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Colorectal cancer (CRC), a common malignant tumor of the digestive tract, has a high incidence and mortality rate. Several recent studies have found that aging is associated with the increasing risk of cancer. Nevertheless, the expression status and function of age-related genes in CRC is still not well understood. In the study, we comprehensively analyzed the gene expression data of CRC patients from The Cancer Genome Atlas (TCGA) database. Age-related differential expression genes (age-related DEGs) in tumor tissues compared with normal tissues of CRC were further identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of age-related DEGs were performed by clusterProfiler of R. Afterwards, we used the STRING database to map the protein–protein interaction network of DEGs. We constructed prognostic model through univariate and multivariate COX regression analyses, and further evaluated their predictive power. The prognostic gene signature-related functional pathways were explored by gene set enrichment analysis (GSEA). The weighted gene co-expression network analysis (WGCNA) was used to identify key module associated with two prognostic gene signatures. Finally, we used the Metascape to perform functional enrichment analysis of genes in the key module. A total of 279 age-related DEGs were identified from the TCGA database. GO and KEGG enrichment analysis showed that the age-related DEGs were enriched in the Modulation of chemical synaptic transmission and Neuroactive ligand–receptor interaction. Moreover, we established a novel age-related gene signature (DLX2 and PCOLCE2) for overall survival in CRC, which was further predicted in both the training and validation sets. The results of GSEA demonstrated that numerous disease-related pathways were enriched in the high-risk group. We identified 43 genes related to the DLX2 and PCOLCE2 by the WGCNA co-expression network. We also found that these 43 genes were enriched in the cancer-related pathways. To sum up, the study identified an age-related gene signature for predicting the prognosis of CRC patients, which is conducive to the identification of novel prognostic molecular markers. [ABSTRACT FROM AUTHOR]

Asphalt binder is the main material for road pavement and building construction. It is a complex mixture composed of a large number of hydrocarbons with different molecular weights. The study of asphalt binders and asphalt concretes from a molecular perspective is an important means to understand the intricate properties of asphalt. Molecular dynamics simulation is based on Newton's law and predicts the microscopic performance of materials by calculating the intra- and intermolecular interactions. The asphalt binder can be divided into four components: saturates, aromatics, resins, and asphaltenes (SARA). A new molecular model of asphalt was proposed and verified in this study. Eight molecules selected from the literature were used to represent the four components of asphalt. The AMBER Cornell Extension Force Field was applied in this study to model building and the calculation of properties. The density of the asphalt model was calculated and compared with experimental results for validity verifications. The results show that the purposed model can be used to calculate the microscopic properties of the asphalt binder because the density of the model is close to the real value in the field. Besides, the proportions of different molecules in the model were adjusted to predict the relationship between the asphalt binder density and the hydrocarbon ratios and heteroatom contents of the molecular model. Moreover, the glass transition temperature of the asphalt binder model is predicted by the simulation of the heating process. The range of the glass transition temperature is determined by calculating the relationship between specific volume and temperature, and the calculated range is close to the experimental value. [ABSTRACT FROM AUTHOR]

Life history theory predicts that animals often produce fewer offspring of larger size and indicate a stronger trade-off between the number and size of offspring to cope with increasing environmental stress. In order to evaluate this prediction, we tested the life history characteristics of Bufo minshanicus at eight different altitudes on the eastern Tibetan Plateau, China. Our results revealed a positive correlation between female SVL and clutch size or egg size, revealing that larger females produce more and larger eggs. However, high-altitude toads seem to favor more offspring and smaller egg sizes when removing the effect of female SVL, which is counter to theoretical predictions. In addition, there was an overall significantly negative relationship between egg size and clutch size, indicative of a trade-off between egg size and fecundity. Therefore, we suggest that higher fecundity, rather than larger egg size, is a more effective reproductive strategy for this species of anuran living at high-altitude environments. [ABSTRACT FROM AUTHOR]

