Model-based Analysis of ChIP-Seq (MACS) is a computational algorithm for identifying genome-wide protein-DNA interaction from ChIP-Seq data. MACS combines multiple modules to process aligned ChIP-Seq ...reads for either transcription factor or histone modification by removing redundant reads, estimating fragment length, building signal profile, calculating peak enrichment, and refining and reporting peak calls. In this protocol, we provide a detailed demonstration of how to apply MACS to analyze ChIP-Seq datasets related to protein-DNA interactions in embryonic stem cells (ES cells). Instruction on how to interpret and visualize the results is also provided. MACS is an open-source and is available from http://github.com/taoliu/MACS.
Background and Aim
Irritable bowel syndrome (IBS) is a highly prevalent chronic functional gastrointestinal disorder. Recent studies have showed increasing important role of gut microbiota in the ...pathophysiological changes of IBS. Our study aims to elaborate the association between intestinal flora with the genesis and the development of IBS.
Methods
Illumina high‐throughput sequencing technology was applied to investigate microbial communities of IBS patients and healthy donors. Stool specimens from the IBS‐D patients were equally premixed and implanted into germ free C57B/6 mice to construct IBS animal model, and the normal group was also transplanted with normal premixed feces. The post‐transplant defecation and intra‐epithelial lymphocyte counts were evaluated. Microbial communities were also checked by the illumina high‐throughput sequencing technology.
Results
Fifteen genuses significantly different were found expressed in the gut flora of IBS patients, and six genuses showed significantly different abundances between the stool specimens of mice of IBS group and normal group. Among these differences, Parasutterella expression was remarkably different in both screening and validation experiments and also related to chronic intestinal inflammation; therefore, Parasutterella expression is considered in association with the development and progression of IBS.
Conclusion
Parasutterella may be related with the genesis and development of IBS and also associated with chronic intestinal inflammation in IBS patients.
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Neuro-oncological ventral antigen 1 (Nova1) is a neuron-specific RNA-binding protein in human paraneoplastic opsoclonus-myoclonus ataxia accompanying with malignant tumors, but its role in ...hepatocellular carcinoma (HCC) remains elusive. In this study, we found that overexpressed intratumoral Nova1 was associated with poor survival rate and increased recurrence rate of HCC, especially early recurrence, and was an independent prognostic factor for overall survival rate and tumor recurrence. HCC cell lines over-expressing Nova1 exhibited greater potentials in cell proliferation, invasion and migration, while knockdown of Nova1 had the opposite effects. All these findings indicate that Nova1 may act as a prognostic marker for poor outcome and high recurrence in HCC.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Developing noble‐metal‐free electrocatalysts is important to industrially viable ammonia synthesis through the nitrogen reduction reaction (NRR). However, the present transition‐metal ...electrocatalysts still suffer from low activity and Faradaic efficiency due to poor interfacial reaction kinetics. Herein, an interface‐engineered heterojunction, composed of CoS nanosheets anchored on a TiO2 nanofibrous membrane, is developed. The TiO2 nanofibrous membrane can uniformly confine the CoS nanosheets against agglomeration, and contribute substantially to the NRR performance. The intimate coupling between CoS and TiO2 enables easy charge transfer, resulting in fast reaction kinetics at the heterointerface. The conductivity and structural integrity of the heterojunction are further enhanced by carbon nanoplating. The resulting C@CoS@TiO2 electrocatalyst achieves a high ammonia yield (8.09×10−10 mol s−1 cm−2) and Faradaic efficiency (28.6 %), as well as long‐term durability.
Junction box: An interface‐engineered heterojunction, composed of carbon‐nanoplated CoS@TiO2 nanofibrous membrane, is developed for the nitrogen reduction reaction. The resulting C@CoS@electrocatalyst achieves strikingly high ammonia yield (8.09×10−10 mol s−1 cm−2) and Faradaic efficiency (28.6 %), as well as long‐term durability.
