A Rapid Segmentation-Insensitive "Digital Biopsy" Method for Radiomic Feature Extraction: Method and Pilot Study Using CT Images of Non-Small Cell Lung Cancer.

Quantitative imaging approaches compute features within images' regions of interest. Segmentation is rarely completely automatic, requiring time-consuming editing by experts. We propose a new paradigm, called "digital biopsy," that allows for the collection of intensity- and texture-based features from these regions at least 1 order of magnitude faster than the current manual or semiautomated methods. A radiologist reviewed automated segmentations of lung nodules from 100 preoperative volume computed tomography scans of patients with non-small cell lung cancer, and manually adjusted the nodule boundaries in each section, to be used as a reference standard, requiring up to 45 minutes per nodule. We also asked a different expert to generate a digital biopsy for each patient using a paintbrush tool to paint a contiguous region of each tumor over multiple cross-sections, a procedure that required an average of <3 minutes per nodule. We simulated additional digital biopsies using morphological procedures. Finally, we compared the features extracted from these digital biopsies with our reference standard using intraclass correlation coefficient (ICC) to characterize robustness. Comparing the reference standard segmentations to our digital biopsies, we found that 84/94 features had an ICC >0.7; comparing erosions and dilations, using a sphere of 1.5-mm radius, of our digital biopsies to the reference standard segmentations resulted in 41/94 and 53/94 features, respectively, with ICCs >0.7. We conclude that many intensity- and texture-based features remain consistent between the reference standard and our method while substantially reducing the amount of operator time required

Quality evaluation of mycelial Antrodia camphorata using high-performance liquid chromatography (HPLC) coupled with diode array detector and mass spectrometry (DAD-MS)

<p>Abstract</p> <p>Background</p> <p><it>Antrodia camphorata </it>(AC) is an important fungus native to Taiwanese forested regions. Scientific studies have demonstrated that extracts of AC possess a variety of pharmacological functions. This study aims to identify the full profile fingerprint of nucleosides and nucleobases in mycelial AC and to assess the quality of two commercial mycelial AC products.</p> <p>Methods</p> <p>High-performance liquid chromatography coupled with diode array detector and mass spectrometry was employed to identify the major components in mycelial AC. The chemical separation was carried out using a gradient program on a reverse phase Alltima C₁₈AQ analytical column (250 × 4.6 mm, 5 μm) with the mobile phase consisting of deionized water and methanol.</p> <p>Results</p> <p>Ten nucleosides and nucleobases, two maleimide derivatives, and a sterol were identified as the major constituents in mycelial AC. These groups of chemical compounds constitute the first chromatographic fingerprint as an index for quality assessment of this medicinal fungus.</p> <p>Conclusions</p> <p>This study provides the first chromatographic fingerprint to assess the quality of mycelial AC.</p

The formation of a nanohybrid shish-kebab (NHSK) structure in melt-processed composites of poly (ethylene terephthalate) (PET) and multi-walled carbon nanotubes (MWCNTs)

The combination of synchrotron Small- and Wide-Angle X-ray scattering (SAXS/WAXS), and thermal analysis was used to follow the evolution of crystalline morphology and crystallization kinetics in a series of melt-processed composites of poly(ethylene terephthalate) (PET) and multiwall carbon nanotubes (MWCNT). The as-extruded PET-MWCNT composites underwent both hot and cold isothermal crystallizations where a final oriented nanohybrid shish-kebab (NHSK) crystalline structure was observed. An oriented NHSK structure was seen to persist even after melting and recrystallization of the composites. From the scattering data, we propose a model whereby the oriented MWCNTs act as heterogeneous nucleation surfaces (shish) and the polymer chains wrap around them and the crystallites (kebabs) grow epitaxially outwards during crystallization. However, depending on crystallization temperature, unoriented crystallites also grow in the polymer matrix, resulting in a combination of a NHSK and lamellar morphology. In contrast, the neat PET homopolymer showed the sporadic nucleation of a classic unoriented lamellar structure under the same isothermal crystallization conditions. These results provide a valuable insight into the distinctive modification of the crystalline morphology of melt-processed polymer-MWCNT composites prior to any secondary processing, having a significant impact on the use of MWCNTs as fillers in the processing and modification of the physical and mechanical properties of engineering polymers

