[Spatio-temporal Evolution of Drought and Its Impact on Key Resources in the Important Ecological Functional Area: A Case Study in the Yellow River Basin].

This study explored the characteristics of spatial and temporal changes in drought in the Yellow River Basin from 2001 to 2020 based on TVPDI, surface runoff, vegetation net primary productivity, and grain yield data. Further, the effects of drought on water resources, grain resources, and vegetation resources were also analyzed using data spatialization methods, slope trend analysis, and Pearson correlation analysis. The results showed that:① The spatial distribution of drought in the Yellow River basin was stepped from southeast to northwest, and 60.6 % of the basin was in drought. The overall trend of drought in the basin was decreasing annually, and 94 % of the basin was gradually changing from drought to wet conditions, and the trend of drought from spring to winter decreased first and then increased. ② From the spatial and temporal changes in important resources in the basin, 53 % of the key surface runoff areas showed an increasing trend and were mainly located in the southwest of the basin; the net primary productivity (NPP) of vegetation and grain yield of food resources also showed an increasing trend. ③ Drought and the three types of resources showed significant spatial correlations, and the higher the degree of drought, the more significant the effects on surface runoff, vegetation productivity, and grain yield. However, the important resources in areas that had become wetter in recent years had not increased significantly, which indicated that the effects of drought on the three types of important resources had a time lag, and their lags had significant differences in spatial distribution and geographical differentiation patterns. This study has important theoretical implications for agricultural production, drought mitigation, and ecological conservation in the Yellow River Basin.

BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models.

BACKGROUND: In the CRISPR-Cas9 system, the efficiency of genetic modifications has been found to vary depending on the single guide RNA (sgRNA) used. A variety of sgRNA properties have been found to be predictive of CRISPR cleavage efficiency, including the position-specific sequence composition of sgRNAs, global sgRNA sequence properties, and thermodynamic features. While prevalent existing deep learning-based approaches provide competitive prediction accuracy, a more interpretable model is desirable to help understand how different features may contribute to CRISPR-Cas9 cleavage efficiency. RESULTS: We propose a gradient boosting approach, utilizing LightGBM to develop an integrated tool, BoostMEC (Boosting Model for Efficient CRISPR), for the prediction of wild-type CRISPR-Cas9 editing efficiency. We benchmark BoostMEC against 10 popular models on 13 external datasets and show its competitive performance. CONCLUSIONS: BoostMEC can provide state-of-the-art predictions of CRISPR-Cas9 cleavage efficiency for sgRNA design and selection. Relying on direct and derived sequence features of sgRNA sequences and based on conventional machine learning, BoostMEC maintains an advantage over other state-of-the-art CRISPR efficiency prediction models that are based on deep learning through its ability to produce more interpretable feature insights and predictions.

Association between sleep duration and chest pain in US adults: A cross-sectional study.

Objective: Herein, we purposed to explore the association of sleep duration with chest pain among adults in US. Methods: This research work enrolled 13,274 subjects in the National Health and Nutrition Examination Survey (NHANES) from 2011 to 2018. The association of sleep duration with chest pain among adults in US was evaluated by Multivariable logistic regression. Results: To elucidate the association, we made adjustments for gender, BMI, diabetes, smoking status, drinking status, race, marital status, annual family income, hyperlipoidemia, Hypertension. Chest pain incidence decreased by 5% [OR = 0.95 (0.93, 0.98), p = 0.0004] for an increase in sleep duration by 1 h. A generalized additive model (GAM) was used to reseal a U-shaped relationship of sleep duration with incident chest pain. When duration of sleep was <6.5 h, chest pain incidence negatively correlated to sleep duration [OR = 0.77 (0.72, 0.82) P < 0.0001]. However, when sleep duration was ≥6.5 h, chest pain incidence rose with escalating sleep duration [OR = 1.07 (1.03, 1.11) p = 0.0014]. Conclusions: Duration of sleep was established to be independently linked with an increase in the occurrence of chest pain. Excessive sleep, as much as insufficient sleep, increases the risk of chest pain. Both excessive sleep and insufficient sleep are associated with an increased risk of chest pain.

