Optimized kernel minimum noise fraction transformation for hyperspectral image classification

This paper presents an optimized kernel minimum noise fraction transformation (OKMNF) for feature extraction of hyperspectral imagery. The proposed approach is based on the kernel minimum noise fraction (KMNF) transformation, which is a nonlinear dimensionality reduction method. KMNF can map the original data into a higher dimensional feature space and provide a small number of quality features for classification and some other post processing. Noise estimation is an important component in KMNF. It is often estimated based on a strong relationship between adjacent pixels. However, hyperspectral images have limited spatial resolution and usually have a large number of mixed pixels, which make the spatial information less reliable for noise estimation. It is the main reason that KMNF generally shows unstable performance in feature extraction for classification. To overcome this problem, this paper exploits the use of a more accurate noise estimation method to improve KMNF. We propose two new noise estimation methods accurately. Moreover, we also propose a framework to improve noise estimation, where both spectral and spatial de-correlation are exploited. Experimental results, conducted using a variety of hyperspectral images, indicate that the proposed OKMNF is superior to some other related dimensionality reduction methods in most cases. Compared to the conventional KMNF, the proposed OKMNF benefits significant improvements in overall classification accuracy

Asymmetric response of soil methane uptake rate to land degradation and restoration: Data synthesis

Land degradation and restoration profoundly affect soil CH(4)uptake capacity in terrestrial ecosystems. However, a comprehensive assessment of the response of soil CH(4)uptake to land degradation and restoration at global scale is not available. Here, we present a global meta-analysis with a database of 228 observations from 83 studies to investigate the effects of land degradation and restoration on the capacity of soil CH(4)uptake. We found that land degradation significantly decreased the capacity of soil CH(4)uptake, except the conversion of pasture to cropland where the soil CH(4)uptake rate showed no response. In contrast, all types of land restoration significantly increased the capacity of soil CH(4)uptake. Interestingly, the response of soil CH(4)uptake rate to land degradation and restoration was asymmetric: the increased soil CH(4)uptake rate in response to the land restoration was smaller compared to the decrease in CH(4)uptake rate induced by the land degradation. The effect of land degradation on soil CH(4)uptake rate was not dependent on the time since land use change, but the CH(4)sink strength increased with the time since land restoration. The response of soil CH(4)uptake rate to both land degradation and restoration was predominantly regulated by changes in the soil water-filled pore space, soil bulk density, and pH, whereas alterations in the substrate quantity and quality had negligible effect. Additionally, the effects of land degradation and restoration on soil CH(4)uptake were strongly related to the mean annual precipitation and soil texture. Overall, our results provide novel insights for understanding of how land degradation and restoration can affect the CH(4)sink strength of upland soils, and more importantly, our findings are beneficial to take measures to enhance the potential of soil CH(4)uptake in response to global land use change

Prognostic values of ALDOB expression and 18F-FDG PET/CT in hepatocellular carcinoma

PurposeThe glycolytic enzyme fructose 1,6-bisphosphate aldolase B (ALDOB) is aberrantly expressed and impacts the prognosis in hepatocellular carcinoma (HCC). Hepatic ALDOB loss leads to paradoxical upregulation of glucose metabolism, favoring hepatocellular carcinogenesis. Nevertheless, the relationship between ALDOB expression and 18F-fluorodeoxyglucose (18F-FDG) uptake, and their effects on HCC prognosis remain unclear. We evaluated whether ALDOB expression is associated with 18F-FDG uptake and their impacts on HCC prognosis prediction.MethodsChanges in ALDOB expression levels and the prognostic values in HCC were analyzed using data from The Cancer Genome Atlas (TCGA) database. Ultimately, 34 patients with HCC who underwent 18F-FDG positron emission tomography/computed tomography (PET/CT) preoperatively were enrolled in this retrospective study. ALDOB expression was determined using immunohistochemistry (IHC) staining, and the maximum standardized uptake value (SUVmax) of HCC was calculated from the 18F-FDG PET/CT scans. The relationship between ALDOB expression and SUVmax was examined, and their impacts on overall survival were evaluated using Cox proportional hazards models and Kaplan–Meier survival analysis. ALDOB overexpression in HUH7 and 7721 cells was used to analyze its role in tumor metabolism.ResultsAccording to TCGA database, the ALDOB mRNA level was downregulated in HCC compared to normal tissue, and significantly shortened overall survival in HCC patients. ALDOB protein expression was similarly decreased in IHC findings in HCC than that in adjacent normal tissues (P<0.05) and was significantly associated with tumor size (P<0.001), high tumor-node-metastasis stage (P=0.022), and elevated SUVmax (P=0.009). ALDOB expression in HCC was inversely correlated with SUVmax (r=-0.454; P=0.012), and the optimal SUVmax cutoff value for predicting its expression was 4.15. Prognostically, low ALDOB expression or SUVmax ≥3.9 indicated shorter overall survival time in HCC. Moreover, COX regression analysis suggested high SUVmax as an independent prognostic risk factor for HCC (P=0.036). HCC patients with negative ALDOB expression and positive SUVmax (≥3.9) were correlated with worse prognosis. ALDOB overexpression in HCC cells significantly decreases 18F-FDG uptake and lactate production.ConclusionSUVmax in HCC patients is inversely correlated with ALDOB expression, and 18F-FDG PET/CT may be useful for ALDOB status prediction. The combined use of ALDOB expression and 18F-FDG PET/CT data can provide additional information on disease prognosis in HCC patients

FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in Arabidopsis

[EN] Receptor-like kinase FERONIA (FER) plays a crucial role in plant response to small molecule hormones [e.g., auxin and abscisic acid (ABA)] and peptide signals [e.g., rapid alkalinization factor (RALF)]. It remains unknown how FER integrates these different signaling events in the control of cell growth and stress responses. Under stress conditions, increased levels of ABA will inhibit cell elongation in the roots. In our previous work, we have shown that FER, through activation of the guanine nucleotide exchange factor 1 (GEF1)/4/10-Rho of Plant 11 (ROP11) pathway, enhances the activity of the phosphatase ABA Insensitive 2 (ABI2), a negative regulator of ABA signaling, thereby inhibiting ABA response. In this study, we found that both RALF and ABA activated FER by increasing the phosphorylation level of FER. The FER loss-of-function mutant displayed strong hypersensitivity to both ABA and abiotic stresses such as salt and cold conditions, indicating that FER plays a key role in ABA and stress responses. We further showed that ABI2 directly interacted with and dephosphorylated FER, leading to inhibition of FER activity. Several other ABI2-like phosphatases also function in this pathway, and ABA-dependent FER activation required PYRABACTIN RESISTANCE (PYR)/PYR1-LIKE (PYL)/REGULATORY COMPONENTS OF ABA RECEPTORS (RCAR)-A-type protein phosphatase type 2C (PP2CA) modules. Furthermore, suppression of RALF1 gene expression, similar to disruption of the FER gene, rendered plants hypersensitive to ABA. These results formulated a mechanism for ABA activation of FER and for cross-talk between ABA and peptide hormone RALF in the control of plant growth and responses to stress signals.We thank Dr. Alice Cheung, Dr. Daniel Moura, Grossniklaus Ueli, Dr. Jigang Li, and Dr. Nieng Yan for providing plant, ABI1 antibody, or plasmid materials, and Dr. Legong Li for assistance in laser confocal microscopy. This work was supported by grants from National Natural Science Foundation of China (NSFC-31400232, 31571444), the State Key Laboratory of Molecular Developmental Biology (2015-MDB-KF-12), the Fundamental Research Funds for the Central Universities of China, and a grant from the National Science Foundation.Chen, J.; Yu, F.; Liu, Y.; Du, C.; Li, X.; Zhu, S.; Wang, X.... (2016). FERONIA interacts with ABI2-type phosphatases to facilitate signaling cross-talk between abscisic acid and RALF peptide in Arabidopsis. Proceedings of the National Academy of Sciences. 113(37):E5519-E5527. https://doi.org/10.1073/pnas.1608449113SE5519E55271133

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

<span style="font-size:13.0pt;font-family: "Times New Roman";mso-fareast-font-family:"Times New Roman";mso-ansi-language: EN-US;mso-fareast-language:EN-US;mso-bidi-language:AR-SA" lang="EN-US">Preparation and characterization of high surface area α-AlF₃</span>

927-930High surface area -AlF3 has been prepared by a carbon hard template method, Wherein -Al2O3 is immersed with sucrose aqueous solution and the dried mixture thermally treated under N2 flow at 450 oC to obtain the C@-Al2O3. C@-Al2O3 can be completely transformed to C@-AlF3 with hydrogen fluoride at 400 oC. After the carbon template in C@-AlF3 is removed by high temperature combustion, a high surface area -AlF3 (66 m2 g-1) is obtained. It is found that the fluorination process is crucial for the resulting -AlF3. Although high fluorination temperature is favorable to the formation of -AlF3, it also results in the decline of surface area.</span

Influence of neoadjuvant chemotherapy on prognosis of patients with synovial sarcoma

Abstract Background This study aimed to explore the clinical efficacy of neoadjuvant chemotherapy combined with surgery in primary synovial sarcoma of the limbs and trunk through retrospective analysis of patients with primary synovial sarcoma of the limbs and trunk treated by this treatment in our hospital. Methods A total of 89 patients diagnosed with synovial sarcoma were enrolled in this study between January 2005 and December 2011 in PLA General Hospital. Most of the patients received neoadjuvant chemotherapy combined with operative treatment (84.3%), 10.1% of them received adjuvant chemotherapy combined with operative treatment, and only 5.6% received merely operative treatment. The influence on the prognosis of patients with synovial sarcoma was analyzed by the statistics overall survival (OS), progression-free survival (PFS), local control (LC), and freedom from distant metastasis (FFDM). Results The median follow-up time was 68.6 months. The 5-year OS, 5-year PFS, 5-year LC, and 5-year FFDM of the patients were 80.2, 60.5, 78.8, and 80.8%, respectively. The OS of the patients with a tumor size >5 cm was lower (91.4 vs 73.1%, P < 0.05). Besides, the OS and FFDM of neoadjuvant chemotherapy were better than those of adjuvant chemotherapy (84.5 vs 55.6%, P = 0.015, and 83.8 vs 55.6%, P = 0.028, respectively). However, there was no significant difference in the LC and PFS. Conclusions Neoadjuvant chemotherapy was beneficial for patients with synovial sarcoma, and it could improve survival time and control distant metastasis. Tumor size was an important factor influencing patients’ prognosis