The role of 5-methylcytosine (m5C) in tumor initiation and progression has been increasingly recognized. However, the precise association between the regulation of m5C and the progression, metastasis, and prognosis of head and neck squamous cell carcinoma (HNSCC) has not yet been fully explored. Data from 545 HNSCC patients obtained from The Cancer Genome Atlas (TCGA) database were analyzed. Unsupervised cluster analysis was conducted using the expression levels of m5C regulatory genes. Additionally, gene set variation analysis (GSVA), single-sample gene set enrichment analysis (ssGSEA), and Cox regression analysis were utilized. Quantitative reverse transcription polymerase chain reaction (RT-qPCR), colony formation assay, transwell experiments and western blots were performed in the HNSCC cell line UM-SCC-17B to assess the expression and functional role of one of the novel signatures, CNFN. Significant expression differences were found in m5C regulatory genes between tumor and normal tissues in HNSCC. Two distinct m5C modification patterns, characterized by substantial prognostic differences, were identified. Cluster-2, which exhibited a strong association with epithelial-mesenchymal transition (EMT), was found to be associated with a poorer prognosis. Based on the m5C clusters and EMT status, differentially expressed genes (DEGs) were identified. Using DEGs, an 8-gene signature (CAMK2N1, WNT7A, F2RL1, AREG, DEFB1, CNFN, TGFBI, and CAV1) was established to develop a prognostic model. The performance of this signature was validated in both the training and external validation datasets, demonstrating its promising efficacy. Furthermore, additional investigations using RT-qPCR on clinical specimens and experimental assays in cell lines provided compelling evidence suggesting that CNFN, one of the genes in the signature, could play a role in HNSCC progression and metastasis through the EMT pathway. This study highlighted the role of m5C in HNSCC progression and metastasis. The relationship between m5C and EMT has been elucidated for the first time. A robust prognostic model was developed for accurately predicting HNSCC patients' survival outcomes. Potential molecular mechanisms underlying these associations have been illuminated through this research. [ABSTRACT FROM AUTHOR]

Due to its challenging manufacturing and intricate morphology, the aluminum alloy transmission intermediate shell used in vehicle transmission has been the focus of many academic studies. In this study, the three-dimensional cutting model is condensed to a two-dimensional cutting model and utilized to simulate the finishing process of an aluminum alloy workpiece using the finite element modeling program DEFORM-3D. Through orthogonal testing and range analysis, the impact of integral end mill side edge parameters on cutting performance was investigated. It is determined that tool chamfering has a greater impact on cutting performance than tool rake and relief angles, that chamfering width has the most impact on cutting force, and that chamfering angle has the greatest impact on cutting temperature. The workpiece's surface roughness is tested during a cutting experiment, and an analysis of the data reveals that the finite element simulation model is accurate and the orthogonal test method is reasonable. The tool chamfer has a greater impact on roughness than the tool rake angle and relief angle. The tool settings are further optimized using the firefly method. By examining the data, it is determined that the prediction model is correct and the optimization model is reasonable. The cutting efficiency is higher and the surface quality is better when the chamfer width is 0.17 mm and the chamfer angle is 7.3° or 18.3°. Therefore, optimizing the side edge parameters of the integral end mill during the finishing process of a thin-walled aluminum alloy shell has practical technical value. [ABSTRACT FROM AUTHOR]

CHARGE syndrome, a rare multiple congenital anomaly condition, is caused by haploinsufficiency of the chromatin remodeling protein gene CHD7 (Chromodomain helicase DNA binding protein 7). Brain abnormalities and intellectual disability are commonly observed in individuals with CHARGE, and neuronal differentiation is reduced in CHARGE patient-derived iPSCs and conditional knockout mouse brains. However, the mechanisms of CHD7 function in nervous system development are not well understood. In this study, we asked whether CHD7 promotes gene transcription in neural progenitor cells via changes in chromatin accessibility. We used Chd7 null embryonic stem cells (ESCs) derived from Chd7 mutant mouse blastocysts as a tool to investigate roles of CHD7 in neuronal and glial differentiation. Loss of Chd7 significantly reduced neuronal and glial differentiation. Sholl analysis showed that loss of Chd7 impaired neuronal complexity and neurite length in differentiated neurons. Genome-wide studies demonstrated that loss of Chd7 leads to modified chromatin accessibility (ATAC-seq) and differential nascent expression (Bru-Seq) of neural-specific genes. These results suggest that CHD7 acts preferentially to alter chromatin accessibility of key genes during the transition of NPCs to neurons to promote differentiation. Our results form a basis for understanding the cell stage-specific roles for CHD7-mediated chromatin remodeling during cell lineage acquisition. [ABSTRACT FROM AUTHOR]