[Seasonal dynamics of the physicochemical properties of biological crusts exopolysaccharides and the microbial community structure]. / 生物结皮胞外多糖理化特性及菌群结构的季节动态.

Exopolysaccharides (EPS), an important substance of cyanobacteria in resisting stresses, are the main form of carbon storage in biocrusts and play an important role in material cycling and stability of biocrusts. In this study, the biocrusts in different seasons (January, April, July, October) were collected from Gurbantunggut Desert, and the dynamics of EPS content, composition, morphological characteristics and microbial community structures were analyzed. The results showed that: 1) The excretion of EPS showed obvious seasonal dynamics. The EPS contents in January, April, July and October were 81.72, 52.46, 76.77, 70.54 µg·cm-2, and the chlorophyll a contents were 2.7, 4.94, 4.2 and 5.98 µg·cm-2, respectively. Cyanobacteria allocated more fixed organic carbon to EPS in winter and summer, and more to their own biomass accumulation in spring and autumn. 2) EPS in biocrusts of each season was composed of seven kinds of monosaccharides. The sum of relative mole percentages of glucose and galactose was 46%-56%, much higher than the other five monosaccharides. The monosaccharide compositions of EPS were significantly affected by temperature and precipitation. There was no significant difference in the Fourier infrared spectra of EPS in biocrusts across different seasons. 3) The observation results of atomic force microscope showed that more filamentous and thick rope-like structures occurred in EPS in July and October, while the EPS showed block-like morphology in January and April. 4) The results of 16S rDNA high-throughput sequencing showed that Cyanobacteria and Microcoleus were the dominant bacterial phyla and genus in biocrusts in all the four seasons, with significantly higher relative abundance than other bacterial phyla and genera. The relative abundance of Proteobacteria was significantly positively correlated with the relative mole percentages of fucose and galactose, indicating that the composition of monosaccharides affected heterotrophic bacteria in crusts. In deserts, environmental factors such as temperature and moisture changed significantly across seasons. The physicochemical properties of biocrust exopolysaccharides and the seasonal dynamics of bacterial communities were controlled by multiple factors, such as temperature, moisture, and light.

DNAcycP: a deep learning tool for DNA cyclizability prediction.

DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simultaneously. Using the loop-seq data, we develop a software tool, DNAcycP, based on a deep-learning approach for intrinsic DNA cyclizability prediction. We demonstrate DNAcycP predicts intrinsic DNA cyclizability with high fidelity compared to the experimental data. Using an independent dataset from in vitro selection for enrichment of loopable sequences, we further verified the predicted cyclizability score, termed C-score, can well distinguish DNA fragments with different loopability. We applied DNAcycP to multiple species and compared the C-scores with available high-resolution chemical nucleosome maps. Our analyses showed that both yeast and mouse genomes share a conserved feature of high DNA bendability spanning nucleosome dyads. Additionally, we extended our analysis to transcription factor binding sites and surprisingly found that the cyclizability is substantially elevated at CTCF binding sites in the mouse genome. We further demonstrate this distinct mechanical property is conserved across mammalian species and is inherent to CTCF binding DNA motif.

The Hypertension Related Gene G-Protein Coupled Receptor Kinase 4 Contributes to Breast Cancer Proliferation.

