A refined therapeutic plan based on the machine-learning prognostic model of liver hepatocellular carcinoma.

To deeply explore new strategy of the individual therapy for the patients with liver hepatocellular carcinoma (LIHC), we observed gene expression profile in patients with LIHC and made a comprehensive analysis of the inflammation-related phenotypes, we detected a set of characteristic genes associated with the biological activities of tumor cells, among which 3 genes and 2 lncRNAs are tagged on the LIHC prognosis. Then we constructed a novel prognostic model by machine learning, called Inf-PR model, and evaluated the drug sensitivity and immune targets by a series of bioinformatics tools. Ten-fold cross-validation testified that the model achieved excellent performance on prediction and classification of prognostic risks, which was not only able to get more reliable prognosis information than the age, gender, grade and stage, but also exceeded those previously reported similar models. Accordingly, drug sensitivity was detected in different prognostic risk groups, the result displayed that 10 FDA-approved small molecular drugs including lovastatin and sorafenib had higher sensitivities and perturbativities in the high-risk group, and other 15 drugs including doxorubicin and lenvatinib had better sensitivities and perturbativities in the low-risk group. Moreover, it suggested the patients with high risk would better combine with immunotherapy than those with low risk. Taken together, this study presents a new individual precision strategy about drug and target selection to treat LIHC based on this evaluation model, which is a powerful supplement for current anti-tumor therapy.

Optical sequencing of single synthetic polymers.

Microscopic sequences of synthetic polymers play crucial roles in the polymer properties, but are generally unknown and inaccessible to traditional measurements. Here we report real-time optical sequencing of single synthetic copolymer chains under living polymerization conditions. We achieve this by carrying out multi-colour imaging of polymer growth by single catalysts at single-monomer resolution using CREATS (coupled reaction approach toward super-resolution imaging). CREATS makes a reaction effectively fluorogenic, enabling single-molecule localization microscopy of chemical reactions at higher reactant concentrations. Our data demonstrate that the chain propagation kinetics of surface-grafted polymerization contains temporal fluctuations with a defined memory time (which can be attributed to neighbouring monomer interactions) and chain-length dependence (due to surface electrostatic effects). Furthermore, the microscopic sequences of individual copolymers reveal their tendency to form block copolymers, and, more importantly, quantify the size distribution of individual blocks for comparison with theoretically random copolymers. Such sequencing capability paves the way for single-chain-level structure-function correlation studies of synthetic polymers.

Pathogenic fungi shape the fungal community, network complexity, and pathogenesis in kiwifruit.

Kiwifruit decay caused by endophytic fungi is affected by exogenous pathogens that trigger changes in fungal community composition and interact with the endophytic fungal community. Four fungal pathogens of kiwifruit were identified. These were Aspergillus japonicus, Aspergillus flavus, Botryosphaeria dothidea, and Penicillium oxalicum. Except for P. oxalicum, the remaining three species represent newly described pathogens of kiwifruit. All four fungal species caused disease and decay in mature kiwifruit. Results of the fungal community analysis indicated that three pathogens that A. japonicus, A. flavus and P. oxalicum were the most dominant, however, other fungal species that did not cause disease symptoms were also present. Positive interactions between fungal species were found in asymptomatic, symptomatic, and infected kiwifruit. The ability of all four pathogens to infect kiwifruit was confirmed in an inoculation experiment. The presence of any one of the four identified pathogens accelerated decay development and limited the postharvest longevity of harvested kiwifruit. Results of the study identified and confirmed the ability of four fungal species to infect and cause decay in harvested kiwifruit. Changes in the structure and composition of the kiwifruit microbiome during the decay process were also characterized. This provides a foundation for the further study of the microbiome of kiwifruit and their involvement in postharvest diseases.

Fluorescent Carbon Dots for Super-Resolution Microscopy.

