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In systems biology, inference of functional associations among genes is compelling because the construction of functional association networks facilitates biomarker discovery. Specifically, such gene associations in human can help identify putative biomarkers that can be used as diagnostic tools in treating patients. Although biomedical literature is considered a valuable data source for this task, currently only a limited number of webservers are available for mining gene-gene associations from the vast amount of biomedical literature using text mining techniques. Moreover, these webservers often have limited coverage of biomedical literature and also lack efficient and user-friendly tools to interpret and visualize mined relationships among genes. To address these limitations, we developed GAIL (Gene-gene Association Inference based on biomedical Literature), an interactive webserver that infers human gene-gene associations from Gene Ontology (GO) guided biomedical literature mining and provides dynamic visualization of the resulting association networks and various gene set enrichment analysis tools. We evaluate the utility and performance of GAIL with applications to gene signatures associated with systemic lupus erythematosus and breast cancer. Results show that GAIL allows effective interrogation and visualization of gene-gene networks and their subnetworks, which facilitates biological understanding of gene-gene associations. GAIL is available at . [ABSTRACT FROM AUTHOR]

Multi-arm multi-stage designs, in which multiple active treatments are compared to a control and accumulated information from interim data are used to add or remove arms from the trial, may reduce development costs and shorten the drug development timeline. As such, this adaptive update is a natural complement to Bayesian methodology in which the prior clinical belief is sequentially updated using the observed probability of success. Simulation is often required for planning clinical trials to accommodate the complexity of the design and to optimize key design characteristics. This paper addresses two key limiting factors in simulations, namely the computational burden and the time needed to obtain results. We first introduce a generic process for simulating Bayesian multi-arm multi-stage designs with binary endpoints. Then, to address the computational burden and time, we optimize the method for calculating the posterior probability and posterior predictive probability of success. [ABSTRACT FROM AUTHOR]

Abstract China's fallow compensation policy is known to be relatively simple and unsophisticated, and in much need of improvement. In seeking such improvement, this paper designed some alternative compensation schemes that include recultivation insurance, priority right of participation in the fallowing work or free agricultural inputs, but lower income subsidy, and reported on a choice experiment of alternatives with 421 peasant-farming households in Chaling County, Hunan Province – a fallow area of heavy-metal-contaminated farmland. A mixed logit model was used to compare the choices made between pilot and non-pilot villages, and the influencing factors involved. The results showed that most farmers preferred the alternative compensation schemes to the current policy, and income subsidy was not the only factor affecting their choices, which indicated recultivation insurance and a longer period of free agricultural inputs were also important. However, the preferences differed between pilot and non-pilot village farmers, in which the pilot village farmers were more willing to accept less income subsidy in favor of increased recultivation insurance and an extended period of free agricultural inputs. By contrast, non-pilot village farmers preferred to adopt an alternative compensation scheme with a priority right of participation in the fallowing work and high level of income subsidy. The possible reason for the differences was that the publicity and training activities provided by the government had changed the preferences of pilot village farmers. Generally, the effects of various forms of economic compensation and single cash payment were different about fallow compensation policy, and the preferences of farmers from different backgrounds might also vary from person to person. Different regions needed to design the fallow compensation policy according to practical problems in the use of farmland and farmers' preferences. Highlights • Choice experiment is used to compare the preference between pilot and non-pilot village farmers. • The effects of various forms of economic compensation and single cash payment are different. • The preferences of farmers from different backgrounds may be different. • Extra attention should be given to works such as fallow publicity and training. [ABSTRACT FROM AUTHOR]