Structure evolution in poly(ethylene terephthalate) (PET) - Multi-walled carbon nanotube (MWCNT) composite films during <i>in-situ</i> uniaxial deformation

Combined small- and wide-angle X-ray scattering (SAXS/WAXS), mechanical and thermal techniques have been used to follow the morphology evolution in a series of poly(ethylene terephthalate) (PET) multiwall carbon nanotube (MWCNT) composite films during quasi solid-state uniaxial deformation at low strain rates. Uniaxially deformed PET-MWCNT films displayed improved mechanical properties compared with unfilled PET films. SAXS/WAXS data revealed a well oriented lamellar structure for unfilled PET films. In contrast, the PET-MWCNT composites revealed a nanohybrid shish-kebab (NHSK) morphology, with reduced orientation and crystallinity. Mechanistically, this morphology development is attributed to the MWCNTs acting as shish for the epitaxial growth of PET crystallites. Furthermore, nucleation and crystal growth occurs in the PET matrix, but MWCNTs ultimately inhibit crystallite development and hinder a final lamellar structure developing. The results show unequivocally the role MWCNTs play as nanofillers, in the morphology development, thermal and mechanical properties in composite polymer films

Evaluation of global fire simulations in CMIP6 Earth system models

Fire is the primary form of terrestrial ecosystem disturbance on a global scale and an important Earth system process. Most Earth system models (ESMs) have incorporated fire modeling, with 19 out of them submitting model outputs of fire-related variables to the Coupled Model Intercomparison Project Phase 6 (CMIP6). This study provides the first comprehensive evaluation of CMIP6 historical fire simulations by comparing them with multiple satellite-based products and charcoal-based historical reconstructions. Our results show that most CMIP6 models simulate the present-day global burned area and fire carbon emissions within the range of satellite-based products. They also capture the major features of observed spatial patterns and seasonal cycles, the relationship of fires with precipitation and population density, and the influence of El Ni&ntilde;o-Southern Oscillation (ENSO) on the interannual variability of tropical fires. Regional fire carbon emissions simulated by the CMIP6 models from 1850 to 2010 generally align with the charcoal-based reconstructions, although there are regional mismatches, such as in southern South America and eastern temperate North America prior to the 1910s and in temperate North America, eastern boreal North America, Europe, and boreal Asia since the 1980s. The CMIP6 simulations have addressed three critical issues identified in the CMIP5: (1) the simulated global burned area less than half of the observations, (2) the failure to reproduce the high burned area fraction observed in Africa, and (3) the weak fire seasonal variability. Furthermore, the CMIP6 models exhibit improved accuracy in capturing the observed relationship between fires and both climatic and socioeconomic drivers, and better align with the historical long-term trends indicated by charcoal-based reconstructions in most regions worldwide. However, the CMIP6 models still fail to reproduce the decline in global burned area and fire carbon emissions observed over the past two decades, mainly attributed to an underestimation of anthropogenic fire suppression, and the spring peak in fires in the Northern Hemisphere mid-latitudes, mainly due to an underestimation of crop fires. In addition, the model underestimates the fire sensitivity to wet-dry conditions, indicating the need to improve fuel wetness estimation. Based on these findings, we present specific guidance for fire scheme development and suggest the post-processing methodology for using CMIP6 multi-model outputs to generate reliable fire projection products

Incorporating connectivity into conservation planning for the optimal representation of multiple species and ecosystem services

Funding was provided by the Rainforest Trust foundation. Support was also provided by the Sabah Forest Department, Forest Research Centre, the South East Asia Rainforest Research Partnership, the U.N. Development Programme, the Universiti Malaysia Sabah (FRGS0414-STWN-1/2015), PACOS Trust, BC Initiative, the Natural Environment Research Council UK (grant NE/R009597/1), and the Universities of Aberdeen, Montana, and York. We are grateful to the numerous researchers that collected the data used in our analyses, as well as the local communities and government staff who manage forested areas across Sabah.Peer reviewedPostprin

