Progress in research on the role played by myeloid-derived suppressor cells in liver diseases.

Myeloid-derived suppressor cells (MDSCs) refer to a group of immature myeloid cells with potent immunosuppressive capacity upon activation by pathological conditions. Because of their potent immunosuppressive ability, MDSCs have garnered extensive attention in the past few years in the fields of oncology, infection, chronic inflammation and autoimmune diseases. Research on MDSCs in liver diseases has gradually increased, and their potential therapeutic roles will be further explored. This review presents a summary of the involvement and the role played by MDSCs in liver diseases, thus identifying their potential targets for the treatment of liver diseases and providing new directions for liver disease-related research.

Prognostic Prediction Value and Biological Functions of Non-Apoptotic Regulated Cell Death Genes in Lung Adenocarcinoma.

Objective To explore the potential biological functions and prognostic prediction values of non-apoptotic regulated cell death genes (NARCDs) in lung adenocarcinoma.Methods Transcriptome data of lung adenocarcinoma were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. We identified differentially expressed NARCDs between lung adenocarcinoma tissues and normal tissues with R software. NARCDs signature was constructed with univariate Cox regression analysis and the least absolute shrinkage and selection operator Cox regression. The prognostic predictive capacity of NARCDs signature was assessed by Kaplan-Meier survival curve, receiver operating characteristic curve, and univariate and multivariate Cox regression analyses. Functional enrichment of NARCDs signature was analyzed with gene set variation analysis, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes. In addition, differences in tumor mutational burden, tumor microenvironment, tumor immune dysfunction and exclusion score, and chemotherapeutic drug sensitivity were analyzed between the high and low NARCDs score groups. Finally, a protein-protein interaction network of NARCDs and immune-related genes was constructed by STRING and Cytoscape software. Results We identified 34 differentially expressed NARCDs associated with the prognosis, of which 16 genes (ATIC, AURKA, CA9, ITGB4, DDIT4, CDK5R1, CAV1, RRM2, GAPDH, SRXN1, NLRC4, GLS2, ADRB2, CX3CL1, GDF15, and ADRA1A) were selected to construct a NARCDs signature. NARCDs signature was identified as an independent prognostic factor (P < 0.001). Functional analysis showed that there were significant differences in mismatch repair, p53 signaling pathway, and cell cycle between the high NARCDs score group and low NARCDs score group (all P < 0.05). The NARCDs low score group had lower tumor mutational burden, higher immune score, higher tumor immune dysfunction and exclusion score, and lower drug sensitivity (all P < 0.05). In addition, the 10 hub genes (CXCL5, TLR4, JUN, IL6, CCL2, CXCL2, ILA, IFNG, IL33, and GAPDH) in protein-protein interaction network of NARCDs and immune-related genes were all immune-related genes. Conclusion The NARCDs prognostic signature based on the above 16 genes is an independent prognostic factor, which can effectively predict the clinical prognosis of patients of lung adenocarcinoma and provide help for clinical treatment.

Manipulation of amorphous precursors to enhance zeolite nucleation.

Crystallization in media comprised of amorphous precursors is becoming a more common phenomenon for numerous synthetic, biological, and natural materials that grow by a combination of classical and nonclassical pathways. Amorphous phases can exhibit a wide range of physicochemical properties that may evolve during the course of nucleation and crystal growth. This creates challenges for establishing causal relationships between amorphous precursor properties and their effect(s) on the selection of mechanistic pathways of crystallization and ultimately the properties of the crystalline product. In this study, we examine ways to manipulate the composition and colloidal stability of amorphous (alumino)silicate precursors that are prevalent in nanoporous zeolite syntheses. Changes in the amorphous precursor properties are evaluated on the basis of their ability to enhance rates of crystal formation. Here, we use fumed silica as the primary silicon source and examine the effects of infusing the source or growth medium with additional alkali metal, which serves as an inorganic structure-directing agent to facilitate the formation of porous crystal structures. We also assess the impact of adding a polymer additive, which reduces the colloidal stability of precursors, wherein we posit that the confined pockets of solution within the interstitial spaces of the precursor aggregates play an important role in regulating the rate of zeolite crystallization. Three commercially relevant zeolites (mordenite, SSZ-13, and ZSM-5) were selected for this study based on their diverse frameworks and methods of preparation. Our findings reveal that alkali infusion significantly reduces the crystallization times for mordenite and SSZ-13, but has little impact on ZSM-5 synthesis. Conversely, we find that polymer addition markedly enhanced the rates of crystallization among all three zeolites, suggesting that this method may be a general approach to reduce zeolite synthesis times. Given the relatively high costs associated with commercial zeolite production, identifying new methods to improve the efficiency of hydrothermal syntheses can have significant practical implications beyond the fundamental benefits of developing new routes to tailor nonclassical crystallization.