Genomic profiling studies have demonstrated that bladder cancer can be divided into two molecular subtypes referred to as luminal and basal with distinct clinical behaviors and sensitivities to frontline chemotherapy. We analyzed the mRNA expressions of signature luminal and basal genes in bladder cancer tumor samples from publicly available and MD Anderson Cancer Center cohorts. We developed a quantitative classifier referred to as basal to luminal transition (BLT) score which identified the molecular subtypes of bladder cancer with 80–94% sensitivity and 83–93% specificity. In order to facilitate molecular subtyping of bladder cancer in primary care centers, we analyzed the protein expressions of signature luminal (GATA3) and basal (KRT5/6) markers by immunohistochemistry, which identified molecular subtypes in over 80% of the cases. In conclusion, we provide a tool for assessment of molecular subtypes of bladder cancer in routine clinical practice. [ABSTRACT FROM AUTHOR]

Patients who undergo orthotopic liver transplantation often sustain acute kidney injury(AKI). The toll-like receptor 4(TLR4)/Nuclear factor-кB(NF-кB) pathway plays a role in AKI. Dexmedetomidine(Dex) has been shown to attenuate AKI. The current study aimed to determine whether liver transplantation-induced AKI is associated with inflammatory response, and to assess the effects of dexmedetomidine pretreatment on kidneys in rats following orthotopic autologous liver transplantation(OALT). Seventy-seven adult male rats were randomized into 11 groups. Kidney tissue histopathology and levels of blood urea nitrogen(BUN) and serum creatinine(SCr) were evaluated. Levels of TLR4, NF-κB, tumor necrosis factor-α, and interleukin-1β levels were measured in kidney tissues. OALT resulted in significant kidney functional impairment and tissue injury. Pre-treatment with dexmedetomidine decreased BUN and SCr levels and reduced kidney pathological injury, TLR4 expression, translocation of NF-κB, and cytokine production. The effects of dexmedetomidine were reversed by pre-treatment with atipamezole and BRL44408, but not ARC239. These results were confirmed by using α2A-adrenergic receptor siRNA which reversed the protective effect of dexmedetomidine on attenuating NRK-52E cells injury induced by hypoxia reoxygenation. In conclusion, Dexmedetomidine-pretreatment attenuates OALT-induced AKI in rats which may be contributable to its inhibition of TLR4/MyD88/NF-κB pathway activation. The renoprotective effects are related to α2A-adrenergic receptor subtypes. [ABSTRACT FROM AUTHOR]

Many cell types migrate in response to naturally generated electric fields. Furthermore, it has been suggested that the external application of an electric field may be used to intervene in and optimize natural processes such as wound healing. Precise cell guidance suitable for such optimization may rely on predictive models of cell migration, which do not generalize. Here, we present a machine learning model that can forecast directedness of cell migration given a timeseries of previous directedness and electric field values. This model is trained using time series galvanotaxis data of mammalian cranial neural crest cells obtained through time-lapse microscopy of cells cultured at 37 °C in a galvanotaxis chamber at ambient pressure. Next, we show that our modeling approach can be used for a variety of cell types and experimental conditions with very limited training data using transfer learning methods. We adapt the model to predict cell behavior for keratocytes (room temperature, ~ 18–20 °C) and keratinocytes (37 °C) under similar experimental conditions with a small dataset (~ 2–5 cells). Finally, this model can be used to perform in silico studies by simulating cell migration lines under time-varying and unseen electric fields. We demonstrate this by simulating feedback control on cell migration using a proportional–integral–derivative (PID) controller. This data-driven approach provides predictive models of cell migration that may be suitable for designing electric field based cellular control mechanisms for applications in precision medicine such as wound healing. [ABSTRACT FROM AUTHOR]

