[Controversy of primary tumor resection for stage IV colorectal cancer]

Primary tumor resection (PTR) is currently recommended for patients with unresectable stage IV colorectal cancer (CRC) who present symptoms related to their primary tumor (eg, obstruction, perforation, significant bleeding). The role of PTR in asymptomatic patients remains controversial. This article will review the role of PTR in incurable stage IV CRC, including the advantages and risks, with emphasis on identifying patients who may benefit from this palliative intervention.

Dysprosium(iii) complexes with a square-antiprism configuration featuring mononuclear single-molecule magnetic behaviours based on different β-diketonate ligands and auxiliary ligands

Three mononuclear SMMs derived from three β-diketonate ligands and auxiliary ligands have been synthesized.

An Ag(i) energetic metal–organic framework assembled with the energetic combination of furazan and tetrazole: synthesis, structure and energetic performance

A novel 3D Ag(i) energetic MOF assembled with a furazan derivative (4,4′-oxybis[3,3′-(1H-5-tetrazol)]furazan) shows low sensitivity, good thermostability and ultrahigh detonation pressure and detonation velocity.

Copper-based energetic MOFs with 3-nitro-1H-1,2,4-triazole: solvent-dependent syntheses, structures and energetic performances

Three energetic compounds assembled with 3-nitro-1H-1,2,4-triazole have exemplified that coordinated solvent molecules may have a vital effect on the detonation properties.

Contrast-Enhanced Ultrasonography Features of Breast Malignancies with Different Sizes: Correlation with Prognostic Factors

This study was to investigate the correlation between contrast-enhanced ultrasonography (CEUS) characteristics with prognostic factors in breast cancers with different sizes. A retrospective analysis of CEUS characteristics of 104 pathologically proven malignant lesions from 104 women was conducted. Lesions were divided into two groups according to their size measured by US (Group 1: maximum diameter ≤20 mm; Group 2: maximum diameter >20 mm). Features including enhancement degree, order and pattern, enlargement of the enhancement area, and penetrating vessels on CEUS were evaluated. Pathologic prognostic factors, including estrogen and progesterone receptor status, and the expression of c-erb-B2, p53, Ki-67, and VEGF were assessed. Comparison of enhancement pattern parameters between Group 1 and Group 2 showed statistically significant differences (P < 0.0001). A significant correlation was found between enlargement of the enhancement area and ER positivity in Group 1 (P = 0.032). In Group 2 the absence of penetrating vessels was significantly associated with VEGF negativity (P = 0.022) and ER negativity (P = 0.022). Centripetal enhancement reflected VEGF negativity (P = 0.033) in lesions with diameter >20 mm. Thus, breast cancers with different sizes show different CEUS features; small breast cancers show homogeneous enhancement pattern while cancers with diameter >20 mm show homogeneous enhancement pattern. Some CEUS characteristics of differently sized breast cancers could be correlated with prognostic factors, which may be useful in prognosis assessment.

Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing

RNA-Seq technology has been widely applied to transcriptomics, genomics, molecular marker development, and functional gene studies. In the genome, microsatellites are simple sequence repeats (SSR) with a high degree of polymorphism that are used as DNA markers in many molecular genetic studies. Using traditional methods such as magnetic bead enrichment, only a few microsatellite markers have been isolated. Coilia nasus is an anadromous, small-to-moderately sized fish species that is famous as an important fishery resource. Here, we have identified a large number of microsatellites from the fish brains by using Illumina sequencing. About 20 million Illumina reads were assembled into 148,845 unigenes. A total of 13,038 SSR motifs were identified via analysis of 3,958,293,117 (3.96 Gb) nucleotides to produce a comprehensive transcript dataset for the C. nasus brain, including mono-, di-, tri-, tetra-, and penta-repeat motifs. The most abundant type of repeat motif was di-nucleotide (42.97%), followed by mono-nucleotide (38.86%), tri-nucleotide (16.21%), tetra-nucleotide (1.83%), and penta-nucleotide (0.05%) repeat units, which is similar to the results obtained in studies in other species. These data provide a base of sequence information to improve molecular-assisted markers to study C. nasus genetic diversity.

[Association between RIPK4 relative copy number and prognosis of colorectal cancer patient after oxaliplatin-based chemotherapy]

OBJECTIVE

To investigate the association between receptor-interacting kinase protein 4 (RIPK4) relative copy number (RCN) and prognosis of stage III( colorectal cancer (CRC) patients treated with oxaliplatin-based chemotherapy.