Spatial distribution and source apportionment of polycyclic aromatic hydrocarbons in typical oasis soil of north-western China and the bacterial community response.

Oases environments in oases to be sensitive to anthropogenic activity because of ecological fragility. Polycyclic aromatic hydrocarbon (PAH) pollution resulting from anthropogenic activity leads to ecological degradation in oases. To examine the impact of anthropogenic activity on the oasis ecological environment, the present study focused on the spatial distribution and source apportionment of soil PAHs and bacterial community responses in typical oases in Xinjiang, China. The results showed that the soil PAH level were higher in the city centres of Urumqi (9-6340 µg kg-1), Aksu (8-957 µg kg-1) and Korla (8-1103 µg kg-1) and lower in the centres of Hotan city (11-268 µg kg-1) and Qira county (7-163 µg kg-1). Source apportionment suggested that gasoline emissions, diesel emissions, vehicle emissions, coal combustion, coke processing and biomass burning were the sources of soil PAHs. The integrated lifetime cancer risks of soil PAH exceeding the guideline safety values (10-6) recommended by United States Environmental Protection Agency. The ingestion and dermal exposure pathways caused the greatest health risk (contribution ≤82%). Additionally, in the soil with low PAH concentrations, the richness and evenness of the soil bacterial community were great, and the molecular ecological network (MEN) structure was complex. Among populations, Proteobacteria and Actinobacteria (relative abundance ≥17%) are the main dominant species in the bacterial communities and the keystone species in the MEN.

Explore the effects of pulmonary fibrosis on sperm quality and the role of the PI3K/Akt pathway based on rat model.

Researches were reported that respiratory diseases can lead to male infertility; however, it is unclear whether there is a relationship between pulmonary fibrosis (PF) and male infertility. This study examined the influence of PF on sperm quality and its mechanisms. The key signalling pathway of male infertility caused by PF was predicted based on bioinformatics research. After modelling, we evaluated semen quality. Real-time quantitative polymerase chain reaction and Western blotting were used to measure the protein and mRNA expression levels of phosphatidylinositol 3-kinase (PI3K), phosphorylation-protein kinase B (p-Akt) and B-cell lymphoma 2 (Bcl2) in rat testicular cells. Compared with group A (48.77 ± 4.67; 59.77 ± 4.79), the sperm concentration and total sperm viability of group B (8.44 ± 1.71; 15.39 ± 3.48) showed a downward trend (p < 0.05). Western blotting showed that the protein expressions of PI3K, p-Akt and Bcl2 in the testes of group B (0.30 ± 0.06; 0.27 ± 0.05; 0.15 ± 0.03) was significantly lower than those of group A (0.71 ± 0.07; 0.72 ± 0.06; 0.50 ± 0.06) (p < 0.05). The hypoxic environment induced by PF can inhibit the expression of PI3K, p-Akt and Bcl2 protein and eventually cause dysfunctional spermatogenesis.

Oasis sustainability assessment in arid areas using GRACE satellite data.