PURPOSE: Clinical studies have shown that breast cancer risk is increased in hypertensive women. The underlying molecular mechanism remains undetermined. The current study tests our hypothesis that G protein coupled receptor kinase 4 (GRK4) is a molecule that links hypertension and breast cancer. GRK4 plays an important role in regulation of renal sodium excretion. Sustained activation of GRK4 as in the circumstances of single nucleotide polymorphism (SNPs) causes hypertension. Expression of GRK4 in the kidney is regulated by cMyc, an oncogene that is amplified in breast cancer. METHODS: Western analysis was used to evaluate GRK4 protein expression in seven breast cancer cell lines. GRK4 gene single nucleotide polymorphism in breast cancer cell lines and in breast cancer cDNA arrays were determined using TaqMan Genotyping qPRC. The function of GRK4 was evaluated in MCF-7 cells with cMyc knock-down and GRK4 re-expression and in MDA-MB-468 cells expressing inducible GRK4 shRNA lentivirus constructs. Nuclei counting and 5-Bromo-2'-deoxy-uridine (BrdU) labeling were used to evaluate cell growth and proliferation. RESULTS: Genotyping of GRK4 SNPs in breast cancer cDNA arrays (n = 94) revealed that the frequency of carrying two hypertension related SNPs A142 V or R65 L is threefold higher in breast cancer patients than in healthy people (P = 7.53E-11). GRK4 protein is expressed in seven breast cancer cell lines but not the benign mammary epithelial cell line, MCF-10A. Three hypertension related SNPs in the GRK4 gene were identified in the breast cancer cell lines. Except for BT20, all other breast cancer lines have 1-3 GRK4 SNPs of which A142 V occurs in all 6 lines. MDA-MB-468 cells contain homozygous A142 V and R65 L SNPs. Knocking down cMyc in MCF-7 cells significantly reduced the growth rate, which was rescued by re-expression of GRK4. We then generated three stable GRK4 knock-down MDA-MB-468 lines using inducible lentiviral shRNA vectors. Doxycycline (Dox) induced GRK4 silencing significantly reduced GRK4 mRNA and protein levels, growth rates, and proliferation. As a marker of cell proliferation, the percentage of BrdU-labeled cells decreased from 45 ± 3% in the cells without Dox to 32 ± 5% in the cells treated with 0.1 µg/mL Dox. CONCLUSIONS: GRK4 acts as an independent proliferation promotor in breast cancer. Our results suggest that targeted inhibition of GRK4 could be a new therapy for both hypertension and breast cancer.

Establishment and Clinical Application of the Concept of Invalid Extraction Rates in Follicular Unit Extraction.

OBJECTIVE: This study aims to establish the concept of invalid extraction rates in follicular unit extraction and evaluate its clinical value. METHODS: The present study involved 30 patients with alopecia. Three young surgeons (nominated A, B, and C) each performed follicular unit extraction on a randomly selected portion of the donor site of each patient for ten minutes. The outcomes were separately recorded and calculated, and converted to an invalid extraction rate for each surgeon using the formula, "invalid extraction rate = 1 - successfully extracted follicular units/actually extracted units × 100%." RESULTS: The follicular unit invalid extraction efficiency of each surgeon gradually declined. The average efficiency level of surgeon B was evaluated as excellent, while the levels of surgeons A and C were evaluated as good. CONCLUSION: With experience, surgeons can speed up the process of follicular unit extraction and gradually increase performance quality through both extraction speed and success rate.

RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.

Ribosome profiling, also known as Ribo-seq, has become a popular approach to investigate regulatory mechanisms of translation in a wide variety of biological contexts. Ribo-seq not only provides a measurement of translation efficiency based on the relative abundance of ribosomes bound to transcripts, but also has the capacity to reveal dynamic and local regulation at different stages of translation based on positional information of footprints across individual transcripts. While many computational tools exist for the analysis of Ribo-seq data, no method is currently available for rigorous testing of the pattern differences in ribosome footprints. In this work, we develop a novel approach together with an R package, RiboDiPA, for Differential Pattern Analysis of Ribo-seq data. RiboDiPA allows for quick identification of genes with statistically significant differences in ribosome occupancy patterns for model organisms ranging from yeast to mammals. We show that differential pattern analysis reveals information that is distinct and complimentary to existing methods that focus on translational efficiency analysis. Using both simulated Ribo-seq footprint data and three benchmark data sets, we illustrate that RiboDiPA can uncover meaningful pattern differences across multiple biological conditions on a global scale, and pinpoint characteristic ribosome occupancy patterns at single codon resolution.