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Lithium–sulfur (Li–S) batteries hold the promise of the next generation energy storage system beyond state‐of‐the‐art lithium‐ion batteries. Despite the attractive gravimetric energy density (WG), ...the volumetric energy density (WV) still remains a great challenge for the practical application, based on the primary requirement of Small and Light for Li–S batteries. This review highlights the importance of cathode density, sulfur content, electroactivity in achieving high energy densities. In the first part, key factors are analyzed in a model on negative/positive ratio, cathode design, and electrolyte/sulfur ratio, orientated toward energy densities of 700 Wh L−1/500 Wh kg−1. Subsequently, recent progresses on enhancing WV for coin/pouch cells are reviewed primarily on cathode. Especially, the “Three High One Low” (THOL) (high sulfur fraction, high sulfur loading, high density host, and low electrolyte quantity) is proposed as a feasible strategy for achieving high WV, taking high WG into consideration simultaneously. Meanwhile, host materials with desired catalytic activity should be paid more attention for fabricating high performance cathode. In the last part, key engineering technologies on manipulating the cathode porosity/density are discussed, including calendering and dry electrode coating. Finally, a future outlook is provided for enhancing both WV and WG of the Li–S batteries.
The volumetric energy density (WV) of lithium–sulfur batteries is critical for mobile applications. Key factors that dominate WV progress on WV research are analyzed, and technologies for tuning cathode structure are discussed. A “three‐high one‐low (THOL)” strategy is proposed for high WV and gravimetric energy density (WG), and catalytic hosts are important to unlock the sulfur electroactivity.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Recently, many new diagnostic biomarkers have been developed for colorectal cancer. We chose 2 methods with high diagnostic efficiency, the detection of serum microRNA and metabolomics based on gas ...chromatography/mass spectrometry (GC/MS), and aimed to establish appropriate models. We reviewed the diagnostic value of all microRNA identified by previous diagnostic tests. We selected appropriate microRNA to validate their diagnostic efficiency, and determined the optimal combination. We included 85 patients with colorectal cancer (CRC) and 78 healthy controls (HC) and detected the expression of the microRNA. GC/MS analysis was conducted, and we used 3 multivariate statistical methods to establish diagnostic models. The concentrations of carcinoembryonic antigen (CEA) and carbohydrate antigen 19‐9 (CA19‐9) were detected for comparison with the novel models. Ultimately, 62 published studies and 63 microRNA were included in this review. MiR‐21, miR‐29a, miR‐92a, miR‐125b and miR‐223 were selected to further validate their diagnostic value. The serum levels of the 5 microRNA in CRC patients were significantly higher than those in the HC. The combination of miR‐21, miR‐29a, miR‐92a and miR‐125b had the highest area under the curve (AUC) at 0.952, with a sensitivity of 84.7% and a specificity of 98.7%. The GC/MS analysis exhibited an excellent diagnostic value and the AUC reached 1.0. With regard to traditional biomarkers, the AUC of CEA and CA19‐9 were 0.808 and 0.705, respectively. The application prospects are good for microRNA and metabolomics as new diagnostic methods because of their high diagnostic value compared with traditional biomarkers.
The combination of miR‐21, miR‐29a, miR‐92a and miR‐125b had the highest area under the curve (AUC) at 0.952 with a sensitivity of 84.7% and a specificity of 98.7%. The GC/MS analysis exhibited an excellent diagnostic value and the AUC reached 1.0. There is a good application prospect for microRNAs and metabolomics as new diagnostic methods because of their high diagnostic value compared with traditional biomarkers.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
Recently, a new class of 2D materials, i.e., transition metal carbides, nitrides, and carbonitrides known as MXenes, is unveiled with more than 20 types reported one after another. Since they are ...flexible and conductive, MXenes are expected to compete with graphene and other 2D materials in many applications. Here, a general route is reported to simple self‐assembly of transition metal oxide (TMO) nanostructures, including TiO2 nanorods and SnO2 nanowires, on MXene (Ti3C2) nanosheets through van der Waals interactions. The MXene nanosheets, acting as the underlying substrate, not only enable reversible electron and ion transport at the interface but also prevent the TMO nanostructures from aggregation during lithiation/delithiation. The TMO nanostructures, in turn, serve as the spacer to prevent the MXene nanosheets from restacking, thus preserving the active areas from being lost. More importantly, they can contribute extraordinary electrochemical properties, offering short lithium diffusion pathways and additional active sites. The resulting TiO2/MXene and SnO2/MXene heterostructures exhibit superior high‐rate performance, making them promising high‐power and high‐energy anode materials for lithium‐ion batteries.
Transition metal oxide (TMO) nanostructures are self‐assembled on MXene nanosheets in tetrahydrofuran through van der Waals interactions, resulting in novel TMO/MXene heterostructures. Due to remarkable morphological and functional synergy, the TMO/MXene heterostructures exhibit superior high‐rate performance, which rank them as promising anode materials for fast and stable lithium storage.