Many cell types migrate in response to naturally generated electric fields. Furthermore, it has been suggested that the external application of an electric field may be used to intervene in and optimize natural processes such as wound healing. Precise cell guidance suitable for such optimization may rely on predictive models of cell migration, which do not generalize. Here, we present a machine learning model that can forecast directedness of cell migration given a timeseries of previous directedness and electric field values. This model is trained using time series galvanotaxis data of mammalian cranial neural crest cells obtained through time-lapse microscopy of cells cultured at 37 °C in a galvanotaxis chamber at ambient pressure. Next, we show that our modeling approach can be used for a variety of cell types and experimental conditions with very limited training data using transfer learning methods. We adapt the model to predict cell behavior for keratocytes (room temperature, ~ 18–20 °C) and keratinocytes (37 °C) under similar experimental conditions with a small dataset (~ 2–5 cells). Finally, this model can be used to perform in silico studies by simulating cell migration lines under time-varying and unseen electric fields. We demonstrate this by simulating feedback control on cell migration using a proportional–integral–derivative (PID) controller. This data-driven approach provides predictive models of cell migration that may be suitable for designing electric field based cellular control mechanisms for applications in precision medicine such as wound healing. [ABSTRACT FROM AUTHOR]

Plants belonging to family Paeoniaceae are not only economically important ornamental plants but also medicinal plants used as an important source of traditional Chinese medicine. Owing to the complex network evolution and polyploidy evolution of this family, its systematics and taxonomy are controversial and require a detailed investigation. In this study, three complete chloroplast genomes of sect. Paeonia, one of the sections of Paeonia, were sequenced and then analysed together with 16 other published chloroplast genomes of Paeoniaceae species. The total lengths of the chloroplast genomes of these species were 152,153–154,405 bp. A total of 82–87 protein-coding genes, 31–40 tRNA genes and 8 rRNA genes were annotated. Bioinformatics analysis revealed 61–74 simple sequence repeats (SSRs) in the chloroplast genomes, most of which have A/T base preference. Codon usage analysis showed that A/U-ending codons were more positive than C/G-ending codons, and a slight bias in codon usage was observed in these species. A comparative analysis of these 19 species of Paeoniaceae was then conducted. Fourteen highly variable regions were selected for species relationship study. Phylogenetic analysis revealed that the species of sect. Paeonia gathered in one branch and then divided into different small branches. P. lactiflora, P. anomala, P. anomala subsp. veitchii and P. mairei clustered together. P. intermedia was related to P. obovata and P. obovata subsp. willmottiae. P. emodi was the sister to all other species in the sect. Paeonia. [ABSTRACT FROM AUTHOR]

Sarcomatoid clear-cell renal cell carcinomas (sRCC) are associated with dismal prognosis. Genomic alterations associated with sarcomatoid dedifferentiation are poorly characterized. We sought to define the genomic landscape of sRCC and uncover potentially actionable therapeutic targets. We assessed the genomic landscape of sRCC using targeted panel sequencing including patients with microdissected sarcomatoid and epithelial components. Along with common genomic alterations associated with clear-cell histology, we found that Hippo was one of the most frequently altered pathways in these tumours. Hippo alterations were differentially enriched in sRCC compared to non-sRCC. Functional analysis showed that Hippo members mutations were associated with higher nuclear accumulation of YAP/TAZ, core effectors of the Hippo pathway. In a NF2-mutant sRCC model, YAP1 knockdown and NF2 reconstitution suppressed cell proliferation, tumour growth and invasion, both in vitro and in vivo. Overall, we show that Hippo pathway alterations are a feature of sRCC, and enable the exploration of the Hippo pathway as a novel potential therapeutic target. [ABSTRACT FROM AUTHOR]