An oasis is an important habitat for humans, plants, and wildlife in arid desert areas. The sustainability of an oasis is crucial for a smooth regional ecological functioning and healthy economic development. However, the overexploitation of groundwater will result in unsustainable oasis development. Due to the lack of long-term groundwater monitoring data, the impact of groundwater level changes on the sustainability of an oasis has not been studied extensively. In the present study, we used the ground water storage anomaly (GWSA) in combination with the Gravity Recovery and Climate Experiment (GRACE) and the Global Land Data Assimilation System (GLDAS) for the rapid identification of oasis sustainability, which has been tested and evaluated in Hotan and Qira oasis located in arid areas. The results showed that (1) the GWSA is a suitable and reliable indicator for trend change analysis in small-scale oasis and, (2) additionally, M-K test results for long-term trend change of GWSA showed a positive correlation with water resource carrying capacity (WRCC). These results suggest that GWSA can be used as a reliable index for the rapid assessment of oasis sustainability status in arid areas. Moreover, the potential applicability of GRACE satellite data in evaluating the groundwater sustainability in arid areas lacking proper data has also been proved in this study. These findings have provided a foundation to evaluate the sustainability status of an oasis and set a reference point to formulate future policies for the oasis.

Accelerating the Crystallization of Zeolite SSZ-13 with Polyamines.

Tailoring processes of nucleation and growth to achieve desired material properties is a pervasive challenge in synthetic crystallization. In systems where crystals form via nonclassical pathways, engineering materials often requires the controlled assembly and structural evolution of colloidal precursors. In this study, we examine zeolite SSZ-13 crystallization and show that several polyquaternary amines function as efficient accelerants of nucleation, and, in selected cases, tune crystal size by orders of magnitude. Among the additives tested, polydiallyldimethylammonium (PDDA) was found to have the most pronounced impact on the kinetics of SSZ-13 formation, leading to a 4-fold reduction in crystallization time. Our findings also reveal that enhanced nucleation occurs at an optimal PDDA concentration where a combination of light-scattering techniques demonstrate these conditions lead to polymer-induced aggregation of amorphous precursors and the promotion of (alumino)silicate precipitation from the growth solution. Here, we show that relatively low concentrations of polymer additives can be used in unique ways to dramatically enhance SSZ-13 crystallization rates, thereby improving the overall efficiency of zeolite synthesis.

Enhanced Selectivity and Stability of Finned Ferrierite Catalysts in Butene Isomerization.

Designing zeolite catalysts with improved mass transport properties is crucial for restrictive networks of either one- or two-dimensional pore topologies. Here, we demonstrate the synthesis of finned ferrierite (FER), a commercial zeolite with two-dimensional pores, where protrusions on crystal surfaces behave as pseudo nanoparticles. Catalytic tests of 1-butene isomerization reveal a 3-fold enhancement of catalyst lifetime and an increase of 12 % selectivity to isobutene for finned samples compared to corresponding seeds. Electron tomography was used to confirm the identical crystallographic registry of fins and seeds. Time-resolved titration of Brønsted acid sites confirmed the improved mass transport properties of finned ferrierite compared to conventional analogues. These findings highlight the advantages of introducing fins through facile and tunable post-synthesis modification to impart material properties that are otherwise unattainable by conventional synthesis methods.

Finned zeolite catalysts.

There is growing evidence for the advantages of synthesizing nanosized zeolites with markedly reduced internal diffusion limitations for enhanced performances in catalysis and adsorption. Producing zeolite crystals with sizes less than 100 nm, however, is non-trivial, often requires the use of complex organics and typically results in a small product yield. Here we present an alternative, facile approach to enhance the mass-transport properties of zeolites by the epitaxial growth of fin-like protrusions on seed crystals. We validate this generalizable methodology on two common zeolites and confirm that fins are in crystallographic registry with the underlying seeds, and that secondary growth does not impede access to the micropores. Molecular modelling and time-resolved titration experiments of finned zeolites probe internal diffusion and reveal substantial improvements in mass transport, consistent with catalytic tests of a model reaction, which show that these structures behave as pseudo-nanocrystals with sizes commensurate to that of the fin. This approach could be extended to the rational synthesis of other zeolite and aluminosilicate materials.

Improving Ponzi Scheme Contract Detection Using Multi-Channel TextCNN and Transformer.