[Symbiotic bacteria facilitate algal growth and oil biosynthesis in Scenedesmus obliquus]. / å ±ç”ŸèŒä¿ƒè¿›æ–œç”Ÿæ 藻生长和油脂合成.

We isolated bacteria from the phycosphere of Scenedesmus obliques and sequenced 16S rDNAs to establish algae-bacterial co-culture systems. Further, we examined effects of the bacteria on algal growth, and parameters associated with physio-biochemical and oil-producing characteristics of S. obliquus. Seven bacterial strains were isolated, including Micrococcus (strains 1-1, 1-2 and 1-3), Pseudomonas sp. (strains 2-1 and 2-2), Exiguobacterium (strain-3) and Staphylococcus sp. (strain-4). Among them, two bacteria (strain 1-2 and strain 2-1) were characterized as the dominant growth-promoting bacterial strains, which significantly increased algal growth, pigment production, and oil enrichment. After eight days cultivation under microalgal-bacterial (strain 1-2) symbiotic systemat at an initial ratio of 1:10, biomass of S. obliquus was 4.27 g·L-1, about 46.0% higher than that of the control. The contents of chlorophyll a, chlorophyll b and carotenoids were increased by 12.1%, 16.7% and 25.0%, respectively. Oil content was increased by 14.0% and reached to 25.7%, and the oleic acid content was significantly higher than that of the control and up to 16.4%. When co-cultured with Pseudomonas sp. (strain 2-1) for eight days at an initial ratio of 1:5, algal biomass, chlorophyll a, chlorophyll b and carotenoids contents were higher than that of the control by 47.9%, 16.0%, 17.5% and 19.9%, respectively. The total oil (27.1%) and oleic acid (18.2%) contents were increased by 20.4% and 64.0%, respectively. We concluded that Micrococcus (strain 1-2) and Pseudomonas sp. (strain 2-1) could significantly promote algal growth and increase oil production by their beneficial interaction with S. obliques, which could be potentially used in commercial production of S. obliques.

Impact of Thermal History on the Kinetic Response of Thermoresponsive Poly(diethylene glycol monomethyl ether methacrylate)-block-poly(poly(ethylene glycol)methyl ether methacrylate) Thin Films Investigated by In Situ Neutron Reflectivity.

The impact of thermal history on the kinetic response of thin thermoresponsive diblock copolymer poly(diethylene glycol monomethyl ether methacrylate)-block-poly(poly(ethylene glycol) methyl ether methacrylate), abbreviated as PMEO2MA-b-POEGMA300, films is investigated by in situ neutron reflectivity. The PMEO2MA and POEGMA300 blocks are both thermoresponsive polymers with a lower critical solution temperature. Their transition temperatures (TTs) are around 25 °C (TT1, PMEO2MA) and 60 °C (TT2, POEGMA300). Thus, by applying different temperature protocols (20 to 60 or 20 to 40 to 60 °C), the PMEO2MA-b-POEGMA300 thin films experience different thermal histories: the first protocol directly switches from a swollen to a collapsed state, whereas the second one switches first from a swollen to a semicollapsed and finally to a collapsed state. Although the applied thermal histories differ, the response and final state of the collapsed films are very close to each other. After the thermal stimulus, both films present a complicated response composed of an initial shrinkage, followed by a rearrangement. Interestingly, a subsequent reswelling of the collapsed film is only observed in the case of having applied a thermal stimulus of 20 to 40 °C. The normalized film thickness and the D2O amount of each layer in the PMEO2MA-b-POEGMA300 films are consistent at the end of the two different thermal stimuli. Hence, it can be concluded that the thermal history does not influence the final state of the PMEO2MA-b-POEGMA300 films upon heating. Based on this property, these thin films are especially suitable for the temperature switches on the nanoscale, which may experience different thermal histories.

