Description of Short-Range Interactions of Carbon-Based Materials with a Combined AIREBO and ZBL Potential.

An accurate description of short-range interactions among atoms is crucial for simulating irradiation effects in applications related to ion modification techniques. A smooth integration of the Ziegler-Biersack-Littmark (ZBL) potential with the adaptive intermolecular reactive empirical bond-order (AIREBO) potential was achieved to accurately describe the short-range interactions for carbon-based materials. The influence of the ZBL connection on potential energy, force, and various AIREBO components, including reactive empirical bond-order (REBO), Lennard-Jones (LJ), and the torsional component, was examined with configurations of the dimer structure, tetrahedron structure, and monolayer graphene. The REBO component is primarily responsible for the repulsive force, while the LJ component is mainly active in long-range interactions. It is shown that under certain conditions, the torsional energy can lead to a strong repulsive force at short range. Molecular dynamics simulations were performed to study the collision process in configurations of the C-C dimer and bulk graphite. Cascade collisions in graphite with kinetic energies of 1 keV and 10 keV for primary knock-on atoms showed that the short-range description can greatly impact the number of generated defects and their morphology.

Microbiota-induced inflammatory responses in bladder tumors promote epithelial-mesenchymal transition and enhanced immune infiltration.

The intratumoral microbiota can modulate the tumor immune microenvironment (TIME); however, the underlying mechanism by which intratumoral microbiota influences the TIME in urothelial carcinoma of the bladder (UCB) remains unclear. To address this, we collected samples from 402 patients with UCB, including paired host transcriptome and tumor microbiome data, from The Cancer Genome Atlas (TCGA). We found that the intratumoral microbiome profiles were significantly correlated with the expression pattern of epithelial-mesenchymal transition (EMT)-related genes. Furthermore, we detected that the genera Lachnoclostridium and Sutterella in tumors could indirectly promote the EMT program by inducing an inflammatory response. Moreover, the inflammatory response induced by these two intratumoral bacteria further enhanced intratumoral immune infiltration, affecting patient survival and response to immunotherapy. In addition, an independent immunotherapy cohort of 348 patients with bladder cancer was used to validate our results. Collectively, our study elucidates the potential mechanism by which the intratumoral microbiota influences the TIME of UCB and provides a new guiding strategy for the targeted therapy of UCB.NEW & NOTEWORTHY The intratumoral microbiota may mediate the bladder tumor inflammatory response, thereby promoting the epithelial-mesenchymal transition program and influencing tumor immune infiltration.

Socioeconomic status and health-related quality of life after stroke: a systematic review and meta-analysis.

BACKGROUND: Socioeconomic status (SES) is associated with stroke occurrence and survival following stroke but its association with health-related quality of life (HRQoL) following stroke remains uncertain. We performed a systematic review and meta-analysis to examine the association between SES and HRQoL after stroke. METHODS: PubMed, SCOPUS, EMBASE, and Web of Science were searched to identify relevant cohort and case-control studies between January 2000 and May 2022. Two authors screened titles, abstracts and full text articles. One author extracted data from all included studies. Meta-analyses were performed for studies with comparable measurements of SES and HRQoL. Random effects models were used to estimate pooled summary standardised mean differences in HRQoL by SES. RESULTS: Out of 1,876 citations, 39 studies incorporated measurement of overall HRQoL following stroke and were included in the systematic review, with 17 studies included in the meta-analyses. Overall, reports including education, income, occupation and work status effects on HRQoL after stroke were inconsistent among all included 39 studies. In the global meta-analysis of 17 studies, HRQoL among survivors of stroke was lower in the low SES group than in the high SES group (standardised mean difference (SMD) -0.36, 95% CI -0.52, -0.20, p < 0.0001). When using education and income indicators separately, summary effects were similar to those of the global analysis (low versus high education SMD -0.38, 95% CI -0.57, -0.18, p < 0.0001; low versus high income SMD -0.39, 95% CI -0.59, -0.19, p < 0.0001). CONCLUSIONS: Across all SES indicators, people with stroke who have lower SES have poorer overall HRQoL than those with higher SES. Accessibility and affordability of poststroke support services should be taken into consideration when planning and delivering services to people with low SES.

