Total and component forest aboveground biomass inversion via LiDAR-derived features and machine learning algorithms.

Forest aboveground biomass (AGB) and its biomass components are key indicators for assessing forest ecosystem health, productivity, and carbon stocks. Light Detection and Ranging (LiDAR) technology has great advantages in acquiring the vertical structure of forests and the spatial distribution characteristics of vegetation. In this study, the 56 features extracted from airborne LiDAR point cloud data were used to estimate forest total and component AGB. Variable importance-in-projection values calculated through a partial least squares regression algorithm were utilized for LiDAR-derived feature ranking and optimization. Both leave-one-out cross-validation (LOOCV) and cross-validation methods were applied for validation of the estimated results. The results showed that four cumulative height percentiles (AIH 30, AIH 40, AIH 20, and AIH 25), two height percentiles (H 8 and H 6), and four height-related variables (H mean, H sqrt, H mad, and H curt) are ranked more frequently in the top 10 sensitive features for total and component forest AGB retrievals. Best performance was acquired by random forest (RF) algorithm, with R 2 = 0.75, root mean square error (RMSE) = 22.93 Mg/ha, relative RMSE (rRMSE) = 25.30%, and mean absolute error (MAE) = 19.26 Mg/ha validated by the LOOCV method. For cross-validation results, R 2 is 0.67, RMSE is 24.56 Mg/ha, and rRMSE is 25.67%. The performance of support vector regression (SVR) for total AGB estimation is R 2 = 0.66, RMSE = 26.75 Mg/ha, rRMSE = 28.62%, and MAE = 22.00 Mg/ha using LOOCV validation and R 2 = 0.56, RMSE = 30.88 Mg/ha, and rRMSE = 31.41% by cross-validation. For the component AGB estimation, the accuracy from both RF and SVR algorithms was arranged as stem > bark > branch > leaf. The results confirmed the sensitivity of LiDAR-derived features to forest total and component AGBs. They also demonstrated the worse performance of these features for retrieval of leaf component AGB. RF outperformed SVR for both total and component AGB estimation, the validation difference from LOOCV and cross-validation is less than 5% for both total and component AGB estimated results.

Glycomic and transcriptomic response of GSC11 glioblastoma stem cells to STAT3 phosphorylation inhibition and serum-induced differentiation.

A glioblastoma stem cell (GSC) line, GSC11, grows as neurospheres in serum-free media supplemented with EGF (epidermal growth factor) and bFGF (basic fibroblast growth factor), and, if implanted in nude mice brains, will recapitulate high-grade glial tumors. Treatment with a STAT3 (signal transducer and activator of transcription 3) phosphorylation inhibitor (WP1193) or 10% FBS (fetal bovine serum) both led to a decrease in expression of the stem cell marker CD133 in GSC11 cells, but differed in phenotype changes. Altered glycolipid profiles were associated with some differentially expressed glycogenes. In serum treated cells, an overall increase in glycosphingolipids may be due to increased expression of ST6GALNAC2, a sialyltransferase. Serum treated cells express more phosphatidylcholine (PC), short chain sphingomyelin (SM) and unsaturated long chain phosphatidylinositol (PI). Decrease of a few glycosphingolipids in the STAT3 phosphorylation inhibited cells may be linked to decreased transcripts of ST6GALNAC2 and UGCGL2, a glucosylceramide synthase. A rare 3-sulfoglucuronylparagloboside carrying HNK1 (human natural killer-1) epitope was found expressed in the GSC11 and the phenotypically differentiated cells. Its up-regulation correlates with increased transcripts of a HNK1 biosynthesis gene, B3GAT2 after serum treatment. Taken together with a quantitative phosphoproteomic study of the same GSC line (C. L. Nilsson, et al. J. Proteome Res. 2010, 9, 430-443), this report represents the most complete systems biology study of cancer stem cell (CSC) differentiation to date. The synergies derived by the combination of glycomic, transcriptomic and phosphoproteomic data may aid our understanding of intracellular and cell-surface events associated with CSC differentiation.