METHODS

RIPK4 RCN was determined by real-time PCR and then dichotomized into high RIPK4 RCN group(n=35) and low RIPK4 RCN group (n=104) using the third quartile as the cut-off point. Overall survival (OS) and recurrence-free survival (RFS) were compared between high and low RIPK4 RCN groups. The subgroup prognostic analysis was also conducted based on tumor site.

RESULTS

The median follow-up period was 49 months (ranged 4 to 98 months). Patients with high RIPK4 RCN had poorer OS than those with low RIPK4 RCN, which reached marginal significance(median OS, 43.0 months vs. 53.5 months, P=0.074). Meanwhile there was no significant difference of RFS between two groups (P=0.352). In colon cancer subgroup, high RIPK4 RCN was significantly associated with poor OS (median OS, 31.5 months vs. 56.6 months, P=0.015) but not with RFS (P=0.135). In rectal cancer subgroup, RIPK4 RCN was not associated with both OS and RFS (P=0.981, P=0.738). Multivariate analysis revealed that high RIPK4 RCN was an independent prognostic factor of OS in stage III( CRC patients treated with oxaliplatin-based chemotherapy (HR=2.903, 95% CI: 1.275 to 6.610).

CONCLUSION

RIPK4 RCN is significantly associated with OS in stage III( colon cancer patients receiving oxaliplatin-based chemotherapy and may be a novel biomarker that can predict the efficacy of oxaliplatin in colon cancer patients.

Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and Escherichia coli DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for E. coli colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.

Adult cervicomedullary pilocytic astrocytoma: A case report

Pilocytic astrocytoma (PA) is a rare glioma, which generally occurs in children and young adults. In adult patients, the majority of PA tumors are supratentorial. Due to the low morbidity rate of the disease in adults, PA is frequently misdiagnosed and mistreated. In the present study, this rare disease was successfully treated. The study reported the case of a 48-year-old patient with a cervicomedullary occupying lesion, who complained of numbness and pain of the right limbs that persisted for >10 years, with aggravation for 1 month. A magnetic resonance imaging scan showed a sharp cervicomedullary mass extending from the lower medulla to the cervical vertebra C3 level. Intraoperatively, the medulla and upper cervical cord were found to be well-stacked. Immediately after ingression into the spinal cord along the dorsal median sulcus, the tumor mass was detected and had a gray fish-like appearance, moderate blood supply and clear boundary. After intratumoral decompression, total excision was achieved. Postoperative pathological examination confirmed that the tumor was a PA. Following discharge, the patient did not suffer from any symptoms of the lower cranial nerves and was able to walk with limited assistance.

Ultra-sparse metasurface for high reflection of low-frequency sound based on artificial Mie resonances

Acoustic metamaterials offer great flexibility for manipulating sound waves and promise unprecedented functionality, ranging from transformation acoustics, super-resolution imaging to acoustic cloaking. However, the design of acoustic metamaterials with exciting functionality remains challenging with traditional approaches using classic acoustic elements such as Helmholtz resonators and membranes. Here we demonstrate an ultraslow-fluid-like particle with intense artificial Mie resonances for low-frequency airborne sound. Eigenstate analysis and effective parameter retrieval show two individual negative bands in the single-size unit cell, one of which exhibits a negative bulk modulus supported by the monopolar Mie resonance, whereas the other exhibits a negative mass density induced by the dipolar Mie resonance. The unique single-negative nature is used to develop an ultra-sparse subwavelength metasurface with high reflectance for low-frequency sound. We demonstrate a 0.15λ-thick, 15%-filling ratio metasurface with an insertion loss over 93.4%. The designed Mie resonators provide diverse routes to construct novel acoustic devices with versatile applications.

Chemical composition and cytotoxicity of the essential oil from different parts of Datura metel L

The essential oil from different parts of Datura metel L. were extracted using hydrodistillation and GC-MS was used to analyse the essential oil. The main components of flowers were ketone (23.61%) and ethyl palmitate (15.84%). The main components of leaves were ketone (18.84%) and phytol (18.71%). Ketone (39.45%) and phytol (31.32%) were the major components of petioles. Palmitic acid (30.60%) and ethyl linoleate (21.56%) were the major components of seeds. The major ingredient of roots was palmitic acid (52.61%). The main ingredients of the stems were palmitic acid (38.38%) and ethyl linoleate (17.38%). All the different parts of essential oil were screened for cytotoxicity. The roots and stems showed the inhibitory effects against HepG-2 with IC50 levels of 613.88 and 341.12 mg/L. The leaves and roots showed the inhibitory effects against HeLa with IC50 levels of 267.76 and 348.35 mg/L. All the six parts have inhibitory effects against SGC-7901 cell lines.