Conventional fluorescence microscopy is limited by the optical diffraction of light, which results in a spatial resolution of about half of the light's wavelength, approximately to 250-300 nm. The spatial resolution restricts the utilization of microscopes for studying subcellular structures. In order to improve the resolution and to shatter the diffraction limit, two general approaches were developed: a spatially patterned excitation method and a single-molecule localization strategy. The success of super-resolution imaging relies on bright and easily accessible fluorescent probes with special properties. Carbon dots, due to their unique properties, have been used for super-resolution imaging. Considering the importance and fast development of this field, this work focuses on the recent progress and applications of fluorescent carbon dots as probes for super-resolution imaging. The properties of carbon dots for super-resolution microscopy (SRM) are analyzed and discussed. The conclusions and outlook on this topic are also presented.

Glucose detection through surface-enhanced Raman spectroscopy: A review.

Glucose detection is of vital importance to diabetes diagnosis and treatment. Optical approaches in glucose sensing have received much attention in recent years due to the relatively low cost, portable, and mini-invasive or non-invasive potentials. Surface enhanced Raman spectroscopy (SERS) endows the benefits of extremely high sensitivity because of enhanced signals and specificity due to the fingerprint of molecules of interest. However, the direct detection of glucose through SERS was challenging because of poor adsorption of glucose on bare metals and low cross section of glucose. In order to address these challenges, several approaches were proposed and utilized for glucose detection through SERS. This review article mainly focuses on the development of surface enhanced Raman scattering based glucose sensors in recent 10 years. The sensing mechanisms, rational design and sensing properties to glucose are reviewed. Two strategies are summarized as intrinsic sensing and extrinsic sensing. Four general categories for glucose sensing through SERS are discussed including SERS active platform, partition layer functionalized surface, boronic acid based sensors, and enzymatic reaction based biosensors. Finally, the challenges and outlook for SERS based glucose sensors are also presented.

Comparison of the Endophytic Bacterial Microbiota of Asymptomatic and Symptomatic Ginger Rhizomes During the Activation of Adventitious Bud Development.

Bacterial infections are the cause of rhizome rot in ginger (Zingiber officinale). Key members of the endophytic microbial community in ginger rhizomes have not been identified, and their impact on the decay of rhizomes during the activation of adventitious bud development has not been investigated. High-throughput, 16S rRNA amplicon sequencing and inoculation experiments were used to analyze the microbial diversity, community structure and composition, and pathogenicity of isolated bacteria. Our results indicated that the composition of the endophytic microbiota underwent a shift during the progression of rhizome rot disease. Enterobacteriaceae, Lachnospiraceae, and the bacterial genera Clostridium, Bacteroides, Acrobacter, Dysgonomonas, Anaerosinus, Pectobacterium, and Lactococcus were relatively abundant in the bacterial community of rhizomes exhibiting bacterial decay symptoms but were also present in asymptomatic rhizomes. The presence of Enterobacteriaceae and Pseudomonadaceae were positively correlated (ρ = 0.83) at the beginning of the sampling period in the symptomatic group, while a positive correlation (ρ = 0.89) was only observed after 20 days in the asymptomatic group. These data indicate that the co-occurrence of Enterobacteriaceae and Pseudomonadaceae may be associated with the development of ginger rot. Bacterial taxa isolated from ginger rhizomes, such as Enterobacter cloacae, E. hormaechei, and Pseudomonas putida, induced obvious rot symptoms when they were inoculated on ginger rhizomes. Notably, antibiotic-producing bacterial taxa in the Streptococcaceae and Flavobacteriaceae were also relatively abundant in rhizomes with rot and appeared to be linked to the onset of rhizome rot disease. Our results provide important information on the establishment and management of disease in ginger rhizomes.

A dual-control strategy based on electrode material and electrolyte optimization to construct an asymmetric supercapacitor with high energy density.