A calix[4]arene (C4A)-functionalized (phthalocyaninato)(porphyrinato) europium(iii) triple-decker compound (Pc)Eu(Pc)Eu[T(C4A)PP] (1) is firstly designed, synthesized and prepared into well-organized films using a simple solution-processing quasi-Langmuir-Shäfer (QLS) method. The QLS film of 1 on an ITO (film 1/ITO) electrode, serving as a host–guest electrochemical recognition layer, is able to establish specific responses/interactions toward organic molecules with biological and drug interest including dopamine (DA), uric acid (UA), tyrosine (Tyr), tryptophan (Trp) and Acetaminophen (APAP), depending mainly on the matching degree of molecular dimensions between the analytes and the C4A cavity in addition to their chemical nature. More significantly, the film 1/ITO electrode shows a wide linear range of electrochemical detection (from 0.1 to 100 μM) to DA and APAP, with a high sensitivity of 53.0 and 94.3 μA mM−1 and a very low detection limit of 25 and 11 nM for DA and APAP, respectively, representing the best result among the nonenzymatic organic semiconductor-based biosensors. In particular, the film 1/ITO electrode exhibits excellent stability, reproducibility, high selectivity, and anti-interference nature for the detection of both DA and APAP, indicating the great potential of calix[n]arene macrocycle-modified tetrapyrrole rare earth sandwich compounds in the field of ultrasensitive and specific nonenzymatic sensors. [ABSTRACT FROM AUTHOR]

An amphiphilic perylenetetracarboxylic diimide derivative (APDI) is designed and synthesized. The highly ordered APDI/CdS hybrid film was obtained successfully via a novel layer-by-layer approach by using a simple H 2 S-vapor annealing over each layer of APDI/Cd 2+ Langmuir-Shäfer film fabricated from Langmuir monolayer of APDI molecules formed on the surface of CdCl 2 aqueous solution. Examination by spectroscopic methods revealed APDI molecules in the hybrid film adopt a typical H aggregation mode whereas those in pure film adopt a slipped co-facial stacking mode in an “edge-on” conformation. The wurtzite CdS nanoparticles have been incorporated successfully into APDI matrix. The film morphology changed obviously from elongated domains of ca. 70 nm in length in pure APDI film to small nanoparticles of ca. 55 nm in diameter in APDI/CdS hybrid film. In particular, energy transfer from CdS to APDI has been established in the hybrid film. [ABSTRACT FROM AUTHOR]

Two series of new Schiff base compounds were synthesized. For Schiff base compounds with a pyridine nitrogen atom in 4-position (7a–e), their supramolecular hydrogen bonding complexes show good liquid crystal properties. However, no liquid crystal property is observed for8a–e. Results of theoretical calculations demonstrate that it is the intermolecular hydrogen bond of Schiff base compounds (8a–e) that prevents the formation of supramolecular hydrogen bonding. The Schiff base compounds, with terminal alkoxy chains, can recognize Cu2+selectively with a color change. Nevertheless, others cannot recognize Cu2+. [ABSTRACT FROM AUTHOR]

Summary: Integration of genetic studies for multiple phenotypes is a powerful approach to improving the identification of genetic variants associated with complex traits. Although it has been shown that leveraging shared genetic basis among phenotypes, namely pleiotropy, can increase statistical power to identify risk variants, it remains challenging to effectively integrate genome-wide association study (GWAS) datasets for a large number of phenotypes. We previously developed graph-GPA, a Bayesian hierarchical model that integrates multiple GWAS datasets to boost statistical power for the identification of risk variants and to estimate pleiotropic architecture within a unified framework. Here we propose a novel improvement of graph-GPA which incorporates external knowledge about phenotype-phenotype relationship to guide the estimation of genetic correlation and the association mapping. The application of graph-GPA to GWAS datasets for 12 complex diseases with a prior disease graph obtained from a text mining of biomedical literature illustrates its power to improve the identification of risk genetic variants and to facilitate understanding of genetic relationship among complex diseases. [ABSTRACT FROM AUTHOR]

