Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

Global Prevalence of Helicobacter pylori Infection and Incidence of Gastric Cancer Between 1980 and 2022.

BACKGROUND & AIMS: We aimed to assess the secular trend of the global prevalence of Helicobacter pylori (H pylori) infection in adults and children/adolescents and to show its relation to that of gastric cancer incidence. METHODS: We performed a systematic review and meta-analysis to calculate overall prevalence, adjusted by multivariate meta-regression analysis. The incidence rates of gastric cancer were derived from the Global Burden of Disease Study and Cancer Incidence in Five Continents. RESULTS: Of the 16,976 articles screened, 1748 articles from 111 countries were eligible for analysis. The crude global prevalence of H pylori has reduced from 52.6% (95% confidence interval [CI], 49.6%-55.6%) before 1990 to 43.9% (95% CI, 42.3%-45.5%) in adults during 2015 through 2022, but was as still as high as 35.1% (95% CI, 30.5%-40.1%) in children and adolescents during 2015 through 2022. Secular trend and multivariate regression analyses showed that the global prevalence of H pylori has declined by 15.9% (95% CI, -20.5% to -11.3%) over the last 3 decades in adults, but not in children and adolescents. Significant reduction of H pylori prevalence was observed in adults in the Western Pacific, Southeast Asian, and African regions. However, H pylori prevalence was not significantly reduced in children and adolescents in any World Health Organization regions. The incidence of gastric cancer has decreased globally and in various countries where the prevalence of H pylori infection has declined. CONCLUSIONS: The global prevalence of H pylori infection has declined during the last 3 decades in adults, but not in children and adolescents. The results raised the hypothesis that the public health drive to reduce the prevalence of H pylori as a strategy to reduce the incidence of gastric cancer in the population should be confirmed in large-scale clinical trials.

SWEET: a single-sample network inference method for deciphering individual features in disease.

Recently, extracting inherent biological system information (e.g. cellular networks) from genome-wide expression profiles for developing personalized diagnostic and therapeutic strategies has become increasingly important. However, accurately constructing single-sample networks (SINs) to capture individual characteristics and heterogeneity in disease remains challenging. Here, we propose a sample-specific-weighted correlation network (SWEET) method to model SINs by integrating the genome-wide sample-to-sample correlation (i.e. sample weights) with the differential network between perturbed and aggregate networks. For a group of samples, the genome-wide sample weights can be assessed without prior knowledge of intrinsic subpopulations to address the network edge number bias caused by sample size differences. Compared with the state-of-the-art SIN inference methods, the SWEET SINs in 16 cancers more likely fit the scale-free property, display higher overlap with the human interactomes and perform better in identifying three types of cancer-related genes. Moreover, integrating SWEET SINs with a network proximity measure facilitates characterizing individual features and therapy in diseases, such as somatic mutation, mut-driver and essential genes. Biological experiments further validated two candidate repurposable drugs, albendazole for head and neck squamous cell carcinoma (HNSCC) and lung adenocarcinoma (LUAD) and encorafenib for HNSCC. By applying SWEET, we also identified two possible LUAD subtypes that exhibit distinct clinical features and molecular mechanisms. Overall, the SWEET method complements current SIN inference and analysis methods and presents a view of biological systems at the network level to offer numerous clues for further investigation and clinical translation in network medicine and precision medicine.

Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn.