Hepatitis and hepatocellular carcinoma are serious human diseases. Here, we examined the in vivo and in vitro inhibitory effect of extracts of Qizhu decoction (a traditional Chinese medicine) on hepatitis caused by diethylnitrosamine or hepatitis B virus and on diethylnitrosamine-induced hepatocellular carcinoma. The results showed that both the aqueous and ethanol extracts (QC and QS, respectively) of Qizhu decoction significantly inhibited hepatic inflammation and liver cancer induced by diethylnitrosamine or hepatitis B virus by suppressing NF-κB signaling and decreasing the levels of TNF-α and IL-1β. Both QC and QS inhibited the proliferation and migration of primary cancer hepatocytes by reducing cyclin B1, cyclin D1 and N-cadherin expression and increasing E-cadherin expression. QC and QS also promoted the apoptosis of primary cancer hepatocytes by upregulating caspase-3 and downregulating BCL-2 expression. The knockdown of p65 in NF-κB signaling inhibited the ability of QC and QS to significantly reduce the colony formation ability of liver cancer cells. Additionally, QC and QS might significantly inhibit the DNA replication of hepatitis B virus in vivo and in vitro, and we found that corilagin and polydatin were the active compounds of QC and QS. Taken together, our in vitro findings and our results in C57BL/6 mice showed that extracts of Qizhu decoction might inhibit hepatitis and hepatocellular carcinoma by suppressing NF-κB signaling. [ABSTRACT FROM AUTHOR]

Complement activation plays important roles in the pathogenesis of central nervous system (CNS) diseases. Patients face neurological disorders due to the development of complement activation, which contributes to cell apoptosis, brain edema, blood-brain barrier dysfunction and inflammatory infiltration. We previously reported that induced neural stem cells (iNSCs) can promote neurological functional recovery in closed head injury (CHI) animals. Remarkably, we discovered that local iNSC grafts have the potential to modulate CNS inflammation post-CHI. In this study, we aimed to explore the role of systemically delivered iNSCs in complement activation following CNS injury. Our data showed that iNSC grafts decreased the levels of sera C3a and C5a and down-regulated the expression of C3d, C9, active Caspase-3 and Bax in the brain, kidney and lung tissues of CHI mice. Furthermore, iNSC grafts decreased the levels of C3d+/NeuN+, C5b-9+/NeuN+, C3d+/Map2+ and C5b-9+/Map2+ neurons in the injured cortices of CHI mice. Subsequently, we explored the mechanisms underlying these effects. With flow cytometry analysis, we observed a dramatic increase in complement receptor type 1-related protein y (Crry) expression in iNSCs after CHI mouse serum treatment. Moreover, both in vitro and in vivo loss-of-function studies revealed that iNSCs could modulate complement activation via Crry expression. [ABSTRACT FROM AUTHOR]

Pulsatillae radix is a conventional traditional Chinese medicine (TCM) with common name Baitouweng, and has notable effects on inflammation and dysentery. Pulsatilla chinensis (Bge.) Regel is the only source plant of Baitouweng recorded in Chinese Pharmacopoeia, but its adulteration often occurs in the market that possibly affects medicinal efficacy and safety. We have established an internal transcribed spacer 2 (ITS2) barcode library based on 105 plant samples from 12 Pulsatilla species and 10 common adulterants. Results indicate that ITS2 barcoding can accurately distinguish Pulsatilla species from their adulterants. Pulsatilla chinensis can be discriminated from 11 congeneric species by two stable single nucleotide polymorphisms (SNPs) in the ITS2 region. Additionally, a quick specific PCR-RFLP identification assay based on the ITS2 barcode was developed. Using specific primers ITS2/PR1 combined with restriction enzyme Bgl I, Pu. chinensis can rapidly be differentiated from other species via simple and low-cost test procedures. Furthermore, 30 commercial Baitouweng products were tested and only two products were derived from authentic Pu. chinensis. Thus, these two molecular approaches provide practical tools for quick identification of commercial Baitouweng products and can help ensure the safe use of this TCM product. [ABSTRACT FROM AUTHOR]

The adulteration of herbal products is a threat to consumer safety. Here we surveyed the species composition of commercial Rhodiola products using DNA barcoding as a supervisory method. A Rhodiola dietary supplement DNA barcode database was successfully constructed using 82 voucher samples from 10 Rhodiola species. Based on the DNA barcoding standard operating procedure (SOP), we used this database to identify 100 Rhodiolae Crenulatae Radix et Rhizoma decoction piece samples that were purchased from drug stores and hospitals. The results showed that only 36 decoction piece sequences (40%) were authentic R. crenulata, which is recorded in Chinese Pharmacopeia, whereas the other samples were all adulterants and may indicate a potential safety issue. Among the adulterants, 35 sequences (38.9%) were authenticated as R. serrata, nine sequences (10%) were authenticated as R. rosea, which is documented in the United States Pharmacopeia, and the remaining samples were authenticated as other three Rhodiola species. This result indicates decoction pieces that are available in the market have complex origins and DNA barcoding is a convenient tool for market supervision. [ABSTRACT FROM AUTHOR]