The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches

BACKGROUND

Functional annotation of novel proteins is one of the central problems in bioinformatics. With the ever-increasing development of genome sequencing technologies, more and more sequence information is becoming available to analyze and annotate. To achieve fast and automatic function annotation, many computational (automated) function prediction (AFP) methods have been developed. To objectively evaluate the performance of such methods on a large scale, community-wide assessment experiments have been conducted. The second round of the Critical Assessment of Function Annotation (CAFA) experiment was held in 2013-2014. Evaluation of participating groups was reported in a special interest group meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in Boston in 2014. Our group participated in both CAFA1 and CAFA2 using multiple, in-house AFP methods. Here, we report benchmark results of our methods obtained in the course of preparation for CAFA2 prior to submitting function predictions for CAFA2 targets.

RESULTS

For CAFA2, we updated the annotation databases used by our methods, protein function prediction (PFP) and extended similarity group (ESG), and benchmarked their function prediction performances using the original (older) and updated databases. Performance evaluation for PFP with different settings and ESG are discussed. We also developed two ensemble methods that combine function predictions from six independent, sequence-based AFP methods. We further analyzed the performances of our prediction methods by enriching the predictions with prior distribution of gene ontology (GO) terms. Examples of predictions by the ensemble methods are discussed.

CONCLUSIONS

Updating the annotation database was successful, improving the Fmax prediction accuracy score for both PFP and ESG. Adding the prior distribution of GO terms did not make much improvement. Both of the ensemble methods we developed improved the average Fmax score over all individual component methods except for ESG. Our benchmark results will not only complement the overall assessment that will be done by the CAFA organizers, but also help elucidate the predictive powers of sequence-based function prediction methods in general.

LZTFL1 suppresses lung tumorigenesis by maintaining differentiation of lung epithelial cells

Lung cancer is the leading cause of cancer-related death in the United States, and metastatic behavior is largely responsible for this mortality. Mutations in multiple ‘driver' oncogenes and tumor suppressors are known to contribute to the lung tumorigenesis and in some cases represent therapeutic targets. Leucine Zipper Transcription Factor-like 1 (LZTFL1) is located in the chromosome region 3p21.3 where allelic loss and genetic alterations occur early and frequently in lung cancers. Previously, we found that LZTFL1 is downregulated in epithelial tumors, including lung cancer, and functions as a tumor suppressor in gastric cancers. However, the functional role of LZTFL1 in lung oncogenesis is undefined. We show here that downregulation of LZTFL1 expression in non-small cell lung cancer is associated with recurrence and poor survival, whereas re-expression of LZTFL1 in lung tumor cells inhibited extravasation/colonization of circulating tumor cells to the lung and inhibited tumor growth in vivo. Mechanistically, we found that LZTFL1 is expressed in ciliated human bronchial epithelial cells (HBECs) and its expression correlates with HBEC differentiation. LZTFL1 inhibits transforming growth factor β-activated mitogen-activated protein kinase and hedgehog signaling. Alteration of intracellular levels of LZTFL1 resulted in changes of expression of genes associated with epithelial-to-mesenchymal transition (EMT). We conclude that LZTFL1 inhibits lung tumorigenesis, possibly by maintaining epithelial cell differentiation and/or inhibition of signalings that lead to EMT and suggest that reactivation of LZTFL1 expression in tumor cells may be a novel lung cancer therapeutic approach.