With the development of blockchain technologies, many Ponzi schemes disguise themselves under the veil of smart contracts. The Ponzi scheme contracts cause serious financial losses, which has a bad effect on the blockchain. Existing Ponzi scheme contract detection studies have mainly focused on extracting hand-crafted features and training a machine learning classifier to detect Ponzi scheme contracts. However, the hand-crafted features cannot capture the structural and semantic feature of the source code. Therefore, in this study, we propose a Ponzi scheme contract detection method called MTCformer (Multi-channel Text Convolutional Neural Networks and Transofrmer). In order to reserve the structural information of the source code, the MTCformer first converts the Abstract Syntax Tree (AST) of the smart contract code to the specially formatted code token sequence via the Structure-Based Traversal (SBT) method. Then, the MTCformer uses multi-channel TextCNN (Text Convolutional Neural Networks) to learn local structural and semantic features from the code token sequence. Next, the MTCformer employs the Transformer to capture the long-range dependencies of code tokens. Finally, a fully connected neural network with a cost-sensitive loss function in the MTCformer is used for classification. The experimental results show that the MTCformer is superior to the state-of-the-art methods and its variants in Ponzi scheme contract detection.

An Empirical Study of Training Data Selection Methods for Ranking-Oriented Cross-Project Defect Prediction.

Ranking-oriented cross-project defect prediction (ROCPDP), which ranks software modules of a new target industrial project based on the predicted defect number or density, has been suggested in the literature. A major concern of ROCPDP is the distribution difference between the source project (aka. within-project) data and target project (aka. cross-project) data, which evidently degrades prediction performance. To investigate the impacts of training data selection methods on the performances of ROCPDP models, we examined the practical effects of nine training data selection methods, including a global filter, which does not filter out any cross-project data. Additionally, the prediction performances of ROCPDP models trained on the filtered cross-project data using the training data selection methods were compared with those of ranking-oriented within-project defect prediction (ROWPDP) models trained on sufficient and limited within-project data. Eleven available defect datasets from the industrial projects were considered and evaluated using two ranking performance measures, i.e., FPA and Norm(Popt). The results showed no statistically significant differences among these nine training data selection methods in terms of FPA and Norm(Popt). The performances of ROCPDP models trained on filtered cross-project data were not comparable with those of ROWPDP models trained on sufficient historical within-project data. However, ROCPDP models trained on filtered cross-project data achieved better performance values than ROWPDP models trained on limited historical within-project data. Therefore, we recommended that software quality teams exploit other project datasets to perform ROCPDP when there is no or limited within-project data.

Effect of leech-centipede medicine on improving erectile function in diabetes-induced erectile dysfunction rats via PDE5 signalling pathway-related molecules.

CONTEXT: The leech and centipede granules have good curative effects on many diabetic vascular diseases, including diabetes-induced erectile dysfunction (DIED). OBJECTIVE: To explore the effect of leech and centipede on erectile function in rats with diabetes-induced erectile dysfunction and its possible mechanism. MATERIALS AND METHODS: Thirty male Sprague-Dawley DIED rats were randomly divided into the model group (Group M), low-dose group (Group DD), high-dose group (Group DG) and tadalafil group (Group T) (n = 6); diabetic rats were induced by streptozotocin. Apomorphine was used to induce diabetic erectile dysfunction. The 'leech-centipede' granules (0.15 and 0.6 g/kg) were intragastrically administered in the DD and DG groups for 8 weeks. Blood glucose, serum insulin, testosterone, cGMP levels and protein expression changes were measured in each group. RESULTS: After 8 weeks, the erectile function of rats in the DG group significantly improved (1.26 ± 0.73). Penis tissue cGMP levels were higher in the DG group (1.48 ± 0.11) than in the M group (0.58 ± 0.15). Protein and mRNA expression levels of NOS were significantly higher (0.77 ± 0.05; 0.61 ± 0.02) but those of PDE5 (0.43 ± 0.05; 0.61 ± 0.03) were lower in the DG group than in the M group (0.37 ± 0.06; 0.51 ± 0.01; 0.78 ± 0.06; 0.81 ± 0.04). CONCLUSION: The leech-centipede can improve erectile dysfunction in DIED rats by regulating the expression of cGMP, NOS, and PDE5-related molecules in the PDE5 pathway. This study provides a potential mechanism for the treatment of DIED with leech-centipede.