A series of poly(arylene ether)s, (PAEs), carrying a pendant diphenyl phosphoryl group were prepared via the nucleophilic aromatic substitution (NAS) reactions of 3,5-difluorotriphenylphosphine oxide, 6. The difluoro monomer 6 was synthesized via two-step reaction sequence and subsequently characterized by 1H, 13C, 19F, and 31P NMR spectroscopy, GC/MS, and elemental analysis. The reactivity of the electrophilic sites in 6, activated by only a diphenylphosphoryl group located in the meta-position, in 6 was probed via NMR spectroscopy and model reactions and was determined to be sufficient to undergo typical NAS reactions. High molecular weight, amorphous, organic soluble poly(arylene ether)s, bearing a pendant diphenylphosphoryl group, were prepared via the reaction of 6 with a variety of bis-phenols under typical NAS conditions. The poly(arylene ether)s were characterized for structure via the use of 1H, 13C, and 31P NMR spectroscopy while their thermal properties were evaluated using DSC and TGA analysis. The glass transition temperatures ( Tg) of the synthesized PAEs ranged from 143 to 175 °C, while their 5% weight loss temperatures ranged from 467 to 510 °C under nitrogen and from 470 to 526 °C in air. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011 [ABSTRACT FROM AUTHOR]

An alternative approach to an AB2 monomer, N-[3,5-bis(4-hydroxybenzoyl)benzene]-4-fluorophthalimde, 4, for hyperbranched poly(arylene ether ketone imide)s has been developed. The key steps were a para-position selective electrophilic aromatic substitution of fluorobenzene with 5-nitroisophthaloyl dichloride and a subsequent clean conversion of the aryl fluorides to phenol groups using potassium hydroxide as the nucleophile. The overall yield for the synthesis of 4 was 51.6%. [ABSTRACT FROM AUTHOR]

Background: In systems biology, it is of great interest to identify previously unreported associations between genes. Recently, biomedical literature has been considered as a valuable resource for this purpose. While classical clustering algorithms have popularly been used to investigate associations among genes, they are not tuned for the literature mining data and are also based on strong assumptions, which are often violated in this type of data. For example, these approaches often assume homogeneity and independence among observations. However, these assumptions are often violated due to both redundancies in functional descriptions and biological functions shared among genes. Latent block models can be alternatives in this case but they also often show suboptimal performances, especially when signals are weak. In addition, they do not allow to utilize valuable prior biological knowledge, such as those available in existing databases. Results: In order to address these limitations, here we propose PALMER, a constrained latent block model that allows to identify indirect relationships among genes based on the biomedical literature mining data. By automatically associating relevant Gene Ontology terms, PALMER facilitates biological interpretation of novel findings without laborious downstream analyses. PALMER also allows researchers to utilize prior biological knowledge about known gene-pathway relationships to guide identification of gene–gene associations. We evaluated PALMER with simulation studies and applications to studies of pathway-modulating genes relevant to cancer signaling pathways, while utilizing biological pathway annotations available in the KEGG database as prior knowledge. Conclusions: We showed that PALMER outperforms traditional latent block models and it provides reliable identification of novel gene–gene associations by utilizing prior biological knowledge, especially when signals are weak in the biomedical literature mining dataset. We believe that PALMER and its relevant user-friendly software will be powerful tools that can be used to improve existing pathway annotations and identify novel pathway-modulating genes. [ABSTRACT FROM AUTHOR]

Identification of cancer patient subgroups using high throughput genomic data is of critical importance to clinicians and scientists because it can offer opportunities for more personalized treatment and overlapping treatments of cancers. In spite of tremendous efforts, this problem still remains challenging because of low reproducibility and instability of identified cancer subgroups and molecular features. In order to address this challenge, we developed Integrative Genomics Robust iDentification of cancer subgroups (InGRiD), a statistical approach that integrates information from biological pathway databases with high-throughput genomic data to improve the robustness for identification and interpretation of molecularly-defined subgroups of cancer patients. We applied InGRiD to the gene expression data of high-grade serous ovarian cancer from The Cancer Genome Atlas and the Australian Ovarian Cancer Study. The results indicate clear benefits of the pathway-level approaches over the gene-level approaches. In addition, using the proposed InGRiD framework, we also investigate and address the issue of gene sharing among pathways, which often occurs in practice, to further facilitate biological interpretation of key molecular features associated with cancer progression. The R package "InGRiD" implementing the proposed approach is currently available in our research group GitHub webpage ( https://dongjunchung.github.io/INGRID/ ). [ABSTRACT FROM AUTHOR]