Area-level and individual-level socio-economic differences in health-related quality of life trajectories: Results from a 10-year longitudinal stroke study.

BACKGROUND: We examined area-level (aSES) and individual-level (iSES) socio-economic status on trajectories of HRQoL to 10 years following stroke. METHODS: Participants with strokes between 1/5/1996 and 30/4/1999 completed the Assessment of Quality of Life instrument (AQoL, range: -0.04 [worse than death] to 0 [death] to 1 [full health]) at ≥one of 3month, 6-month, 1-year, 2-year, 3-year, 4-year, 5-year, 7-year and 10-year interviews after stroke. Sociodemographic and health information were collected at baseline. We derived aSES from postcode using the Australian Socio-Economic Indexes For Area (2006) (categories: high, medium, low), and iSES from lifetime occupation (categories: non-manual, manual). Multivariable linear mixed effects modelling was used to estimate trajectories of HRQoL over 10 years, by aSES and iSES, adjusting for age, sex, cardiovascular disease, smoking, diabetes, stroke severity, stroke type, and the time influence on age and health conditions. RESULTS: Of 1,686 participants enrolled, we excluded 239 with 'possible' stroke and 284 with missing iSES. Among the remaining 1,163 participants, 1,123 (96.6%) had AQoL assessed at ≥3 timepoints. In multivariable analysis, over time, people in the medium aSES group had mean 0.02 (95% CI -0.06, 0.02) greater reduction in AQoL score, and people in the low aSES group had mean 0.04 (95% CI, -0.07, -0.001) greater reduction, than those in the high aSES group. Manual workers had an average 0.04 (95% CI, -0.07, -0.01) greater reduction in AQoL score over time than non-manual workers. CONCLUSIONS: Over time, HRQoL declines in all people with stroke, declining most rapidly in lower SES groups.

Genomic mapping of metastatic organotropism in lung adenocarcinoma.

We analyzed 2,532 lung adenocarcinomas (LUAD) to identify the clinicopathological and genomic features associated with metastasis, metastatic burden, organotropism, and metastasis-free survival. Patients who develop metastasis are younger and male, with primary tumors enriched in micropapillary or solid histological subtypes and with a higher mutational burden, chromosomal instability, and fraction of genome doublings. Inactivation of TP53, SMARCA4, and CDKN2A are correlated with a site-specific shorter time to metastasis. The APOBEC mutational signature is more prevalent among metastases, particularly liver lesions. Analyses of matched specimens show that oncogenic and actionable alterations are frequently shared between primary tumors and metastases, whereas copy number alterations of unknown significance are more often private to metastases. Only 4% of metastases harbor therapeutically actionable alterations undetected in their matched primaries. Key clinicopathological and genomic alterations in our cohort were externally validated. In summary, our analysis highlights the complexity of clinicopathological features and tumor genomics in LUAD organotropism.

Action Recognition Using a Spatial-Temporal Network for Wild Felines.

Behavior analysis of wild felines has significance for the protection of a grassland ecological environment. Compared with human action recognition, fewer researchers have focused on feline behavior analysis. This paper proposes a novel two-stream architecture that incorporates spatial and temporal networks for wild feline action recognition. The spatial portion outlines the object region extracted by Mask region-based convolutional neural network (R-CNN) and builds a Tiny Visual Geometry Group (VGG) network for static action recognition. Compared with VGG16, the Tiny VGG network can reduce the number of network parameters and avoid overfitting. The temporal part presents a novel skeleton-based action recognition model based on the bending angle fluctuation amplitude of the knee joints in a video clip. Due to its temporal features, the model can effectively distinguish between different upright actions, such as standing, ambling, and galloping, particularly when the felines are occluded by objects such as plants, fallen trees, and so on. The experimental results showed that the proposed two-stream network model can effectively outline the wild feline targets in captured images and can significantly improve the performance of wild feline action recognition due to its spatial and temporal features.

OncoTree: A Cancer Classification System for Precision Oncology.

PURPOSE: Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS: To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS: OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION: OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.