Metal-organic frames (MOFs) are regarded as excellent candidates for supercapacitors that have attracted much attention because of their diversity, adjustability and porosity. However, both poor structural stability in aqueous alkaline electrolytes and the low electrical conductivity of MOF materials constrain their practical implementation in supercapacitors. In this study, bimetallic CoNi-MOF were synthesized to enhance the electrical conductivity and electrochemical activity of nickel-based MOF, as well as the electrochemical performance of the CoNi-MOF in multiple alkaline electrolytes was investigated. The CoNi-MOF/active carbon device, as-fabricated with a 1 M KOH electrolyte, possesses a high energy density of 35 W h kg-1with a power density of 1450 W kg-1, exhibiting outstanding cycling stability of 95% over 10,000 cycles. The design of MOF-based electrode materials and the optimization selection of electrolytes pave the way for constructing high-performance supercapacitors.

Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit.

Alternaria alternata is a pathogen in a wide range of agriculture crops and causes significant economic losses. A strain of A. alternata (Y784-BC03) was isolated and identified from "Hongyang" kiwifruit and demonstrated to cause black spot infections on fruits. The genome sequence of Y784-BC03 was obtained using Nanopore MinION technology. The assembled genome is composed of 33,869,130bp (32.30Mb) comprising 10 chromosomes and 11,954 genes. A total of 2,180 virulence factors were predicted to be present in the obtained genome sequence. The virulence factors comprised genes encoding secondary metabolites, including non-host-specific toxins, cell wall-degrading enzymes, and major transcriptional regulators. The predicted gene clusters encoding genes for the biosynthesis and export of secondary metabolites in the genome of Y784-BC03 were associated with non-host-specific toxins, including cercosporin, dothistromin, and versicolorin B. Major transcriptional regulators of different mycotoxin biosynthesis pathways were identified, including the transcriptional regulators, polyketide synthase, P450 monooxygenase, and major facilitator superfamily transporters.

Preparation of Quasi-Three-Dimensional Porous Ag and Ag-NiO Nanofibrous Mats for SERS Application.

In this study, two new quasi-three-dimensional Surface Enhanced Raman Scattering (SERS) substrates, namely porous Ag and Ag-NiO nanofibrous mats, were prepared using a simple, electrospinning-calcination, two-step synthetic process. AgNO3/polyvinyl pyrrolidone (PVP) and AgNO3/Ni(NO3)2/PVP composites serving as precursors were electrospun to form corresponding precursory nanofibers. Porous Ag and Ag-NiO nanofibers were successfully obtained after a 3-h calcination at 500 °C under air atmosphere, and analyzed using various material characterization techniques. Synthesized, quasi-three-dimensional porous Ag and Ag-NiO nanofibrous mats were applied as SERS substrates, to measure the model compound Rhodamine 6G (R6G), and investigate the corresponding signal enhancement. Furthermore, porous Ag and Ag-NiO nanofibrous mats were employed as SERS substrates for melamine and methyl parathion respectively. Sensitive detection of melamine and methyl parathion was achieved, indicating their feasibility as an active SERS sensing platform, and potential for food safety and environmental monitoring. All the results suggest that the electrospinning-calcination, two-step method offers a new, low cost, high performance solution in the preparation of SERS substrates.

Natural or Natural-Synthetic Hybrid Polymer-Based Fluorescent Polymeric Materials for Bio-imaging-Related Applications.

Fluorescent polymeric materials such as hydrogels and particles have been attracting attention in many biomedical applications including bio-imaging, optical sensing, tissue engineering, due to their good biocompatibility, biodegradability, and advanced optical property. This review article aims at summarizing recent progress in fluorescent hydrogels and particles based on natural polymers or natural-synthetic hybrid polymers as the building blocks with a concentration on their bio-imaging-related applications. The challenges and future perspectives for the development of natural or natural-synthetic hybrid polymer-based fluorescent hydrogels and particles are also presented.

A Biocompatible and Biodegradable Protein Hydrogel with Green and Red Autofluorescence: Preparation, Characterization and In Vivo Biodegradation Tracking and Modeling.