Abstract The mixing of land uses lies at the core of understanding their characteristics in cities. Some existing land use mix measures have been used to quantify the mix degree from different perspectives. However, these existing indices mainly cover only two dimensions of the land use mix concept, namely, distance and quantity, and cannot effectively delineate the picture of land use mix. Thus, we propose a new quantification framework of land use mix by involving a third dimension, that is, the "attribute" level of the land use mix concept. On the basis of this framework, we develop a novel measure called (weighted) vector-based mix degree index (VMDI/WVMDI) to address the compatibility mix degree by incorporating the compatibility relations between different land uses. This novel measure adopts vector land use data and compatibility relations. To some extent, VMDI/WVMDI can overcome some of the deficiencies of existing land use mix measures. We select Guangzhou as a study area in evaluating the proposed measure. In addition, the "head/tail breaks" classification scheme is employed for results with heavy-tailed distribution. By using this scheme, we clearly identify several clustered regions of land use mix in Guangzhou, which might be useful for urban planners and policy makers. Compared with some traditional measures, VMDI/WVMDI can be more efficient in depicting the compatibility relation between land use parcels. Highlights • A more effective quantification framework of land use mix is proposed. • A novel measure is developed to address the compatibility mix degree among different land uses. • The "Head/tail breaks" classification scheme is adopted to reveal the underlying scaling pattern of outcomes in Guangzhou. • By comparing with previous measures, this measure shows some superior at the quantification of compatibility relations. [ABSTRACT FROM AUTHOR]

The maximal procedure is a restricted randomization method that maximizes the number of feasible allocation sequences under the constraints of the maximum tolerated imbalance and the allocation sequence length. It assigns an equal probability to all feasible sequences. However, its implementation is not easy due to the lack of the Markovian property of the conditional allocation probabilities. In this paper, we propose the asymptotic maximal procedure, which replaces the sequence-length-dependent conditional allocation probabilities with their asymptotic values. The new randomization procedure is compared with the original maximal procedure and few other randomization procedures with the maximum tolerated imbalance via simulations and is found to be a practical choice for future clinical trials. [ABSTRACT FROM AUTHOR]

[Display omitted] • We evaluated urban land-use intensity from input, density and output. • The spillover effects of urban land-use intensity on CO 2 emissions were explored. • A machine learning method (BPNN) was proposed to predict CO 2 emissions. Currently, China will promote county towns' urbanization, and few studies have analyzed spatial effects of urban land-use intensity on CO 2 emissions and predicted CO 2 emissions at the county level accurately. Here, taking data from 2010 to 2015 at the county level of Zhejiang Province as an example, we analyzed the spatial effect of urban land-use intensity from three aspects of input, density and output on CO 2 emissions by the spatial Durbin model (SDM). And then a machine learning method of Back Propagation Neural Network (BPNN) was proposed to predict CO 2 emissions for 2035 nonlinearly under the different promotions of urban land-use intensity. The main result and conclusion showed that: (1) The spillover effects of urban land-use density were negatively related to CO 2 emissions, and urban land-use output intensity showed positive spillover effects on CO 2 emissions; (2) The prediction of BPNN showed that the improvement of urban land-use intensity would not be effective in CO 2 emissions reductions for southwestern counties with both low levels of urbanization and urban land-use intensity; (3) It was effective in CO 2 emissions reduction by slowing down the growth rate of urban land-use capital input intensity, especially for the northeast region which was developed by the port economy. Our study encouraged a regional differentiated urban land-use intensity improvement strategy for Zhejiang to achieve low carbon development. [ABSTRACT FROM AUTHOR]