Prospective Genotyping of Hepatocellular Carcinoma: Clinical Implications of Next-Generation Sequencing for Matching Patients to Targeted and Immune Therapies.

PURPOSE: Prior molecular profiling of hepatocellular carcinoma (HCC) has identified actionable findings that may have a role in guiding therapeutic decision-making and clinical trial enrollment. We implemented prospective next-generation sequencing (NGS) in the clinic to determine whether such analyses provide predictive and/or prognostic information for HCC patients treated with contemporary systemic therapies. EXPERIMENTAL DESIGN: Matched tumor/normal DNA from patients with HCC (N = 127) were analyzed using a hybridization capture-based NGS assay designed to target 341 or more cancer-associated genes. Demographic and treatment data were prospectively collected with the goal of correlating treatment outcomes and drug response with molecular profiles. RESULTS: WNT/ß-catenin pathway (45%) and TP53 (33%) alterations were frequent and represented mutually exclusive molecular subsets. In sorafenib-treated patients (n = 81), oncogenic PI3K-mTOR pathway alterations were associated with lower disease control rates (DCR, 8.3% vs. 40.2%), shorter median progression-free survival (PFS; 1.9 vs. 5.3 months), and shorter median overall survival (OS; 10.4 vs. 17.9 months). For patients treated with immune checkpoint inhibitors (n = 31), activating alteration WNT/ß-catenin signaling were associated with lower DCR (0% vs. 53%), shorter median PFS (2.0 vs. 7.4 months), and shorter median OS (9.1 vs. 15.2 months). Twenty-four percent of patients harbored potentially actionable alterations including TSC1/2 (8.5%) inactivating/truncating mutations, FGF19 (6.3%) and MET (1.5%) amplifications, and IDH1 missense mutations (<1%). Six percent of patients treated with systemic therapy were matched to targeted therapeutics. CONCLUSIONS: Linking NGS to routine clinical care has the potential to identify those patients with HCC likely to benefit from standard systemic therapies and can be used in an investigational context to match patients to genome-directed targeted therapies.See related commentary by Pinyol et al., p. 2021.

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.

A new phenylethanoid glucoside from Plantago depressa Willd.

Chemical research of Plantago depressa Willd. led to one new phenylethanoid glucoside with α-L-rhamnosyl (1 → 2)-ß-D-glucose structure, together with four known compounds. These five compounds (1-5) were isolated from the family Plantaginaceae for the first time; the chemotaxonomic significance of cerebrosides was also discussed.

Ethylene inhibits darkness-induced stomatal closure by scavenging nitric oxide in guard cells of Vicia faba.

The plant hormone ethylene regulates many aspects of plant growth and development. Despite the well-known relationship between ethylene and stress signalling, the involvement of ethylene in regulating stomatal movement is not completely explored. Here, the role and association between nitric oxide (NO) reduction and the inhibition of darkness-induced stomatal closure by ethylene was studied. Physiological data are provided that both ethylene-releasing compound 2-chloroethylene phosphonic acid (ethephon, ETH) and 1-aminocyclopropane-1-carboxylic acid (ACC), the immediate precursor of ethylene, reduced the levels of NO in Vicia faba L. guard cells, and then induced stomatal opening in darkness. In addition, ACC and ETH not only reduced NO levels in guard cells caused by exogenous NO (derived from sodium nitroprusside, SNP) in light, but also abolished NO that had been generated during a dark period and promoted stomatal opening. Interestingly, 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (cPTIO) and hemoglobin (Hb), NO scavenger and the potent scavenger of NO/carbon monoxide (CO), respectively, also reduced NO levels by SNP and darkness. However, the above-mentioned effects of ACC and ETH were dissimilar to that of nitric oxide synthase (enzyme commission 1.14.13.39) inhibitor NG-nitro-L-Arg-methyl ester (L-NAME), which could neither reduce NO levels by SNP nor abolish NO that had been generated in the dark. Thus, it is concluded that ethylene reduces the levels of NO in V. faba guard cells via a pattern of NO scavenging, then induces stomatal opening in the dark.