Quantitative phosphoproteomic analysis of the STAT3/IL-6/HIF1alpha signaling network: an initial study in GSC11 glioblastoma stem cells.

Initiation and maintenance of several cancers including glioblastoma (GBM) may be driven by a small subset of cells called cancer stem cells (CSCs). CSCs may provide a repository of cells in tumor cell populations that are refractory to chemotherapeutic agents developed for the treatment of tumors. STAT3 is a key transcription factor associated with regulation of multiple stem cell types. Recently, a novel autocrine loop (IL-6/STAT3/HIF1alpha) has been observed in multiple tumor types (pancreatic, prostate, lung, and colon). The objective of this study was to probe perturbations of this loop in a glioblastoma cancer stem cell line (GSC11) derived from a human tumor by use of a JAK2/STAT3 phosphorylation inhibitor (WP1193), IL-6 stimulation, and hypoxia. A quantitative phosphoproteomic approach that employed phosphoprotein enrichment, chemical tagging with isobaric tags, phosphopeptide enrichment, and tandem mass spectrometry in a high-resolution instrument was applied. A total of 3414 proteins were identified in this study. A rapid Western blotting technique (<1 h) was used to confirm alterations in key protein expression and phosphorylation levels observed in the mass spectrometric experiments. About 10% of the phosphoproteins were linked to the IL-6 pathway, and the majority of remaining proteins could be assigned to other interlinked networks. By multiple comparisons between the sample conditions, we observed expected changes and gained novel insights into the contribution of each factor to the IL6/STAT3/HIF1alpha autocrine loop and the CSC response to perturbations by hypoxia, inhibition of STAT3 phosphorylation, and IL-6 stimulation.

Polar lipid remodeling and increased sulfatide expression are associated with the glioma therapeutic candidates, wild type p53 elevation and the topoisomerase-1 inhibitor, irinotecan.

We report changes in gene and polar lipid expression induced by adenovirus-delivered wild-type (wt) p53 gene and chemotherapy of U87 MG glioblastoma cells, a treatment known to trigger apoptosis and cell cycle arrest. Sulfatides (sulfonated glycolipids) were most highly modulated by wild-type p53 treatment; however, no changes were observed in expression levels of mRNA for genes involved in sulfatide metabolism, indicating post-transcriptional control of sulfatide synthesis. Modulation of the aglycones of GD1 and GM1b was observed in wild-type p53-treated cells. The treatment also leads to an increase in phospholipids such as phosphatidyl inositols, phosphatidyl serines, phosphatidyl glycerols, and phosphatidyl ethanolamines, especially hydroxylated phospholipids. These dramatic changes in the composition of cellular glycolipids in response to p53 gene expression and cytotoxic chemotherapy treatment indicate the large role that they play in cell signaling. The use of the human glioma cell line U87 appears to be an excellent model system both in tissue culture and in intracranial murine xenograft models to further characterize the role of sulfatides in modulating glioma responsivity to therapeutic agents.

Forest structure dependency analysis of L-band SAR backscatter.

Forest structure plays an important role in forest biomass inversion using synthetic aperture radar (SAR) backscatter. Synthetic aperture radar (SAR) sensors with long-wavelength have the potentiality to provide reliable and timely forest biomass inversion for their ability of deep penetration into the forest. L-band SAR backscatter shows useful for forest above-ground biomass (AGB) estimation. However, the way that forest structure mediating the biomass-backscatter affects the improvement of the related biomass estimation accuracy. In this paper, we have investigated L-band SAR backscatter sensitivity to forests with different mean canopy density, mean tree height and mean DBH (diameter at breast height) at the sub-compartment level. The forest species effects on their relationship were also considered in this study. The linear correlation coefficient R, non-linear correlation parameter, Maximal Information Coefficient (MIC), and the determination coefficient R2 from linear function, Logarithmic function and Quadratic function were used in this study to analyze forest structural properties effects on L-band SAR backscatter. The HV channel, which is more sensitive than HH to forest structure parameters, was chosen as the representative of SAR backscatter. 6037 sub-compartment were involved in the analysis. Canopy density showed a great influence on L-band backscatter than mean forest height and DBH. All of the R between canopy density and L-band backscatter were greater than 0.7 during the forest growth cycle. The sensitivity of L-band backscatter to mean forest height depends on forest canopy density. When canopy density was lower than 0.4, R values between mean forest height are smaller than 0.5. In contrast, the values of R were greater than 0.8 if canopy density was higher than 0.4. The sensitivity SAR backscatter to DBH fluctuated with canopy density, but it only showed obvious sensitivity when canopy density equals to 0.6, where both the linear and non-liner correlation values are higher than others. However, their effects on L-bang HV backscatter are affected by forest species, the effects on three forest structural parameters depend on tree species.