Mobilizable antibiotic resistance genes are present in dust microbial communities.

The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.

Thermoresponsive Diblock Copolymer Films with a Linear Shrinkage Behavior and Its Potential Application in Temperature Sensors.

The linear shrinkage behavior in thermoresponsive diblock copolymer films and its potential application in temperature sensors are investigated. The copolymer is composed of two thermoresponsive blocks with different transition temperatures (TTs): di(ethylene glycol) methyl ether methacrylate (MEO2MA; TT1 = 25 °C) and poly(ethylene glycol) methyl ether methacrylate (OEGMA300; TT2 = 60 °C) with a molar ratio of 1:1. Aqueous solutions of PMEO2MA-b-POEGMA300 show a three-stage transition upon heating as seen with optical transmittance and small-angle X-ray scattering: dissolution (T < TT1), self-assembled micelles with core-shell structure (TT1 < T < TT2), and aggregation of collapsed micelles (T > TT2). Due to the restrictions in the polymer chain arrangement introduced by the solid Si substrate, spin-coated PMEO2MA-b-POEGMA300 films exhibit an entirely different internal structure and transition behavior. Neutron reflectivity shows the absence of an ordered structure normal to the Si substrate in as-prepared PMEO2MA-b-POEGMA300 films. After exposure to D2O vapor for 3 h and then increasing the temperature above its TT1 and TT2, the ordered structure is still not observed. Only a D2O enrichment layer is formed close to the hydrophilic Si substrate. Such PMEO2MA-b-POEGMA300 films show a linear shrinkage between TT1 and TT2 in a D2O vapor atmosphere. This special behavior can be attributed to the synergistic effect between the restrained collapse of the PMEO2MA blocks by the still swollen POEGMA300 blocks and the impedance of chain arrangement by the Si substrate. Based on this unique behavior, spin-coated PMEO2MA-b-POEGMA300 films are further prepared into a temperature sensor by implementing Ag electrodes. Its resistance decreases linearly with temperature between TT1 and TT2.

MicroRNA-498 promotes proliferation, migration, and invasion of prostate cancer cells and decreases radiation sensitivity by targeting PTEN.

Prostate cancer (PCa) remains the secondary highest cause of cancer-related death in the United States in men. It has been reported that microRNAs can serve as key regulators in tumor development and progression in various cancers including PCa. In this study, we examined the effect of miR-498 on proliferation, radiosensitivity, invasion, and migration of PCa cells. The proliferation of LNCaP and DU-145 PCa cells with altered expression of miR-498 was evaluated by MTT assay. The invasion and migration of LNCaP and DU-145 PCa cells were assess by matrigel invasion assay and transwell migration assay. The protein expression level in PCa cells was examined by western blot. The function of miR-498 on radiation-induced apoptosis in LNCaP and DU-145 PCa cells was detected by Caspase-Glo3/7 assay. Forced expression of miR-498 improved the proliferation, invasion and migration in PCa cells. Furthermore, miR-498 decreased the sensitivity of PCa cells after ionizing radiation treatment. MiR-498 reduced the radiation-induced apoptosis in PCa cells by regulation of BAX and Bcl-2 expression. Meanwhile, miR-498 altered the expression of E-cadherin, N-cadherin, snail, and Vimentin in both LNCaP and DU-145 PCa cells and regulated epithelial to mesenchymal transition (EMT). Further study showed that aberrant expression of miR-498 changed the expression levels of phosphatase and tensin homolog and p-AKT in LNCaP and DU-145 PCa cells. In a summary, miR-498 displayed important roles in tumor development and progression in PCa cells, and might act as a potential prognostic biomarker and predict radiotherapy response in PCa.