Methane emissions during storage of different treatments from cattle manure in Tianjin.

Many studies on methane emissions from animal manure have revealed that animal manure is a major source of methane emissions to the atmosphere that can have negative consequences for people, animals and environment. In general, the release of methane can be influenced by the type of feed taken by animals, temperature, manure characteristics and so on. This study aimed at quantifying and comparing methane release from dairy manure with different piling treatments. Four treatments were designed including manure piling height 30, 45, 60 cm and adding 6 cm manure every day until the piling height was 60 cm. Static chamber method and gas chromatography were adopted to measure the methane emissions from April to June in 2009. Methane emission rates of all four manure treatments were low in the first week and then increased sharply until reaching the peak values. Subsequently, all the methane emission rates decreased and fluctuated within the steady range till the end of the experiment. Wilcoxon nonparametric tests analysis indicated that methane emission rate was greatly influenced by manure piling height and manner. There were no significant relationships between methane emission rates and the temperatures of ambience and heap. However, regression analysis showed that the quadratic equations were found between emission rates of all treatments and the gas temperature in the barrels.

Effects of diode laser irradiation on smear layer removal from root canal walls and apical leakage after obturation.

OBJECTIVE: The objective of this study was to investigate the rise in temperature in root surfaces during and immediately after diode laser irradiation, to observe morphological changes of root canal wall after irradiation, and to evaluate the apical leakage after irradiation and obturation in vitro. BACKGROUND DATA: There have been very few reports on root canal treatment by 980-nm wavelength diode laser. METHODS: Sixty-six extracted human single-rooted teeth were instrumented up to size 60 K-file, and then randomly divided into three groups of 22 teeth each. Groups 1 and 2 were irradiated with a diode laser at 5 W for 7 sec using fibers of diameters 550 and 365 microm, respectively. Group 3 was not irradiated, and served as a control. The rise in temperature on root surfaces of the teeth in groups 1 and 2 were measured by thermography. Six teeth in each group were bisected longitudinally and observed morphologically. Other teeth were obturated and immersed in rhodamine B solution, and the degree of apical leakage was evaluated longitudinally and transversally. RESULTS: A maximum temperature rise of 8.1( degrees )C was recorded in group 1. The smear layer in the laser-treated groups was evaporated and removed, resulting in clean root canal walls, which was significantly superior to the control group (p < 0.05). After obturation, the laser-treated groups showed significantly less apical leakage than the control group (p < 0.05). CONCLUSIONS: These results indicate that the diode laser is useful for removing smear layer and debris from root canal walls, and reducing apical leakage after obturation in vitro, and suggest that it would be useful for root canal treatment in clinic.

Persistent organochlorine residues in sediments of Haihe River and Dagu Drainage River in Tianjin, China.

Persistent organochlorine compounds were analyzed by means of GC-ECD in surface sediment samples from two selected rivers in Tianjin, Haihe River and Dagu Drainage River. A total of 16 surface sediment sites were selected along the both rivers. The frequency of detection of T-HCH and T-DDT in sediment samples both was up to 100%, which illustrated that the contamination of HCH and DDT was widespread in Haihe and Dagu Drainage Rivers. Results indicated that the concentrations of various pesticides in sediments from Haihe River were in the range of 3.30-75.96 ng/g dw for T-HCH and 1.57-211.57 ng/g dw for T-DDT. Compared with Haihe River, Dagu Drainage River was contaminated by HCHs and DDTs along the all locations and the values of T-HCH and T-DDT residues in sediments ranged from 2.30 to 124.61 ng/g dw and from 11.28 to 237.30 ng/g dw, respectively. The possible pollution sources were analyzed through monitoring results of organochlorine pesticides(OCPs) residues in sediments from the two rivers. The investigation also indicated that HCH was still used as pesticide in Tianjin partial area.

[General principles of urban ecological land classification and planning].

Urban ecological land planning is a difficult and urgent task in city layout. This paper presented the definition of urban ecological land, and according the definition, divided the urban ecological land into two groups, i. e., ecological land for service, and ecological land for functioning. Based on the principles of city layout, some measures to plan these two urban ecological land groups were proposed.