Reversible and High-Temperature-Stabilized Strain in (Pb,La)(Zr,Sn,Ti)O3 Antiferroelectric Ceramics.

Antiferroelectric (AFE) materials have a tremendous advantage as smart materials and large-strain actuators due to their unique reversible characteristic electric-field-induced strain (electrostrain) responses in comparison to piezoelectric effect and electrostriction. A key limitation to today's AFE actuators, however, is the poor temperature stability of electrostrain. In this work, a large reversible strain of 0.4% and an excellent thermal stability with a variation within ±5.5% from 20 to 190 °C were achieved for (Pb0.97La0.02)(Zr0.85Sn0.08Ti0.07)O3 (PLZST) AFE ceramics. A room-temperature electrostrain of 0.71% was obtained in virgin PLZST ceramics. It is intriguing to observe inconsistent strain curves between the first and further measured cycles, implying an incomplete reversible field-induced AFE-ferroelectric phase transition. A sharp electrostrain response in milliseconds was realized in the as-prepared PLZST ceramics. In addition, a phenomenological explanation was proposed to explain the extraordinary phenomena. Our results may shed light on the origin of the superior strain behaviors in AFE materials from the view of microscopic structure and macroscopic properties, and probably improve the understanding of the AFE phase transition.

Giant Negative Electrocaloric Effect in (Pb,La)(Zr,Sn,Ti)O3 Antiferroelectrics Near Room Temperature.

(Pb0.97La0.02)(Zr xSn0.94- xTi0.06)O3 (PLZST) antiferroelectric ceramics with x = 0.75-0.90 have been fabricated and found to be a novel electrocaloric material system with a giant negative electrocaloric effect (Δ T = -11.5 K) and a large electrocaloric strength (|Δ T/Δ E| = 0.105 K cm kV-1) near room temperature. Additionally, the PLZST antiferroelectric ceramic also exhibits a large positive electrocaloric effect around the Curie temperature. The giant negative effect and the coexistence of both positive and negative electrocaloric effects in one material indicate a promising possibility to develop mid- to large-scale solid-state cooling devices with high efficiency.

Delta24-hyCD adenovirus suppresses glioma growth in vivo by combining oncolysis and chemosensitization.

Replication-competent adenoviruses could provide an efficient method for delivering therapeutic genes to tumors. The most promising strategies among adenovirus-based oncolytic systems are designed to exploit free E2F-1 activity in cancer cells, which in the absence of pRb activates transcription and regulates the expression of genes involved in differentiation, proliferation, and apoptosis. We previously developed Delta24, an E1A-mutant, conditionally replicative oncolytic adenovirus. Here, we examine the ability of a second-generation Delta24 (Delta24-hyCD) engineered to express a humanized form of the Saccharomyces cerevisiae cytosine deaminase gene (hyCD). Real-time quantitative PCR, Western blotting, thin-layer chromatography, and radioisotope quantitative enzymatic assays confirmed the production of a catalytically active hyCD enzyme in the setting of an oncolytic infection in vitro; other experiments assessing local production of 5-fluorouracil and a concomitant bystander effect showed improved cytotoxicity. The IC50 dose of 5-fluorocytosine (5-FC) required for a complete cytopathic effect by the Delta24-hyCD virus was fivefold lower than with Delta24 alone in U251MG and U87MG malignant glioma (MG) cell lines. Intratumoral treatment of mice bearing intracranial U87MG xenografts with Delta24-hyCD+5-FC significantly improved survival, confirming that Delta24-hyCD with 5-FC is a more efficient anticancer tool than Delta24 alone. Histopathologically, Delta24-hyCD replication was accompanied by progressively augmented oncolysis and drug-induced necrosis. These findings demonstrate that Delta24-hyCD with concomitant systemic 5-FC is a significant improvement over the earlier Delta24 oncolytic tumor-selective strategy for therapy of experimental gliomas.