Reducing contributions from non-neuronal sources is a crucial step in functional magnetic resonance imaging (fMRI) connectivity analyses. Many viable strategies for denoising fMRI are used in the literature, and practitioners rely on denoising benchmarks for guidance in the selection of an appropriate choice for their study. However, fMRI denoising software is an ever-evolving field, and the benchmarks can quickly become obsolete as the techniques or implementations change. In this work, we present a denoising benchmark featuring a range of denoising strategies, datasets and evaluation metrics for connectivity analyses, based on the popular fMRIprep software. The benchmark prototypes an implementation of a reproducible framework, where the provided Jupyter Book enables readers to reproduce or modify the figures on the Neurolibre reproducible preprint server (https://neurolibre.org/). We demonstrate how such a reproducible benchmark can be used for continuous evaluation of research software, by comparing two versions of the fMRIprep. Most of the benchmark results were consistent with prior literature. Scrubbing, a technique which excludes time points with excessive motion, combined with global signal regression, is generally effective at noise removal. Scrubbing was generally effective, but is incompatible with statistical analyses requiring the continuous sampling of brain signal, for which a simpler strategy, using motion parameters, average activity in select brain compartments, and global signal regression, is preferred. Importantly, we found that certain denoising strategies behave inconsistently across datasets and/or versions of fMRIPrep, or had a different behavior than in previously published benchmarks. This work will hopefully provide useful guidelines for the fMRIprep users community, and highlight the importance of continuous evaluation of research methods.

Tungsten Nitride (W5N6): An Ultraresilient 2D Semimetal.

Two-dimensional transition metal nitrides offer intriguing possibilities for achieving novel electronic and mechanical functionality owing to their distinctive and tunable bonding characteristics compared to other 2D materials. We demonstrate here the enabling effects of strong bonding on the morphology and functionality of 2D tungsten nitrides. The employed bottom-up synthesis experienced a unique substrate stabilization effect beyond van-der-Waals epitaxy that favored W5N6 over lower metal nitrides. Comprehensive structural and electronic characterization reveals that monolayer W5N6 can be synthesized at large scale and shows semimetallic behavior with an intriguing indirect band structure. Moreover, the material exhibits exceptional resilience against mechanical damage and chemical reactions. Leveraging these electronic properties and robustness, we demonstrate the application of W5N6 as atomic-scale dry etch stops that allow the integration of high-performance 2D materials contacts. These findings highlight the potential of 2D transition metal nitrides for realizing advanced electronic devices and functional interfaces.

Inference of single-cell network using mutual information for scRNA-seq data analysis.

BACKGROUND: With the advance in single-cell RNA sequencing (scRNA-seq) technology, deriving inherent biological system information from expression profiles at a single-cell resolution has become possible. It has been known that network modeling by estimating the associations between genes could better reveal dynamic changes in biological systems. However, accurately constructing a single-cell network (SCN) to capture the network architecture of each cell and further explore cell-to-cell heterogeneity remains challenging. RESULTS: We introduce SINUM, a method for constructing the SIngle-cell Network Using Mutual information, which estimates mutual information between any two genes from scRNA-seq data to determine whether they are dependent or independent in a specific cell. Experiments on various scRNA-seq datasets with different cell numbers based on eight performance indexes (e.g., adjusted rand index and F-measure index) validated the accuracy and robustness of SINUM in cell type identification, superior to the state-of-the-art SCN inference method. Additionally, the SINUM SCNs exhibit high overlap with the human interactome and possess the scale-free property. CONCLUSIONS: SINUM presents a view of biological systems at the network level to detect cell-type marker genes/gene pairs and investigate time-dependent changes in gene associations during embryo development. Codes for SINUM are freely available at https://github.com/SysMednet/SINUM .

Elucidating Singlet-Fission-Born Multiexciton Dynamics via Molecular Engineering: A Dilution Principle Extended to Quintet Triplet Pair.

Multiexciton in singlet exciton fission represents a critical quantum state with significant implications for both solar cell applications and quantum information science. Two distinct fields of interest explore contrasting phenomena associated with the geminate triplet pair: one focusing on the persistence of long-lived correlation and the other emphasizing efficient decorrelation. Despite the pivotal nature of multiexciton processes, a comprehensive understanding of their dependence on the structural and spin properties of materials is currently lacking in experimental realizations. To address this gap in knowledge, molecular engineering was employed to modify the TIPS-tetracene structures, enabling an investigation of the structure-property relationships in spin-related multiexciton processes. In lieu of the time-resolved electron paramagnetic resonance technique, two time-resolved magneto-optical spectroscopies were implemented for quantitative analysis of spin-dependent multiexciton dynamics. The utilization of absorption and fluorescence signals as complementary optical readouts, in the presence of a magnetic field, provided crucial insights into geminate triplet pair dynamics. These insights encompassed the duration of multiexciton correlation and the involvement of the spin state in multiexciton decorrelation. Furthermore, simulations based on our kinetic models suggested a role for quintet dilution in multiexciton dynamics, surpassing the singlet dilution principle established by the Merrifield model. The integration of intricate model structures and time-resolved magneto-optical spectroscopies served to explicitly elucidate the interplay between structural and spin properties in multiexciton processes. This comprehensive approach not only contributes to the fundamental understanding of these processes but also aligns with and reinforces previous experimental studies of solid states and theoretical assessments.