Potential mechanism of Achyranthis bidentatae radix plus semen vaccariae granules in the treatment of diabetes mellitus-induced erectile dysfunction in rats utilizing combined experimental model and network pharmacology.

CONTEXT: Achyranthes bidentata Blume (Amaranthaceae) (ABR) and semen vaccariae (SV) are used commonly in the clinical treatment of erectile dysfunction in males with diabetes mellitus (DMED) to strengthen the kidney and promote blood circulation, and often achieve good curative effects. OBJECTIVE: Explore mechanistic details of ABR + SV treatment against DMED. MATERIALS AND METHODS: Prediction of key targets by network pharmacology. A rat model of DM was established by streptozotocin injection (55 mg/kg). Apomorphine (100 µg/kg) was injected into rats to screen the DMED model. Group C (n = 6) and group M (n = 6) were gavaged with deionized water; group T (n = 6) was given Achyranthis bidentatae radix-semen vaccariae granule suspension (2.5 g/kg). It lasted 8 weeks. Real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blotting (WB) were used to measure the expression of tissue-related proteins and mRNA. RESULTS: The predicted key targets are albumin (ALB), caspase-3 (CASP3), vascular endothelial growth factor A (VEGFA), angiotensin-converting enzyme (ACE), and endothelial nitric oxide synthase (eNOS). Compared with the M group (0.52 ± 0.04; 0.50 ± 0.03; 0.49 ± 0.02; 0.23 ± 0.03), CASP3, VEGFA, and ACE protein expression reduced in the T group (0.39 ± 0.06; 0.34 ± 0.03; 0.39 ± 0.03), and eNOS protein expression increased (0.34 ± 0.03). CONCLUSION: ABR + SV can improve erectile function in DMED rats. This study provides a potential mechanism for the treatment of DMED with ABR + SV and can benefit from more patients.

[Asthma affects erectile function in rats: An experimental study].

Objective: To investigate the impact of asthma on erectile function in rats and the expressions of related proteins. METHODS: Male rats were injected intraperitoneally with ovalbumin solution to induce asthma followed by subcutaneous injection of apomorphine at 100 µg/kg into the neck, and then observed for reduced frequency or loss of penile erection. Based on the results of observation, a model of asthma-induced ED (AED) was made in 6 of the animals, and another 6 normal male rats were taken as controls. The histomorphology of the corpus cavernosum was observed by HE staining, and the mRNA and protein expressions of phosphodiesterase 5 (PDE5) and nitric oxide synthase 3 (eNOS) in the testis tissue were determined by RT-qPCR and Western blot. RESULTS: Compared with the normal controls, the rats in the AED model group showed disorderly distribution of sinusoids and decreased density of endothelial and smooth muscle cells in the corpus cavernosum. The mRNA and protein expressions of PDE5 were significantly higher (P < 0.05), while those of eNOS remarkably lower in the AED model than in the control group (P < 0.05). CONCLUSIONS: Asthma can induce ED and change the histomorphology of the corpus cavernosum in rats by affecting the expressions of PDE5 and eNOS proteins.

Few-Unit-Cell MFI Zeolite Synthesized using a Simple Di-quaternary Ammonium Structure-Directing Agent.

Synthesis of a pentasil-type zeolite with ultra-small few-unit-cell crystalline domains, which we call FDP (few-unit-cell crystalline domain pentasil), is reported. FDP is made using bis-1,5(tributyl ammonium) pentamethylene cations as structure directing agent (SDA). This di-quaternary ammonium SDA combines butyl ammonium, in place of the one commonly used for MFI synthesis, propyl ammonium, and a five-carbon nitrogen-connecting chain, in place of the six-carbon connecting chain SDAs that are known to fit well within the MFI pores. X-ray diffraction analysis and electron microscopy imaging of FDP indicate ca. 10 nm crystalline domains organized in hierarchical micro-/meso-porous aggregates exhibiting mesoscopic order with an aggregate particle size up to ca. 5 µm. Al and Sn can be incorporated into the FDP zeolite framework to produce active and selective methanol-to-hydrocarbon and glucose isomerization catalysts, respectively.

BreakID: genomics breakpoints identification to detect gene fusion events using discordant pairs and split reads.