Expression of ssDNA in mammalian cells.

Antisense therapy involves the use of antisense oligonucleotides for altering targeted gene function. However, the low efficiency of cell delivery of antisense oligonucleotides has limited the efficacy of antisense therapeutic approaches. RNA-based antisense or ribozyme oligonucleotides can be either synthesized endogenously (e.g., by a viral vector) or delivered exogenously. However, there is presently no vector delivery system available for DNA-based oligonucleotides. Recently, a novel ssDNA expression vector that can generate intracellularly any ssDNA molecule, such as antisense oligonucleotide or DNA enzyme, has been developed in our laboratory. Here we describe an improved expression vector based on the first-generation two-vector system. To test this new expression vector, we chose to express a single-stranded "10-23" DNA enzyme targeting c-raf mRNA in the human lung carcinoma A549 cell line. After introduction into cells by transient transfection, c-raf-cleaving DNA enzymes produced by this expression vector can significantly suppress the expression of c-raf mRNA. Furthermore, the expressed c-raf DNA enzymes induced cell apoptosis, as indicated by genomic DNA fragmentation assay. Our study further demonstrates the feasibility of using this novel ssDNA expression technology to produce intracellularly any sequence of interest, including antisense oligonucleotides and DNA enzyme molecules.

Tumor invasion after treatment of glioblastoma with bevacizumab: radiographic and pathologic correlation in humans and mice.

Patients with recurrent malignant glioma treated with bevacizumab, a monoclonal antibody to vascular endothelial growth factor (VEGF), alone or in combination with irinotecan have had impressive reductions in MRI contrast enhancement and vasogenic edema. Responses to this regimen, as defined by a decrease in contrast enhancement, have led to significant improvements in progression-free survival rates but not in overall survival duration. Some patients for whom this treatment regimen fails have an uncharacteristic pattern of tumor progression, which can be observed radiographically as an increase in hyperintensity on T2-weighted or fluid-attenuated inverse recovery (FLAIR) MRI. To date, there have been no reports of paired correlations between radiographic results and histopathologic findings describing the features of this aggressive tumor phenotype. In this study, we correlate such findings for 3 illustrative cases of gliomas that demonstrated an apparent phenotypic shift to a predominantly infiltrative pattern of tumor progression after treatment with bevacizumab. Pathologic examination of abnormal FLAIR areas on MRI revealed infiltrative tumor with areas of thin-walled blood vessels, suggesting vascular "normalization," which was uncharacteristically adjacent to regions of necrosis. High levels of insulin-like growth factor binding protein-2 and matrix metalloprotease-2 expression were seen within the infiltrating tumor. In an attempt to better understand this infiltrative phenotype associated with anti-VEGF therapy, we forced a highly angiogenic, noninvasive orthotopic U87 xenograft tumor to become infiltrative by treating the mice with bevacizumab. This model mimicked many of the histopathologic findings from the human cases and will augment the discovery of alternative or additive therapies to prevent this type of tumor recurrence in clinical practice.

Method for lipidomic analysis: p53 expression modulation of sulfatide, ganglioside, and phospholipid composition of U87 MG glioblastoma cells.