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A conceptually new, metal‐free electrocatalyst, black phosphorus (BP) is presented, which is further downsized to quantum dots (QDs) for larger surface areas, and thus, more active sites than the ...bulk form. However, BP QDs are prone to agglomeration, which inevitably results in the loss of active sites. Besides, their poor conductivity is not favorable for charge transport during electrolysis. To solve these problems, an electrochemically active, electrically conductive matrix, black tin oxide (SnO2−x) nanotubes, is employed for the first time. Through facile self‐assembly, BP QDs are stably confined on the SnO2−x nanotubes due to Sn‐P coordination, resulting in a robust, double‐active electrocatalyst. Benefiting from their synergistic superiority, the BP@SnO2−x nanotubes deliver impressively high ammonia yield and Faradaic efficiency, which represent a successful attempt toward advanced hybrid electrocatalysts for ambient nitrogen fixation.
Through facile self‐assembly, black phosphorus quantum dots are stably confined on SnO2−x nanotubes, which serve as an electrocatalytically active and electrically conductive matrix. Benefiting from their synergistic superiority, the two components result in a robust, double‐active electrocatalyst delivering impressively high ammonia yield and Faradaic efficiency.
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Black phosphorus quantum dots (BP QDs) are facilely loaded on MXene nanosheets through van der Waals self-assembly. On the one hand, the BP QDs possess large surface areas and abundant active sites, ...offering fairly high electrocatalytic activity. On the other hand, the MXene nanosheets serve as a 2D substrate to confine the BP QDs, preventing them from aggregation and, thus, electrolyte inaccessibility. They can further provide excellent electronic conductivity and superior structural robustness. The BP QDs, in turn, act as a spacer to isolate the nanosheets from restacking, thus preserving the active sites from being lost. The resulting BP QDs/MXene nanohybrids, as a bifunctional electrocatalyst, exhibit remarkable synergy in both hydrogen and oxygen evolution reactions (HER/OER) in alkaline media. Specifically, an overpotential of 360 mV ( vs. RHE) and a Tafel slope of 64.3 mV dec −1 are achieved for the OER, and an overpotential of 190 mV ( vs. RHE) and a Tafel slope of 83.0 mV dec −1 for the HER in 1.0 M KOH solution are achieved. These values are significantly lower than those of their components (BP QDs and MXene nanosheets) and even approach those of commercialized RuO 2 or Pt/C. When the BP QDs/MXene nanohybrids are employed as both the cathode and anode in a full cell for overall water splitting, a current density of 10 mA cm −2 is quickly reached at a potential of only 1.78 V. Additionally, the underlying mechanism of the superior electrocatalytic performance of the BP QDs/MXene nanohybrids is fundamentally explored by density functional theory calculations.
Co3O4/nitrogen‐doped carbon hollow spheres (Co3O4/NHCSs) with hierarchical structures are synthesized by virtue of a hydrothermal method and subsequent calcination treatment. NHCSs, as a hard ...template, can aid the generation of Co3O4 nanosheets on its surface; while SiO2 spheres, as a sacrificed‐template, can be dissolved in the process. The prepared Co3O4/NHCS composites are investigated as the electrode active material. This composite exhibits an enhanced performance than Co3O4 itself. A higher specific capacitance of 581 F g−1 at 1 A g−1 and a higher rate performance of 91.6% retention at 20 A g−1 are achieved, better than Co3O4 nanorods (318 F g−1 at 1 A g−1 and 67.1% retention at 20 A g−1). In addition, the composite is employed as a positive electrode to fabricate an asymmetric supercapacitor. The device can deliver a high energy density of 34.5 Wh kg−1 at the power density of 753 W kg−1 and display a desirable cycling stability. All of these attractive results make the unique hierarchical Co3O4/NHCS core–shell structure a promising electrode material for high‐performance supercapacitors.
The Co3O4/N‐doped carbon hollow sphere (Co3O4/NHCS) with a core–shell structure, where Co3O4 nanosheets serve as the shell and NHCS as the core, has large surface area and hierarchical porous structure. The asymmetric supercapacitor assembled with Co3O4/NHCS as a positive electrode and activated carbon as a negative electrode exhibits an excellent electrochemical performance.
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