Pro-Apoptotic Effects of Estetrol on Long-Term Estrogen-Deprived Breast Cancer Cells and at Low Doses on Hormone-Sensitive Cells.

PURPOSE: Postmenopausal women with estrogen receptor-positive breast cancers often respond initially to tamoxifen or aromatase inhibitor therapy. Resistance to these treatments usually develops within 12 to 18 months. Clinical studies have demonstrated that high-dose estrogen can induce regression of these endocrine-resistant tumors. However, side-effects of high-dose estradiol (E2) or diethylstilbestrol (DES) limit their usage. Estetrol (E4) is the most abundant estrogen during pregnancy and has a long half-life and a low potential for side-effects. Estetrol might then provide benefits similar to DES on tumor regression but with lesser toxicity. METHODS: In this study, we systematically evaluated the effects of E4 on cell proliferation and apoptosis in wild-type MCF-7 and long-term estrogen-deprived (LTED) MCF-7 cells and compared its effects with E2 and estriol (E3). RESULTS: Estetrol induced apoptosis in LTED cells but stimulated growth of MCF-7 cells at concentrations from 10-11 to 10-8 M. These effects of E4 are similar to those of E2 but require much higher doses. Differing from E2, E4 at 10-12 M induced apoptosis in MCF-7 cells and another pregnancy estrogen, E3, acted similarly. No antagonistic effect of E4 or E3 against E2 occurred when they were combined. CONCLUSIONS: The pro-apoptotic effects of E4 and E3 on LTED cells and at low doses on MCF-7 cells indicate that these steroids could be used as therapeutic agents for endocrine-resistant or sensitive breast cancer.

Functional Phosphine Derivatives Having Stationary and Flexible Chiralities: Their Preparation and Chirality Controlling.

Various functional secondary and tertiary phosphines, or their derivatives, containing stationary chiral phosphorus and flexible chiral axis were prepared, which could be further modified to afford diversely chelating ligands. The flexible axial chirality was fixed by stereogenic phosphorus via a cyclic linkage of chemical bonds or coordination with a metallic ion.

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis.

RNA degradation affects RNA-seq quality when profiling transcriptional activities in cells. Here, we show that transcript degradation is both gene- and sample-specific and is a common and significant factor that may bias the results in RNA-seq analysis. Most existing global normalization approaches are ineffective to correct for degradation bias. We propose a novel pipeline named DegNorm to adjust the read counts for transcript degradation heterogeneity on a gene-by-gene basis while simultaneously controlling for the sequencing depth. The robust and effective performance of this method is demonstrated in an extensive set of simulated and real RNA-seq data.

Enhanced Stain Removal and Comfort Control Achieved by Cross-Linking Light and Thermo Dual-Responsive Copolymer onto Cotton Fabrics.

Enhanced capabilities of stain removal and comfort control are simultaneously achieved by the light and thermo dual-responsive copolymer poly(triethylene glycol methyl ether methacrylate- co-ethylene glycol methacrylate- co-acrylamide azobenzene) (P(MEO3MA- co-EGMA- co-AAAB)) cross-linked on cotton fabrics. P(MEO3MA- co-EGMA- co-AAAB) is synthesized by sequential atom transfer radical polymerization with a molar ratio of 8 (MEO3MA):1 (EGMA):1 (AAAB). The MEO3MA units induce a thermoresponsive behavior to the copolymer. The hydrophilicity of the copolymer films can be further improved by the light-induced trans- cis isomerization of the AAAB units with UV radiation. The copolymer is facilely immobilized onto cotton fabrics with 1,2,3,4-butane tetracarboxylic acid as cross-linker. Due to the immobilization of P(MEO3MA- co-EGMA- co-AAAB), the hydrophilicity of the fabric surface is increased under UV radiation. Therefore, by simply installing a UV light source in the washing machine, better capability of stain removal is realized for the cross-linked cotton fabrics. It can prominently reduce the consumption of energy, water, and surfactants in laundry. In addition, the trans-AAAB units of the copolymer cause the cross-linked P(MEO3MA- co-EGMA- co-AAAB) layer to be more hydrophobic under ambient conditions. Hence, the copolymer can more easily collapse and form a porous structure on the fabrics. Thus, the air permeability of cotton fabrics cross-linked with P(MEO3MA- co-EGMA- co-AAAB) is enhanced by 13% at human body temperature as compared to P(MEO3MA- co-EGMA), giving improved comfort control during daily wear.