Distance-based microfluidic paper-based analytical devices (μ PADs) are simple and user-friendly detection platforms for disease screening, environment monitoring and food safety. However, the current distance-based μ PADs still face major challenges of relatively low sensitivity and accuracy. In this work, we propose a novel chromogenic reaction-free distance-based (CRFD) μ PAD strategy for sensitive and accurate quantitation of microRNAs (miRNAs) via viscosity amplification and surface hydrophobicity modulations. The CRFD μ PAD with sampling, indicator (with red ink), and detection zones is scaled with reference patterns. Target miRNA in sample is pre-amplified with rolling circle amplification (RCA) reaction to specifically enhance its viscosity. The difference of flow between target and control is further enlarged on CRFD μ PADs whose surface hydrophobicity is rationally modulated by in situ metal-organic frameworks (MOFs) modification. Meanwhile, the repeatability and flow shape are significantly improved. For a proof-of-concept demonstration, the miR-221 and miR-222 in liver cells lysis were sensitively detected by naked-eye with limits of detection of 0.33 and 0.37 pM, respectively. A smartphone-based auto-reading system (SAS) was developed to further improve the accuracy and convenience, showing greatly reduced relative standard deviation (RSD) of assay from 12.2% to 1.0%. This facile and extensible strategy is promising for rapid detection in complex biosystem. [Display omitted] • Distance-based μ PADs without chromogenic reaction are used for microRNA detection. • Viscosity is specifically amplified by RCA to generate the flow distance difference. • Sensitivity is improved by in situ MOF modification that modulate the surface. • A smartphone-based system is developed to improve the accuracy and convenience. [ABSTRACT FROM AUTHOR]

Abstract: Two new Schiff base compounds, tailed by the fluoroalkoxy, were synthesized in a three-step process. Those supramolecular structures constructed by hydrogen bonding show good liquid crystal properties with higher clear points and wider mesomorphic phase ranges than other analogs containing a terminal alkoxy chain. Investigation of the optical textures by polarizing microscopy reveals that terminal fluorinated substituents convert the nematic phase of supramolecular hydrogen-bonding complexes with terminal alkoxy chains into the smectic A phase of those with terminal fluoroalkoxy chains. [Copyright &y& Elsevier]

The influence of a variety of factors on the photomechanical output of azo-CP2- xx systems is studied, primarily focusing on a sample with a higher crosslink density (30 mol%) and two new, structurally related crosslinked polyimides with modified backbone flexibility/rigidity. This work elucidates the strong coupling between geometrical considerations (reciprocal aspect ratio of cantilever) and the visualized mechanical response (e.g., flexural-torsional response of a cantilever). [ABSTRACT FROM AUTHOR]

The application of organic fertilizer by farmers is an important method for promoting the transition of agricultural production from increasing the yield to improving the quality and safety of agricultural products and realizing the green development of agriculture. The behavior of farmers can have a direct impact on organic fertilizer application, and the active participation of farmers can effectively reduce moral hazards and improve governance efficiency. A consensus appears to have been reached regarding the importance of land property rights stability (LPRS) for farmers' organic fertilizer application (FOFA) in China; however, few studies have focused on the conditions under which LPRS exerts an effect or the extent of the effect. Moreover, the grain-growing purpose and farm size are rarely included as driving factors underlying the impact of LPRS on FOFA; thus, biased estimations are easily formed. This study analyzed the influence mechanism of LPRS on FOFA and its dependent conditions using the 2017 China Rural Household Panel Survey from Zhejiang University and conducted an empirical analysis via a logit model. The results showed that LPRS could enable farmers to apply organic fertilizer, although the degree of its impact will vary due to differences in the grain-growing purpose and farm size. Currently, selling products is not conducive to the application of organic fertilizer and will reduce the positive impact of LPRS on the application of organic fertilizer by farmers, whereas expanding the farm size will enhance the positive impact of LPRS. The government should constantly improve the methods and channels for realizing high-quality and high-priced agricultural products and fully acknowledge the role of market demand in guiding farmers' agricultural production, which will increase their enthusiasm for organic fertilizer application. The government should also improve the contract management system for land transfer to strengthen the ability of farmers to expand their farm size to fully demonstrate the role of large-scale farmers. • Analyze the influencing mechanism of LPRS on FOFA. • Grain-growing purpose and farm size are the driving factors. • Selling grain will reduce the positive impact of LPRS on FOFA. • Expanding farm size will enhance the positive impact of LPRS on FOFA. • High-quality and high-priced agricultural products will encourage FOFA. [ABSTRACT FROM AUTHOR]