Conservation assessment and spatial distribution of endemic orchids in Sabah, Borneo

Orchids are among the most threatened plants due to habitat loss and illegal harvesting for horticultural demands. Sabah is a centre of orchid diversity, with approximately 1300 species of which 250 orchid taxa are endemic to Sabah. In this study, we conducted an IUCN Red List assessment on 136 endemic species and used Maximum Entropy (MaxEnt) to develop species distribution models for 47 species. The species distribution models were developed using presence-only data and six environmental predictors. The accuracy of the models were assessed using the area under the curve (AUC) and models with an AUC of higher than 0.8 stacked together to produce a species richness heatmap. We found that 83% of the researched species were threatened, of which 14 species were assessed to be Critically Endangered, eight species as Endangered and 93 species as Vulnerable. The heatmap shows that all of the species occurred within the Totally Protected Area (TPA) network in western Sabah. The heatmap highlighted the mid-altitude areas adjacent to the Kinabalu and Crocker Range parks and Ulu Sipitang regions as areas with a high species richness that were outside the TPA network. These areas are also important for the conservation of the majority of the species assessed as Critically Endangered and Endangered. Urgent conservation actions are needed to protect these species from extinction. The results from this work will be used as part of an intensive conservation action plan for threatened endemic orchids of Sabah and used to identify important plant areas currently not within the existing TPA networ

Transcriptional Repressive H3K9 and H3K27 Methylations Contribute to DNMT1-Mediated DNA Methylation Recovery

DNA methylation and histone modifications are two major epigenetic events regulating gene expression and chromatin structure, and their alterations are linked to human carcinogenesis. DNA methylation plays an important role in tumor suppressor gene inactivation, and can be revised by DNA methylation inhibitors. The reversible nature of DNA methylation forms the basis of epigenetic cancer therapy. However, it has been reported that DNA re-methylation and gene re-silencing could occur after removal of demethylation treatment and this may significantly hamper the therapeutic value of DNA methylation inhibitors. In this study we have provided detailed evidence demonstrating that mammalian cells possess a bona fide DNA methylation recovery system. We have also shown that DNA methylation recovery was mediated by the major human DNA methyltransferase, DNMT1. In addition, we found that H3K9-tri-methylation and H3K27-tri-methylation were closely associated with this DNA methylation recovery. These persistent transcriptional repressive histone modifications may have a crucial role in regulating DNMT1-mediated DNA methylation recovery. Our findings may have important implications towards a better understanding of epigenetic regulation and future development of epigenetic therapeutic intervention

Gene Expression Profiling on the Molecular Action of Danshen-Gegen Formula in a Randomized Placebo-Controlled Trial of Postmenopausal Women with Hypercholesterolemia

The Danshen-Gegen formula (DG) is a traditional Chinese herbal formula which has long been used to treat cardiovascular disease. DG was found to be a cardiovascular tonic in our recent research. However, a comprehensive investigation of the molecular mechanism of DG in cardiovascular disease has not been performed. The aim of this study was to clarify the transcriptional profiling of genes modulated by DG on postmenopausal women by using DNAmicroarray technology. We obtained 29 whole blood samples both from DG-treated and placebo-treated subjects. Blood lipid profile and intima-media thickness (IMT) were measured. Affymetrix GeneChip was used to identify differentially expressed genes (DEGs), followed by validation by the real-time PCR method. The results showed that DG-treated group has a significant improvement in IMT and lipid profile as compared to placebo-treated group. For the genomic study, the DG-treated group has a higher number of DEGs identified as compared to the placebo-treated group. Two important biological processes of “regulation of systemic arterial blood pressure by hormone” and “regulation of smooth muscle proliferation” have been identified by GePS in the DG-treated group. No significant biological process and cellular components were identified in the placebo-treated group. This genomic study on the molecular action of DG in postmenopausal women gathered sufficient molecular targets and pathways to reveal that DG could improve neointima thickening and hypertension