Functional analysis of gene expression profiling-based prediction in bladder cancer.

The present study aimed to analyze the modification of gene expression in bladder cancer (BC) by identifying significant differentially expressed genes (DEGs) and functionally assess them using bioinformatics analysis. To achieve this, two microarray datasets, GSE24152 (which included 10 fresh tumor tissue samples from urothelial bladder carcinoma patients and 7 benign mucosa samples from the bladder), and GSE42089 (which included 10 tissues samples from urothelial cell carcinoma patients and 8 tissues samples from the normal bladder), were downloaded from the Gene Expression Omnibus database for further analysis. Differentially expressed genes (DEGs) were screened between benign the mucosa and control groups in GSE24152 and GSE42089 datasets. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on overlapping DEGs identified in GSE24152 and GSE42089. Protein-protein interaction (PPI) networks and sub-networks were then constructed to identify key genes and main pathways. GO terms analysis was also performed for the selected clusters. In total, 1,325 DEGs in GSE24152 and 647 DEGs in GSE42089 were screened, in which 619 common DEGs were identified. The DEGs were mainly enriched in pathways and GO terms associated with mitotic and chromosome assembly, including nucleosome assembly, spindle checkpoint and DNA replication. In the interaction network, progesterone receptor (PGR), MAF bZIP transcription factor G (MAFG), cell division cycle 6 (CDC6) and members of the minichromosome maintenance family (MCMs) were identified as key genes. Histones were also considered to be significant factors in BC. Nucleosome assembly and sequence-specific DNA binding were the most significant clustered GO terms. In conclusion, the DEGs, including PGR, MAFG, CDC6 and MCMs, and those encoding the core histone family were closely associated with the development of BC via pathways associated with mitotic and chromosome assembly.

Chinese herbal medicine Shenzhuo Formula treatment in patients with macroalbuminuria secondary to diabetic kidney disease: study protocol for a randomized controlled trial.

BACKGROUND: Diabetic kidney disease (DKD) is a serious complication associated with diabetes mellitus and can cause end-stage renal disease (ESRD). Traditional Chinese medicine (TCM) is widely used in China to treat DKD, and in particular microalbuminuria and macroalbuminuria. This study will address the efficacy and safety of Shenzhuo Formula (SZF), a frequently prescribed TCM, in DKD patients with macroalbuminuria. METHODS/DESIGN: This study is a 24-week, randomized, multi-center, double-blinded, double-dummy, controlled, clinical trial that will include 120 DKD patients aged 18 to 80 years old with a 24-h urinary protein (24-h UP) level of between 0.5 g and 3 g and serum creatinine (SCr) ≤ 133 µmol/L (1.5 mg/dL) and compare SZF to irbesartan. The 24-h UP change from baseline to week 24 will represent the primary endpoint with secondary endpoints including SCr, estimated glomerular filtration rate (eGFR), TCM symptoms, urinary albumin excretion rate (UAER), etc. Safety assessments will also be evaluated. DISCUSSION: This study will provide initial evidence regarding the efficacy and safety of SZF relative to irbesartan in the treatment of DKD patients with macroalbuminuria. TRIAL REGISTRATION: Chinese Clinical Trial Registry, ID: ChiCTR-ICR-15006311 . Registered on 15 April 2015.