Multiple Enol-Keto Isomerization and Excited-State Unidirectional Intramolecular Proton Transfer Generate Intense, Narrowband Red OLEDs.

A novel series of excited-state intramolecular proton transfer (ESIPT) emitters, namely, DPNA, DPNA-F, and DPNA-tBu, endowed with dual intramolecular hydrogen bonds, were designed and synthesized. In the condensed phase, DPNAs exhibit unmatched absorption and emission spectral features, where the minor 0-0 absorption peak becomes a major one in the emission. Detailed spectroscopic and dynamic approaches conclude fast ground-state equilibrium among enol-enol (EE), enol-keto (EK), and keto-keto (KK) isomers. The equilibrium ratio can be fine-tuned by varying the substitutions in DPNAs. Independent of isomers and excitation wavelength, ultrafast ESIPT takes place for all DPNAs, giving solely KK tautomer emission maximized at >650 nm. The spectral temporal evolution of ESIPT was resolved by a state-of-the-art technique, namely, the transient grating photoluminescence (TGPL), where the rate of EK* → KK* is measured to be (157 fs)-1 for DPNA-tBu, while a stepwise process is resolved for EE* → EK* → KK*, with a rate of EE* → EK* of (72 fs)-1. For all DPNAs, the KK tautomer emission shows a narrowband emission with high photoluminescence quantum yields (PLQY, ∼62% for DPNA in toluene) in the red, offering advantages to fabricate deep-red organic light-emitting diodes (OLED). The resulting OLEDs give high external quantum efficiency with a spectral full width at half-maximum (FWHM) as narrow as ∼40 nm centered at 666-670 nm for DPNAs, fully satisfying the BT. 2020 standard. The unique ESIPT properties and highly intense tautomer emission with a small fwhm thus establish a benchmark for reaching red narrowband organic electroluminescence.

Diffusion tensor brain imaging at 0.55T: A feasibility study.

PURPOSE: To investigate the feasibility of diffusion tensor brain imaging at 0.55T with comparisons against 3T. METHODS: Diffusion tensor imaging data with 2 mm isotropic resolution was acquired on a cohort of five healthy subjects using both 0.55T and 3T scanners. The signal-to-noise ratio (SNR) of the 0.55T data was improved using a previous SNR-enhancing joint reconstruction method that jointly reconstructs the entire set of diffusion weighted images from k-space using shared-edge constraints. Quantitative diffusion tensor parameters were estimated and compared across field strengths. We also performed a test-retest assessment of repeatability at each field strength. RESULTS: After applying SNR-enhancing joint reconstruction, the diffusion tensor parameters obtained from 0.55T data were strongly correlated ( R 2 ≥ 0 . 70 $$ {R}^2\ge 0.70 $$ ) with those obtained from 3T data. Test-retest analysis showed that SNR-enhancing reconstruction improved the repeatability of the 0.55T diffusion tensor parameters. CONCLUSION: High-resolution in vivo diffusion MRI of the human brain is feasible at 0.55T when appropriate noise-mitigation strategies are applied.

Dislocation phenomena described with free volume concept and Eyring's rate process theory.

