBook. Feature maps are constructed using the intrinsic correlation of spectral data, and prediction models are developed based on convolutional neural networks. Twenty-one major functional groups for each molecule are successfully identified using binary and multilabel models without expert guidance and feature selection. The multilabel classification model can produce all prediction results simultaneously for rapid characterization. Further analysis of the detailed substructures indicates that our model is capable of obtaining abundant structural information from IR spectra for a comprehensive investigation. The interpretation of our model reveals that the peaks of most interest are similar to those often considered by spectroscopists. In addition to demonstrating great potential for spectral identification, our method may contribute to the development of automated analyses in many fields

Serum IgE anti-dsDNA autoantibodies in patients with proliferative lupus nephritis are associated with tubulointerstitial inflammation

Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the overproduction of multiple autoantibodies. Lupus nephritis (LN), the most common cause of morbidity and mortality, requires early detection. However, only a limited number of serum biomarkers have been associated with the disease activity of LN. Serum IgE anti-dsDNA autoantibodies are prevalent in patients with SLE and may be associated with the pathogenesis of LN. In this study, serum samples from 88 patients with biopsy-proven proliferative LN were collected along with complete clinical and pathological data to investigate the clinical and pathological associations of anti-dsDNA IgE autoantibodies using ELISA. This study found that the prevalence of IgE anti-dsDNA autoantibodies in patients with proliferative LN was 38.6% (34/88). Patients with anti-dsDNA IgE autoantibodies were more prone to acute kidney injury (17/34 vs. 14/54; p = .025). Levels of anti-dsDNA IgE autoantibodies were associated with interstitial inflammation (r = 0.962, p = .017). Therefore, anti-dsDNA IgE autoantibody levels are associated with tubulointerstitial inflammation in patients with proliferative LN.</p

Bridging the Monomer to Polymer Gap in Radical Polymer Design

Radical polymers bearing open-shell moieties at pendant sites exhibit unique redox and optoelectronic properties that are promising for many organic electronic applications. Nevertheless, gaps remain in relating the electronic properties of repeat units, which can be easily calculated, to the condensed-phase charge transport behaviors of these materials. To address this gap, we have performed the first quantum chemical study on a broad swathe of radical polymer design space that explicitly includes the coupling between polymer constraints and radical-mediated intramolecular charge transfer. For this purpose, a chemical space of 64 radical polymer chemistries was constructed based on varying backbone units, open-shell chemistries, and spacer units between the backbone and the radical groups. For each combination of backbone, radical, and spacer, comprehensive conformational sampling was used to calculate expected values of intrachain charge transport using several complementary metrics, including the end-to-end thermal Green’s function, Delta–Wye transformed inverse resistance, and the Kirchhoff transport index. We observe that charge transport in radical polymers is primarily driven by the choice radical chemistry, which influences the optimal choice of backbone chemistry and spacer group that mediate radical alignment and avoid the formation of undesired trap states. Given the limited exploration of radical chemistries beyond the TEMPO radical for this class of materials, these findings suggest tremendous opportunities exist for synthetic exploration in radical polymers

Comparison of the performance of a chemiluminescence assay and an ELISA for detection of anti-GBM antibodies

Objective: Autoantibodies to the α3 chain noncollagen 1 domain of type IV collagen (α3(IV)NC1) are a serological hallmark in the diagnosis of anti-glomerular basement membrane (GBM) disease. The objective of our study was to compare the performance of anti-glomerular basement membrane (GBM) antibody detection by chemiluminescence immunoassay (CIA) and by enzyme-linked immunosorbent assays (ELISAs). Methods: Sera from outpatients who were suspected to have anti-GBM disease and 31 patients with biopsy-proven anti-GBM disease were collected. Thirty normal controls were also included. All samples were tested for anti-GBM antibodies by CIA and commercial ELISA. The anti-GBM antibody-positive samples were confirmed by a homemade ELISA coated with recombinant human α3(IV)NC1. Results: Compared with detection of anti-GBM antibodies with ELISA, detection of anti-GBM antibodies with CIA showed a positivity agreement of 70% and a negativity agreement of 98.6%. Among the 4 patients with different results, the anti-GBM antibody detection by CIA was in agreement with the homemade ELISA coated with recombinant human α3(IV)NC1 and the clinical diagnosis. In 31 patients with anti-GBM disease, good agreement was achieved in the detection of anti-GBM antibodies with CIA, commercial ELISA and the homemade ELISA (100%, 100%). The AUC for CIA and commercial ELISA was 0.987 and 0.966, respectively. Conclusions: The detection of anti-GBM antibodies with CIA demonstrated good sensitivity and specificity and was in good agreement with our homemade ELISA, which seems better than the commercial ELISA in suspected anti-GBM disease patients. The three assays performed in parallel in the diagnosis of anti-GBM disease patients.</p

The clinical and pathological relevance of waxy casts in urine sediment

Although casts in urine may imply the underlying pathogenesis and the diagnosis, the waxy cast is poorly understood yet. We aim to investigate the association between waxy casts and clinicopathological indices. Patients undergone renal biopsy and urine sediment examination were enrolled. Waxy casts referred to those presented with a homogeneous melted wax appearance and pre-waxy casts referred to those in which one or more segments demonstrated a waxy-cast appearance. Multivariable logistic regression was used to assess the factors associated with waxy casts. In 1282 patients, the detection rate of waxy casts was 26.3%. If either waxy or pre-waxy cast was considered as a diagnostic marker for renal insufficiency (eGFR 2), the sensitivity was 0.58 and the specificity was 0.88. If the only waxy cast was considered as the diagnostic marker, the sensitivity was 0.29 and the specificity was 0.97. The patients with waxy or pre-waxy casts had higher blood pressure, more proteinuria, and worse renal function. Waxy or pre-waxy cast was independently associated with eGFR (odds ratio: 0.73 per 10 mL/min/1.73 m2 increase, 95% confidence interval: 0.69–0.77, p p < 0.001) and pathological lesions. Waxy or pre-waxy casts are closely related to impaired renal function. Their presence is a specific indicator of renal insufficiency but is not sensitive enough.</p

Additional file 5 of RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization

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Additional file 8 of RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization

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Unveiling the Molecular Dynamics in a Living Cell to the Subcellular Organelle Level Using Second-Harmonic Generation Spectroscopy and Microscopy

Second-harmonic generation (SHG) microscopy has been proved to be a powerful method for investigating the structures of biomaterials. SHG spectra were also generally used to probe the adsorption and cross-membrane transport of molecules on lipid bilayers in situ and in real time. In this work, we applied SHG and two-photon fluorescence (TPF) spectra to investigate the dynamics of an amphiphilic ion with an SHG and TPF chromophore, D289 (4-(4-diethylaminostyry)-1-methyl-pyridinium iodide), on the surface of human chronic myelogenous leukemia (K562) cells and the subcellular structures inside the cells. The adsorption and cross-membrane transport of D289 into the cells and then into the organelles such as mitochondria were revealed. SHG images were also recorded and used to demonstrate their capability of probing molecular dynamics in organelles in K562 cells. This work demonstrated the first SHG investigation of the cross-membrane transport dynamics on the surface of subcellular organelles. It may also shed light on the differentiation of different types of subcellular structures in cells

Additional file 12 of RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization

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Additional file 10 of RNA interference-mediated silencing of DNA methyltransferase 1 attenuates neuropathic pain by accelerating microglia M2 polarization

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