Because of its good biocompatibility and biodegradability, albumins such as bovine serum albumin (BSA) and human serum albumin (HSA) have found a wide range of biomedical applications. Herein, we report that glutaraldehyde cross-linked BSA (or HSA) forms a novel fluorescent biological hydrogel, exhibiting new green and red autofluorescence in vitro and in vivo without the use of any additional fluorescent labels. UV-vis spectra studies, in conjunction with the fluorescence spectra studies including emission, excitation and synchronous scans, indicated that three classes of fluorescent compounds are presumably formed during the gelation process. SEM, FTIR and mechanical tests were further employed to investigate the morphology, the specific chemical structures and the mechanical strength of the as-prepared autofluorescent hydrogel, respectively. Its biocompatibility and biodegradability were also demonstrated through extensive in vitro and in vivo studies. More interestingly, the strong red autofluorescence of the as-prepared hydrogel allows for conveniently and non-invasively tracking and modeling its in vivo degradation based on the time-dependent fluorescent images of mice. A mathematical model was proposed and was in good agreement with the experimental results. The developed facile strategy to prepare novel biocompatible and biodegradable autofluorescent protein hydrogels could significantly expand the scope of protein hydrogels in biomedical applications.

One-pot and ultrafast synthesis of nitrogen and phosphorus co-doped carbon dots possessing bright dual wavelength fluorescence emission.

Very brief microwave heating of aniline, ethylene diamine, and phosphoric acid in water at ambient pressure generated nitrogen and phosphorus co-doped carbon dots (N,P-CDs) that exhibit bright dual blue (centred at 450 nm; 51% quantum yield) and green (centred at 510 nm, 38% quantum yield) fluorescence emission bands. The N,P-CDs were characterized using TEM, XRD, XPS, IR, UV-vis, and fluorescence spectroscopy, demonstrating their partially crystalline carbon, partially amorphous structures, and the incorporation of O, N, and P into the carbogenic scaffold. The N,P-CDs demonstrated excitation-dependent and nearly pH-independent emission properties. The unique dual emission properties lay the foundation for the use of N,P-CDs in ratiometric sensing applications.

Fluorescence based explosive detection: from mechanisms to sensory materials.

The detection of explosives is one of the current pressing concerns in global security. In the past few decades, a large number of emissive sensing materials have been developed for the detection of explosives in vapor, solution, and solid states through fluorescence methods. In recent years, great efforts have been devoted to develop new fluorescent materials with various sensing mechanisms for detecting explosives in order to achieve super-sensitivity, ultra-selectivity, as well as fast response time. This review article starts with a brief introduction on various sensing mechanisms for fluorescence based explosive detection, and then summarizes in an exhaustive and systematic way the state-of-the-art of fluorescent materials for explosive detection with a focus on the research in the recent 5 years. A wide range of fluorescent materials, such as conjugated polymers, small fluorophores, supramolecular systems, bio-inspired materials and aggregation induced emission-active materials, and their sensing performance and sensing mechanism are the centerpiece of this review. Finally, conclusions and future outlook are presented and discussed.

Fundamental Study of Electrospun Pyrene-Polyethersulfone Nanofibers Using Mixed Solvents for Sensitive and Selective Explosives Detection in Aqueous Solution.

Fluorescent pyrene-polyethersulfone (Py-PES) nanofibers were prepared through electrospinning technique using mixed solvents. The effects of mixed solvent ratio and polymer/fluorophore concentrations on electrospun nanofiber's morphology and its sensing performance were systematically investigated and optimized. The Py-PES nanofibers prepared under optimized conditions were further applied for highly sensitive detection of explosives, such as picric acid (PA), 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), and 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) in aqueous phase with limits of detection (S/N = 3) of 23, 160, 400, and 980 nM, respectively. The Stern-Volmer (S-V) plot for Py excimer fluorescence quenching by PA shows two linear regions at low (0-1 µM) and high concentration range (>1 µM) with a quenching constant of 1.263 × 10(6) M(-1) and 5.08 × 10(4) M(-1), respectively. On the contrary, S-V plots for Py excimer fluorescence quenching by TNT, DNT, and RDX display an overall linearity in the entire tested concentration range. The fluorescence quenching by PA can be attributed to the fact that both photoinduced electron transfer and energy transfer are involved in the quenching process. In addition, pyrene monomer fluorescence is also quenched and exhibits different trends for different explosives. Fluorescence lifetime studies have revealed a dominant static quenching mechanism of the current fluorescent sensors for explosives in aqueous solution. Selectivity study demonstrates that common interferents have an insignificant effect on the emission intensity of the fluorescent nanofibers in aqueous phase, while reusability study indicates that the fluorescent nanofibers can be regenerated. Spiked real river water sample was also tested, and negligible matrix effect on explosives detection was observed. This research provides new insights into the development of fluorescent explosive sensor with high performance.