Dislocation phenomena in solids under simple shear stress are theoretically addressed with the free volume concept and Eyring's rate process theory for obtaining a generic and unified description. The obtained equations do not have any restrictions to specific materials and are compared with various theories and empirical equations like the Hall-Petch and its inverse forms. Moreover, our equations are used to fit experimental data of mechanical properties and dislocation density against grain sizes available in the literature. A good agreement with observations is achieved, indicating that our theoretical framework is sound. Our findings provide a theoretical foundation for the very common dislocation phenomena observed among many solid materials including pure metals, metallic alloys, ceramics, and even geological scale entities, potentially clearing out many inconsistencies and puzzles in the literature.

Theoretical and kinetic study of the H-atom abstraction reactions by H atom from alkyl cyclohexanes.

Reaction kinetics of hydrogen atom abstraction from six alkyl cyclohexanes, methyl cyclohexane (MCH), ethyl cyclohexane (ECH), n-propyl cyclohexane (nPCH), iso-propyl cyclohexane (iPCH), sec-butyl cyclohexane (sBCH) and iso-butyl cyclohexane (iBCH), by the H atom are systematically studied in this work. The M06-2X method combined with the 6-311++G(d,p) basis set is used to perform geometry optimization, frequency analysis and zero-point energy calculations for all species. The intrinsic reaction coordinate (IRC) calculations are performed to confirm the transition states connecting the reactants and products correctly. One-dimensional hindered rotors are used to treat the low frequency torsional models with potentials scanned at the M06-2X/6-31G level of theory. Electronic single-point energy calculations for all reactants, transition states, and products are performed at the QCISD(T)/CBS level of theory. High-pressure limiting rate constants of 39 reaction channels are obtained using conventional transition state theory with asymmetric Eckart tunneling corrections in the temperature range 298.15-2000 K. Reaction rate rules for H-atom abstraction by the H atom from alkyl cyclohexanes on primary, secondary and tertiary carbon sites on both the side chain and ring are provided. The obtained rate constants are given by the Arrhenius expression in the temperature range 500-2000 K, which can be used for the combustion kinetics model development for alkyl cyclohexanes.

The indanone N-H type excited-state intramolecular proton transfer (ESIPT); the observation of a mechanically induced ESIPT reaction.

We report the design and synthesis of indanone derivatives 1-4 with RR'N-H⋯OC intramolecular hydrogen bonds, in which ESIPT takes place and its dynamics and thermodynamics correlate with H-bond strength, facilitated by electron-withdrawing R' groups. Compound 4 (R' = COCF3) shows mechanically induced ESIPT for the first time, where -CF3⋯HN- interaction plays a key role in the non-centrosymmetric crystal packing.

Impact of butylparaben on growth dynamics and microcystin-LR production in Microcystis aeruginosa.

The presence of butylparaben (BP), a prevalent pharmaceutical and personal care product, in surface waters has raised concerns regarding its impact on aquatic ecosystems. Despite its frequent detection, the toxicity of BP to the cyanobacterium Microcystis aeruginosa remains poorly understood. This study investigates the influence of BP on the growth and physiological responses of M. aeruginosa. Results indicate that low concentrations of BP (below 2.5 mg/L) have negligible effects on M. aeruginosa growth, whereas higher concentrations (5 mg/L and 10 mg/L) lead to significant growth inhibition. This inhibition is attributed to the severe disruption of photosynthesis, evidenced by decreased Fv/Fm values and chlorophyll a content. BP exposure also triggers the production of reactive oxygen species (ROS), resulting in elevated activity of antioxidant enzymes. Excessive ROS generation stimulates the production of microcystin-LR (MC-LR). Furthermore, lipid peroxidation and cell membrane damage indicate that high BP concentrations cause cell membrane rupture, facilitating the release of MC-LR into the environment. Transcriptome analysis reveals that BP disrupts energy metabolic processes, particularly affecting genes associated with photosynthesis, carbon fixation, electron transport, glycolysis, and the tricarboxylic acid cycle. These findings underscore the profound physiological impact of BP on M. aeruginosa and highlight its role in stimulating the production and release of MC-LR, thereby amplifying environmental risks in aquatic systems.