Lipidomics can complement genomics and proteomics by providing new insight into dynamic changes in biomembranes; however, few reports in the literature have explored, on an organism-wide scale, the functional link between nonenzymatic proteins and cellular lipids. Here, we report changes induced by adenovirus-delivered wild-type p53 gene and chemotherapy of U87 MG glioblastoma cells, a treatment known to trigger apoptosis and cell cycle arrest. We compare polar lipid changes in treated cells and control cells by use of a novel, sensitive method that employs lipid extraction, one-step liquid chromatography separation, high-resolution mass analysis, and Kendrick mass defect analysis. Nano-LC FT-ICR MS and quadrupole linear ion trap MS/MS analysis of polar lipids yields hundreds of unique assignments of glyco- and phospholipids at sub-ppm mass accuracy and high resolving power (m/Deltam50% = 200 000 at m/z 400) at 1 s/scan. MS/MS data confirm molecular structures in many instances. Sulfatides are most highly modulated by wild-type p53 treatment. The treatment also leads to an increase in phospholipids such as phosphatidyl inositols, phosphatidyl serines, phosphatidyl glycerols, and phosphatidyl ethanolamines. An increase in hydroxylated phospholipids is especially noteworthy. Also, a decrease in the longer chain gangliosides, GD1 and GM1b, is observed in wild-type p53 (treated) cells.

Proteomic investigation of glioblastoma cell lines treated with wild-type p53 and cytotoxic chemotherapy demonstrates an association between galectin-1 and p53 expression.

Global protein analysis of treated and untreated glioblastoma cell lines was performed. Proteomic analysis revealed the identity of proteins that were significantly modulated by the treatment with wild-type TP53 and the cytotoxic chemotherapy SN38. In particular, galectin-1 was found to be negatively regulated by transfection with TP53 and further down-regulated by SN38. Expression level changes were confirmed by Western blot. Subsequent analysis of several high-grade glioma cell lines demonstrated very high levels of galectin-1, regardless if the cell lines contained mutant or wild-type TP53. High expression of galectin-1 in a human orthotopic murine tumor model was also detected by immunohistochemistry and revealed a consistent pattern of preferential expression in peripheral or leading tumor edges. Further examination of galectin-1 expression through microarray analysis in tumor materials from patients confirmed galectin-1 as a valuable biomarker and possible therapeutic target. These results demonstrate the utility of using proteomic approaches to interrogate and identify potential useful targets for cancer therapy by evaluating specific tumor responses, either positive or negative, to various therapies.

Temporal expression of type I interferon receptor in the peri-implantation ovine extra-embryonic membranes: demonstration that human IFNalpha can bind to this receptor.

Interferon-tau (IFNtau), produced by the trophectoderm of ruminant ungulates, binds to the type I IFN receptor (IFNAR) located at the uterine endometrium in a paracrine manner. Since IFNtau attenuates the secretory pattern of an endometrial luteolysin, prostaglandin F2alpha, IFNtau has been considered as a conceptus factor implicated in the process of maternal recognition of pregnancy. Here we report the presence of IFNAR subunit (IFNAR1) in ovine conceptuses during the period of peri-implantation development and demonstrate that 125I-human (h) IFNalpha binds to membrane preparations from ovine corpus luteum and conceptus. Using an antibody against hIFNAR1, immunohistochemical analysis revealed that IFNAR1 protein was present in day 14 and 16 conceptuses (day 0 = day of estrus) and luminal and glandular epithelia of the endometrium. Conceptus membrane proteins analyzed by western blot with the same antibody displayed immunoreactive bands at 95, 60 and 55 kDa while endometrial membrane proteins showed bands at 200, 95 and 55 kDa. Northern blot analysis revealed that IFNAR1 mRNA was present in days 15-19 conceptuses and day 18-19 allantoic membranes. Receptor binding studies indicated that 125I-hIFNalpha binding to day 16, but not earlier, conceptus membrane proteins could be displaced with hIFNalpha or ovine IFNtau. Based on Scatchard analysis, day 16 conceptus membranes contained 28 fmol IFNAR/mg protein with a dissociation constant of 300 pM. Cross-linking experiments demonstrated that 125I-hIFNalpha-receptor complex migrated at 120 kDa, indicating that the receptor component(s) was approximately 100 kDa. These data provide evidence that although the binding does not occur until day 16, ovine conceptuses possess IFNAR1 near or at the time of implantation, suggesting that IFNtau, a factor produced by the trophectoderm of ruminant ungulates, could act on the conceptus in an autocrine manner. In addition to functioning as an antiluteolytic factor, therefore, IFNtau may have a direct effect on conceptus development.