SUMMARY: Here we developed a tool called Breakpoint Identification (BreakID) to identity fusion events from targeted sequencing data. Taking discordant read pairs and split reads as supporting evidences, BreakID can identify gene fusion breakpoints at single nucleotide resolution. After validation with confirmed fusion events in cancer cell lines, we have proved that BreakID can achieve high sensitivity of 90.63% along with PPV of 100% at sequencing depth of 500× and perform better than other available fusion detection tools. We anticipate that BreakID will have an extensive popularity in the detection and analysis of fusions involved in clinical and research sequencing scenarios. AVAILABILITY AND IMPLEMENTATION: Source code is freely available at https://github.com/SinOncology/BreakID. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Comparison of the groundwater microbial community in a salt-freshwater mixing zone during the dry and wet seasons.

To gain a better understanding of the microbial community in salt-freshwater mixing zones, in this study, the influence of seasonal variation on the groundwater microbial community was evaluated by high throughput 16S rDNA gene sequencing. The results showed that notable changes in microbial community occurred in a salt-freshwater mixing zone and the groundwater samples in the dry season were more saline than those in the wet season. The increase in precipitation during the wet season relieved local seawater intrusion. Microbial diversity varied greatly with seasons, while no obvious change pattern was found. Proteobacteria was identified as the dominant phylum in all samples. The genus Hydrogenophaga dominated in the dry season, while the genus Acidovorax dominated in the wet season. Dissolved oxygen affected the diversity of the microbial communities during the dry and wet season, while groundwater level had a strong influence on the structure of microbial communities. Phylogenetic molecular network analysis of the microbial communities indicated that increased seawater intrusion led to a more compact microbial network and strengthening the groundwater microbial interactions.

Assessing water distribution and agricultural expansion in the Cele Oasis, China.

Oases support 90% of the province's inhabitants and produce more than 95% of the social wealth in Xinjiang Province of China. Oases' dependency on water availability from mountainous regions plays a critical factor in the sustainability of agricultural practices and oasis expansion. In this study, we have chosen the Cele Oasis located in the south rim of the Taklimakan Desert, typical of oases in the region, as a case study to examine water availability. With over 97% of Cele's economy tied to agriculture, unfettered expansion of the oasis into the desert has raised concern on water availability. A spatial and temporal analysis of water availability is performed using newly available data to determine whether agricultural production within the Cele Oasis has overexploited available water resources or if feasible expansion of agricultural production is feasible beyond its current boundary. Transferability of the methodology for assessing water availability spatially and temporally will be beneficial to other oases in the arid region that face similar concerns.

Research of stroke combined hyperlipidemia-induced erectile dysfunction in rat model.

Objective: The study was aimed to evaluate the influences of erectile dysfunction (ED) in a rat model of stroke combined with hyperlipidemia (HLP). Methods: Male Sprague-Dawley rats were divided into control and hyperlipidemia (HLP) groups. HLP model was constructed by feeding with high-fat and cholesterol diets. Serum levels of total cholesterol (TC), low density lipoprotein (LDL), high density lipoprotein (HDL), triglyceride (TG), and non-HDL were identified to check the model was success. Stroke model was established by FeCl3. ICP/MAP value was detected to evaluate the erectile function of rats. Serum level of lipoproteins and the expressions of endothelial nitric oxide synthase (eNOS), vascular endothelial growth factor (VEGF) were detected by ELISA. Hematoxylin-eosin (HE) staining of corpus cavernosum and measurement of penis length were utilized to assessment erectile function. Western blot was used. Results: TC, TG, LDL, and non-HDL-C in serum were up-regulated, while HDL level was attenuated. After treatment, the serum lipid level recovered. From the ICP/MAP values, the erectile function of both two treatment groups recovered. The expression of PDE5A was up-regulated, while the levels of eNOS and cGMP were suppressed after surgery. The length of penis was decreased, and corpus cavernosum was damaged following HLP and stroke. However, the erectile function was recovered after treatment. Conclusion: Stroke combined HLP caused ED through NO-cGMP-PDE5 pathway.

Assembly and diploid architecture of an individual human genome via single-molecule technologies.

We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.