Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.

Formalin-fixed paraffin-embedded (FFPE) tissues are widely available specimens for clinical studies. However, RNA degradation in FFPE tissues often restricts their utility. In this study, we determined optimal FFPE preparation conditions, including tissue ischemia at 4°C (<48 h) or 25°C for a short time (0.5 h), 48-h fixation at 25°C and sampling from FFPE scrolls instead of sections. Notably, we observed an increase in intronic reads and a significant change in gene rank based on expression level in the FFPE as opposed to fresh-frozen (FF) samples. Additionally, we found that more reads were mapped to genes associated with chemical stimulus in FFPE samples. Furthermore, we demonstrated that more degraded genes in FFPE samples were enriched in genes with short transcripts and high free energy. Besides, we found 40 housekeeping genes exhibited stable expression in FF and FFPE samples across various tissues. Moreover, our study showed that FFPE samples yielded comparable results to FF samples in dimensionality reduction and pathway analyses between case and control samples. Our study established the optimal conditions for FFPE preparation and identified gene attributes associated with degradation, which would provide useful clues for the utility of FFPE tissues in clinical practice and research.

Evaluation of Walking Comfort in Children's School Travel at Street Scale: A Case Study in Tianjin (China).

(1) Background: school travel is an important part of a child's daily activities. A comfortable walking environment can encourage children to walk to school. The existing methods of evaluating walking environments are not specific to children's walks to school. (2) Methods: this study proposes a method of evaluating walking comfort in children traveling to school at street scale. Related indexes were selected that reflect children's school travel behavior and their needs in street environments based on walking environment audit tools. Factor analysis was then used to calculate the relative weight of each index. (3) Results: the new evaluation method was tested in the neighborhoods around the First Central Primary School in Hedong District, Tianjin, China. The walking comfort for children's school travel was evaluated in eight indexes: effective street width; street flatness; street cleanliness; interface diversity; buffer; shade coverage; green looking ratio; and sound decibels. Different classes and types of streets were found to have various vulnerabilities. (4) Conclusions: this evaluation method can accurately locate the weak spots in streets to improve the local policymakers' perception of street environments, which can greatly facilitate the implementation of precise measures to promote children walking to school.

RETRACTED: Enhanced antitumor efficacy of 5-fluorouracil loaded methoxy poly(ethylene glycol)-poly(lactide) nanoparticles for efficient therapy against breast cancer.

In the present study, a novel nanocarrier was developed for the delivery of anticancer drug to the cancer tissues. For this purpose, 5-FU loaded methoxy poly(ethylene glycol)-poly(lactide) (mPEG-PLA) (5-FU NP) based polymeric nanoparticles was designed to increase the chemotherapeutic efficacy against breast cancers. Nanoprecipitation method was used to prepare the drug-loaded nanoparticles. The nanoparticle was evaluated in terms of DLS, TEM, in vitro release kinetics, and in vivo parameters. The average particle diameter of drug loaded NP was ∼110 nm and exhibited a sustained drug release pattern for up to 120 h. The NP exhibited a pH-response drug release pattern with accelerated release at acidic media. The in vitro cytotoxicity assay showed the enhanced cytotoxicity effect of NP formulations in comparison to free drug. The NP system showed remarkable G2/M phase cell cycle arrest with significant amount of apoptosis cells in late and early phase of flow cytometer analysis. Consistently, NP formulation greatly decreased the tumor burden of mice with no sign of adverse effect. TUNEL assay further confirmed the superior anticancer effect of NP formulations which showed a high number of apoptotic cells. The favorable results obtained from this study highlights the potential application of encapsulated 5-FU NP in the treatment of breast cancers. The remarkable anticancer therapeutic efficacy with negligible toxicity profile of 5-FU NP makes it one of the possible alternative for the successful breast cancer therapy.

[A technique for generating natural color images based on local endmembers].

A method for generating natural color composite of satellite images based on local endmembers of ground features was proposed. First, the reference satellite image which has similar land cover types with the target satellite image is segmented into multiple local patches. Secondly, endmembers of ground features are extracted from each local patch, then we choose better end-members and gather them into a sample set. Thirdly, we use the sample set to build up the relationship between the spectral values of the blue band and the other bands. Finally, the spectrum relationship is used to generate natural color composite of the target image. The verification experiment on Landsat TM5 images shows that the proposed method is reliable and stable to generate the natural color composite of images. The other experiment on IRS-P6 images shows that our method is able to promote for other satellite images. In experiments, we also compared the existing "reference image-image" method and "spectral library-image" method qualitatively and quantificationally, indicating that our method is more precise to simulate spectrums of all kinds of ground features.

[A spatial adaptive algorithm for endmember extraction on multispectral remote sensing image].

Due to the problem that the convex cone analysis (CCA) method can only extract limited endmember in multispectral imagery, this paper proposed a new endmember extraction method by spatial adaptive spectral feature analysis in multispectral remote sensing image based on spatial clustering and imagery slice. Firstly, in order to remove spatial and spectral redundancies, the principal component analysis (PCA) algorithm was used for lowering the dimensions of the multispectral data. Secondly, iterative self-organizing data analysis technology algorithm (ISODATA) was used for image cluster through the similarity of the pixel spectral. And then, through clustering post process and litter clusters combination, we divided the whole image data into several blocks (tiles). Lastly, according to the complexity of image blocks' landscape and the feature of the scatter diagrams analysis, the authors can determine the number of endmembers. Then using hourglass algorithm extracts endmembers. Through the endmember extraction experiment on TM multispectral imagery, the experiment result showed that the method can extract endmember spectra form multispectral imagery effectively. What's more, the method resolved the problem of the amount of endmember limitation and improved accuracy of the endmember extraction. The method has provided a new way for multispectral image endmember extraction.