Application of machine learning techniques in the diagnosis of endometriosis.

OBJECTIVE: The aim of this study is to assess the use of machine learning methodologies in the diagnosis of endometriosis (EM). METHODS: This study included a total of 106 patients with EM and 203 patients with non-EM conditions (like simple cysts and simple uterine fibroids), all admitted to the Shunyi Women's and Children's Hospital of Beijing Children's Hospital between January 2017 and September 2022. All participants were free of comorbidities and their diagnoses were confirmed via postoperative pathology. Comparative analysis was conducted between the EM and non-EM groups. Baseline data were assessed, including white blood cell count, neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio, lymphocyte-to-monocyte ratio, mean platelet volume, hemoglobin, carbohydrate antigen 125 (CA125), carbohydrate antigen 199, coagulation parameters, and other serologic indicators. An optimal predictive model was developed using an artificial intelligence algorithm to determine the presence of EM. The objective is to provide new insights for the clinical diagnosis and treatment of EM. RESULTS: The random forest algorithm demonstrated superior performance when compared to decision trees, LogitBoost, artificial neural networks, naïve Bayes, support vector machines, and linear regression in machine learning methods. Combining CA125 with the NLR yielded a better prediction of EM than using CA125 alone when applying the random forest algorithm. The accuracy of predicting EM with CA125 combined with NLR was 78.16%, with a sensitivity of 86.21% and an area under the curve (AUC) of 0.85 (P < 0.05). In contrast, using CA125 alone resulted in an EM prediction accuracy of 75.8%, with a sensitivity of 79.3% and an AUC of 0.82 (P < 0.05). CONCLUSION: The diagnostic value of serum CA125 combined with the NLR for EM is higher than that of serum CA125 alone. This finding indicates that NLR could serve as a new supplementary biomarker along with serum CA125 in the diagnosis of EM.

Human and rat gonadal 3ß-hydroxysteroid dehydrogenases are suppressed by dithiocarbamate fungicides via interacting with cysteine residues.

Dithiocarbamates have been widely used in various industrial applications, such as insecticides (ferbam) or drug (disulfiram). This study explored the inhibitory effects of dithiocarbamates on human and rat gonadal 3ß-hydroxysteroid dehydrogenases (3ß-HSD) and investigated the structure-activity relationship and mechanistic insights. The inhibitory activity of six dithiocarbamates and thiourea on the conversion of pregnenolone to progesterone was evaluated using human KGN cell and rat testicular microsomes, with subsequent progesterone measurement using HPLC-MS/MS. The study found that among the tested compounds disulfiram, ferbam, and thiram exhibited significant inhibitory activity against human 3ß-HSD2 and rat 3ß-HSD1, with ferbam demonstrating the highest potency. The mode of action for these compounds was characterized, showing mixed inhibition for human 3ß-HSD2 and mixed/noncompetitive inhibition for rat 3ß-HSD1. Additionally, it was observed that dithiothreitol dose-dependently reversed the inhibitory effects of dithiocarbamates on both human and rat gonadal 3ß-HSD enzymes. The study also delved into the penetration of these dithiocarbamates through the human KGN cell membrane and their impact on progesterone production, highlighting their potency in inhibiting human 3ß-HSD2. Furthermore, bivariate correlation analysis revealed a positive correlation of LogP (lipophilicity) with IC50 values for both enzymes. Docking analysis indicated that dithiocarbamates bind to NAD+ and steroid-binding sites, with some interactions with cysteine residues. In conclusion, this study provides valuable insights into the structure-activity relationship and mechanistic aspects of dithiocarbamates as inhibitors of human and rat gonadal 3ß-HSDs, suggesting that these compounds likely exert their inhibitory effects through binding to cysteine residues.

A Preliminary Investigation of the Roles of Endometrial Cells in Endometriosis Development via In Vitro and In Vivo Analyses.