Bimodular high temperature planar oxygen gas sensor.

A bimodular planar O2 sensor was fabricated using NiO nanoparticles (NPs) thin film coated yttria-stabilized zirconia (YSZ) substrate. The thin film was prepared by radio frequency (r.f.) magnetron sputtering of NiO on YSZ substrate, followed by high temperature sintering. The surface morphology of NiO NPs film was characterized by atomic force microscope (AFM) and scanning electron microscope (SEM). X-ray diffraction (XRD) patterns of NiO NPs thin film before and after high temperature O2 sensing demonstrated that the sensing material possesses a good chemical and structure stability. The oxygen detection experiments were performed at 500, 600, and 800°C using the as-prepared bimodular O2 sensor under both potentiometric and resistance modules. For the potentiometric module, a linear relationship between electromotive force (EMF) output of the sensor and the logarithm of O2 concentration was observed at each operating temperature, following the Nernst law. For the resistance module, the logarithm of electrical conductivity was proportional to the logarithm of oxygen concentration at each operating temperature, in good agreement with literature report. In addition, this bimodular sensor shows sensitive, reproducible and reversible response to oxygen under both sensing modules. Integration of two sensing modules into one sensor could greatly enrich the information output and would open a new venue in the development of high temperature gas sensors.

Boron removal from aqueous solution by direct contact membrane distillation.

The removal of boron from aqueous solution by direct contact membrane distillation (DCMD) was studied with self-prepared polyvinylidene fluoride (PVDF) hollow fiber membranes in the present work. The effect of pH, boron concentration, temperature and salt concentration of the feed solution on the boron rejection was investigated. The experimental results indicated that boron rejection was less dependent on the feed pH and salt concentration. DCMD process had high boron removal efficiency (>99.8%) and the permeate boron was below the maximum permissible level even at feed concentration as high as 750 mg/L. Although the permeate flux was enhanced exponentially with the feed temperature increasing, the influence of feed temperature on the boron rejection could be neglected. Finally, the natural groundwater sample containing 12.7 mg/L of boron was treated by DCMD process. The permeate boron kept below 20 microg/L whether the feed was acidified or not, but pre-acidification was helpful to maintain the permeate flux stability. All the experimental results indicated that DCMD could be efficiently used for boron removal from aqueous solution.

Fluoride removal from brackish groundwater by direct contact membrane distillation.

The direct contact membrane distillation applied for fluoride removal from brackish groundwater was investigated. The self-prepared polyvinylidene fluoride membrane exhibited high rejection of inorganic salt solutes. The maximum permeate flux 35.6 kg/(m2 x hr) was obtained with the feed solution at 80 degrees C and the cold distillate water at 20 degrees C. The feed concentration had no significant impact on the permeate flux and the rejection in fluoride. The precipitation of CaCO3 would clog the hollow fiber inlets and foul the membrane surface with increasing concentration factor when natural groundwater was used directly as the feed, which resulted in a rapid decline in the module efficiency. This phenomenon was diminished by acidification of the feed. The experimental results showed that the permeate flux and the quality of obtained distillate kept stable before concentration factor reached 5.0 with the acidified groundwater as feed. The membrane module efficiency began to decline gradually when the feed continued to be concentrated, which can be mainly attributed to the formation of CaF2 deposits on the membrane surface. In addition, a 300 hr continuous fluoride removal experiment of acidified groundwater was carried out with concentration factor at 4.0, the permeate flux kept stable and the permeate fluoride was not detected.