Kampo is the general designation for traditional Japanese herbal medicines, which are recognized as official medicines and listed in the Japanese pharmacopoeia (JP). In most cases, it is difficult to identify the crude drug materials to species level using only traditional identification methods. We report the first online DNA barcode identification system, which includes standard barcode sequences from approximately 95% of the species recorded in the JP (16th edition). This tool provides users with basic information on each crude drug recorded in the JP, DNA barcoding identification of herbal material, and the standard operating procedure (SOP) from sampling to data analysis. ITS2 sequences (psbA-trnH was an alternative when ITS2 could not be amplified) were generated from a total of 576 samples to establish the database. An additional 100 samples (from different medicinal parts, from both single origin and multiple origins and from both retailers and the planting base) were identified using the system. A total of 78% of the test samples were identified as the species listed on their label. This system establishes a model platform for other pharmacopeias from countries like China, Korea, the US and the European Union, for the safe and effective utilization of traditional herbal medicines. [ABSTRACT FROM AUTHOR]

The effects of AURKA overexpression associated with poor clinical outcomes have been attributed to increased cell cycle progression and the development of genomic instability with aneuploidy. We used RNA interference to examine the effects of AURKA overexpression in human bladder cancer cells. Knockdown had minimal effects on cell proliferation but blocked tumor cell invasion. Whole genome mRNA expression profiling identified nicotinamide N-methyltransferase (NNMT) as a downstream target that was repressed by AURKA. Chromatin immunoprecipitation and NNMT promoter luciferase assays revealed that AURKA's effects on NNMT were caused by PAX3-mediated transcriptional repression and overexpression of NNMT blocked tumor cell invasion in vitro. Overexpression of AURKA and activation of its downstream pathway was enriched in the basal subtype in primary human tumors and was associated with poor clinical outcomes. We also show that the FISH test for the AURKA gene copy number in urine yielded a specificity of 79.7% (95% confidence interval [CI] = 74.2% to 84.1%), and a sensitivity of 79.6% (95% CI = 74.2% to 84.1%) with an AUC of 0.901 (95% CI = 0.872 to 0.928; P < 0.001). These results implicate AURKA as an effective biomarker for bladder cancer detection as well as therapeutic target especially for its basal type. [ABSTRACT FROM AUTHOR]

Traditional herbal medicines adulterated and contaminated with plant materials from the Aristolochiaceae family, which contain aristolochic acids (AAs), cause aristolochic acid nephropathy. Approximately 256 traditional Chinese patent medicines, containing Aristolochiaceous materials, are still being sold in Chinese markets today. In order to protect consumers from health risks due to AAs, the hidden assassins, efficient methods to differentiate Aristolochiaceous herbs from their putative substitutes need to be established. In this study, 158 Aristolochiaceous samples representing 46 species and four genera as well as 131 non-Aristolochiaceous samples representing 33 species, 20 genera and 12 families were analyzed using DNA barcodes based on the ITS2 and psbA-trnH sequences. Aristolochiaceous materials and their non-Aristolochiaceous substitutes were successfully identified using BLAST1, the nearest distance method and the neighbor-joining (NJ) tree. In addition, based on sequence information of ITS2, we developed a Real-Time PCR assay which successfully identified herbal material from the Aristolochiaceae family. Using Ultra High Performance Liquid Chromatography-Mass Spectrometer (UHPLC-HR-MS), we demonstrated that most representatives from the Aristolochiaceae family contain toxic AAs. Therefore, integrated DNA barcodes, Real-Time PCR assays using TaqMan probes and UHPLC-HR-MS system provides an efficient and reliable authentication system to protect consumers from health risks due to the hidden assassins (AAs). [ABSTRACT FROM AUTHOR]