Endometriosis is a complex gynecological disease that affects more than 10% of women in their reproductive years. While surgery can provide temporary relief from women's pain, symptoms often return in as many as 75% of cases within two years. Previous literature has contributed to theories about the development of endometriosis; however, the exact pathogenesis and etiology remain elusive. We conducted a preliminary investigation into the influence of primary endometrial cells (ECs) on the development and progression of endometriosis. In vitro studies, they were involved in inducing Lipopolysaccharide (LPS) in rat-isolated primary endometrial cells, which resulted in increased nuclear factor-kappa B (NF-κB) and vascular endothelial growth factor (VEGF) mRNA gene expression (quantitative polymerase chain reaction analysis, qPCR) and protein expression (western blot analysis). Additionally, in vivo studies utilized autogenic and allogeneic transplantations (rat to rat) to investigate endometriosis-like lesion cyst size, body weight, protein levels (immunohistochemistry), and mRNA gene expression. These studies demonstrated that estrogen upregulates the gene and protein regulation of cytoskeletal (CK)-18, transforming growth factor-ß (TGF-ß), VEGF, and tumor necrosis factor (TNF)-α, particularly in the peritoneum. These findings may influence cell proliferation, angiogenesis, fibrosis, and inflammation markers. Consequently, this could exacerbate the occurrence and progression of endometriosis.

Therapeutic Effect of Lecigel, Cetiol®CC, Activonol-6, Activonol-M, 1,3-Propanediol, Soline, and Fucocert® (LCAA-PSF) Treatment on Imiquimod-Induced Psoriasis-like Skin in Mice.

The individual ingredients of 1,3-Propanediol, Soline, and Fucocert® (PSF) are often used as cosmetic formulations in skin care. In addition, the mixture of Lecigel, Cetiol®CC, Activonol-6, and Activonol-M (LCAA) is often used as a cosmetic base. However, whether the combination of LCAA with PSF (LCAA-PSF) exerts a therapeutic effect on psoriasis remains unclear. In this study, mice induced with imiquimod (IMQ) were divided into three groups and administered 100 mg/day of LCAA, 100 mg/day of LCAA-PSF, or Vaseline on the dorsal skin of each mouse. Weight-matched mice treated with Vaseline alone were used as controls. Hematoxylin and eosin (H&E) staining and enzyme-linked immunosorbent assay(ELISA) were used to assess tissue morphology and inflammatory cytokines. RNA sequencing analysis was used to predict the mechanism underlying the action of LCAA-PSF against psoriasis, while immunohistochemical analysis validation was used to identify pertinent molecular pathways. The results demonstrated that LCAA-PSF alleviated IMQ-induced keratinocyte differentiation/ proliferation bydecreasingthe serum levels of inflammatory cytokines such as IL-6, TNF-α, IL-23, and IL-17A and the epidermisof TGFß, Ki67, CK5/6, and VEGF expression, which is associated with angiogenesis and keratinocyte differentiation/ proliferation. These findings highlight the antipsoriatic activity of LCAA-PSF in a psoriasis-like mouse model and suggest this may occurvia the inhibition of inflammatory factor secretionand the TGFß-related signal pathway.

Leveraging Charge-Transfer Interactions in Through-Space-Coupled Pentacene Dendritic Oligomer for Singlet Exciton Fission.

Singlet exciton fission in organic chromophores has received much attention during the past decade. Inspired by numerous spectroscopic studies in the solid state, there have been vigorous efforts to study singlet exciton fission dynamics in covalently bonded oligomers, which aims to investigate underlying mechanisms of this intriguing process in simplified model systems. In terms of through-space orbital interactions, however, most of covalently bonded pentacene oligomers studied so far fall into weakly interacting systems since they manifest chain-like structures based on various (non)conjugated linkers. Therefore, it remains as a compelling question to answer how through-space interactions in the solid state intervene this photophysical process since it is hypersensitive to displacements and orientations between neighboring chromophores. Herein, as one of experimental studies to answer this question, we introduced a tight-packing dendritic structure whose mesityl-pentacene constituents are coupled via moderate through-space orbital interactions. Based on the comparison with a suitably controlled dendritic structure, which is in a weak coupling regime, important mechanistic viewpoints are tackled such as configurational mixings between singlet, charge-transfer, and triplet pair states and the role of chromophore multiplication. We underscore that our through-space-coupled dendritic oligomer in a quasi-intermediate coupling regime provides a hint on the interplay of multiconfigurational excited-states, which might have drawn complexity in singlet exciton fission kinetics throughout numerous solid-state morphologies.

Kinetic Properties Study of H Atom Abstraction by CH3Ȯ2 Radicals from Fuel Molecules with Different Functional Groups.

The detailed kinetic properties of hydrogen atom abstraction by methylperoxy (CH3Ȯ2) radicals from alkanes, alkenes, dienes, alkynes, ethers, and ketones are systematically studied in this work. Geometry optimization, frequency analysis, and zero-point energy corrections were performed for all species at the M06-2X/6-311++G(d,p) level of theory. The intrinsic reaction coordinate calculation was consistently performed to ensure that the transition state connects the correct reactants and products, and one-dimensional hindered rotor scanning results were performed at the M06-2X/6-31G level of theory. The single-point energies of all reactants, transition states, and products were obtained at the QCISD(T)/CBS level of theory. High-pressure-limit rate constants of 61 reaction channels were calculated using conventional transition state theory with asymmetric Eckart tunneling corrections over the temperature range of 298.15-2000 K. Reaction rate rules for H atom abstraction by CH3Ȯ2 radicals from fuel molecules with different functional groups are constructed, which can be used in the development of combustion models of these fuels and fuel types. In addition, the influence of the functional groups on the internal rotation of the hindered rotor is also discussed.

Negative serum (1,3) -ß-D-glucan has a low power to exclude Pneumocystis jirovecii pneumonia (PJP) in HIV-uninfected patients with positive qPCR.

OBJECTIVE: The current study evaluated the diagnostic performance of serum (1,3)-beta-D Glucan (BDG) in differentiating PJP from P. jirovecii-colonization in HIV-uninfected patients with P. jirovecii PCR-positive results. METHODS: This was a single-center retrospective study between 2019 and 2021. The diagnosis of PJP was based on the following criteria: detection of P. jirovecii in sputum or BAL specimen by qPCR or microscopy; Meet at least two of the three criteria: (1) have respiratory symptoms of cough and/or dyspnea, hypoxia; (2) typical radiological picture findings; (3) receiving a complete PJP treatment. After exclusion, the participants were divided into derivation and validation cohorts. The derivation cohort defined the cut-off value of serum BDG. Then, it was verified using the validation cohort. RESULTS: Two hundred and thirteen HIV-uninfected patients were enrolled, with 159 PJP and 54 P. jirovecii-colonized patients. BDG had outstanding specificity, LR, and PPV for PJP in both the derivation (90.00%, 8.900, and 96.43%) and the validation (91.67%, 9.176, and 96.30%) cohorts at ≥ 117.7 pg/mL. However, it had lower sensitivity and NPV in the derivation cohort (89.01% and 72.97%), which was even lower in the validation cohort (76.47% and 57.89%). Of note, BDG ≥ 117.7 pg/mL has insufficient diagnostic efficacy for PJP in patients with lung cancer, interstitial lung disease (ILD) and nephrotic syndrome. And although lymphocytes, B cells, and CD4+ T cells in PJP patients were significantly lower than those in P. jirovecii-colonized patients, the number and proportion of peripheral blood lymphocytes did not affect the diagnostic efficacy of serum BDG. CONCLUSIONS: Serum BDG ≥ 117.7 pg/mL could effectively distinguish P. jirovecii-colonization from infection in qPCR-positive HIV-uninfected patients with infectious diseases, solid tumors (excluding lung cancer), autoimmune or inflammatory disorders, and hematological malignancies. Of note, for patients with lung cancer, ILD, and nephrotic diseases, PJP should be cautiously excluded at BDG < 117.7 pg/mL.