Association of polymorphism within the interleukin-28 receptor alpha gene, but not in interleukin-28B, with lower urinary tract symptoms (LUTS) in Chinese

The aim of this study was to determine the relationship between polymorphisms in the IL-28B and IL-28R genes and lower urinary tract symptoms (LUTS) in Chinese patients. Genomic DNA was extracted from 553 whole blood samples from 233 patients with LUTS resulted from benign prostatic hyperplasia and 320 control subjects. The IL-28B rs12979860 and rs8099917, and IL-28Rα rs10903035 and rs11249006 polymorphisms were genotyped using a polymerase chain reaction-restriction fragment length polymorphism assay. For rs10903035, the frequencies of the "G" allele and the "AG/GG" genotypes in the LUTS group were significantly lower than those in the control group ("G" vs "A": OR = 0.655, 95%CI = 0.506-0.849; AG/GG vs "AA": OR = 0.538, 95%CI = 0.379-0.764, respectively). Combined effects analysis of rs12979860 and rs10903035 showed that the "CC+AG/GG" and "CT+AA" genotypes were significantly less frequent in the LUTS group ("CC+AG/GG" vs "CC+AA": OR = 0.553, 95%CI = 0.381-0.801; "CT+AG/GG" vs "CC+AA": OR = 0.429, 95%CI = 0.198- 0.927, respectively). In addition, the combined effects of the rs8099917 and rs10903035 "TT+AG/GG" and "GT+AG/GG" genotypes were also significantly lower in the LUTS group ("TT+AG/GG" vs "TT+AA": OR = 0.569, 95%CI = 0.395-0.821; "GT+AG/GG" vs "TT+AA": OR = 0.318, 95%CI = 0.128-0.788, respectively). Stratification analysis revealed that the frequencies of the rs11249006 "AG/GG" genotypes in the subgroups of size ≤4.11 and IPSS ≤ 28 were significantly higher than those in the subgroups of size >4.11 and IPSS > 28. Therefore, the IL-28Rαgene polymorphism might be involved in the development of LUTS.

Biocontrol agent Bacillus amyloliquefaciens LJ02 induces systemic resistance against cucurbits powdery mildew

Powdery mildew is a fungal disease found in a wide range of plants and can significantly reduce crop yields. Bacterial strain LJ02 is a biocontrol agent (BCA) isolated from a greenhouse in Tianjin, China. In combination of morphological, physiological, biochemical and phylogenetic analyses, strain LJ02 was classified as a new member of Bacillus amyloliquefaciens. Greenhouse trials showed that LJ02 fermentation broth (LJ02FB) can effectively diminish the occurrence of cucurbits powdery mildew. When treated with LJ02FB, cucumber seedlings produced significantly elevated production of superoxide dismutase, peroxidase, polyphenol oxidase and phenylalanine ammonia lyase as compared to that of the control. We further confirmed that the production of free salicylic acid (SA) and expression of one pathogenesis-related (PR) gene PR-1 in cucumber leaves were markedly elevated after treating with LJ02FB, suggesting that SA-mediated defense response was stimulated. Moreover, LJ02FB-treated cucumber leaves could secrete resistance-related substances into rhizosphere that inhibit the germination of fungi spores and the growth of pathogens. Finally, we separated bacterium and its fermented substances to test their respective effects and found that both components have SA-inducing activity and bacterium plays major roles. Altogether, we identified a BCA against powdery mildew and its mode of action by inducing systemic resistance such as SA signaling pathway.

Increased Expression of TGFβR2 Is Associated with the Clinical Outcome of Non-Small Cell Lung Cancer Patients Treated with Chemotherapy

To investigate the prognostic significance of TGFβR2 expression and chemotherapy in Chinese non-small cell lung cancer (NSCLC) patients, TGFβR2 expression NSCLC was analyzed in silico using the Oncomine database, and subsequently analyzed with quantitative RT-PCR in 308 NSCLC biopsies, 42 of which were paired with adjacent non-neoplastic tissues. Our results show that TGFβR2 expression was also increased in NSCLC biopsies relative to normal tissue samples and correlated with poor prognosis. TGFβR2 expression was also significantly correlated with other clinical parameters such as tumor differentiation, invasion of lung membrane, and chemotherapy. Moreover, overall survival (OS) and disease free survival (DFS) was increased in patients with low TGFβR2 expressing NSCLC and who had undergone chemotherapy. Thus, high expression of TGFβR2 is a significant risk factor for decreased OS and DFS in NSCLC patients. Thus, TGFβR2 is a potential prognostic tumor biomarker for chemotherapy.

Genomic expression profiling and bioinformatics analysis of pancreatic cancer

Pancreatic cancer is a polygenic disease and the fourth leading cause of cancer-associated mortality worldwide; however, the tumorigenesis of pancreatic cancer remains poorly understood. Research at a molecular level, which includes the exploration of biomarkers for early diagnosis and specific targets for therapy, may effectively aid in the diagnosis of pancreatic cancer in its early stages and in the development of targeted molecular-biological approaches for treatment, thus improving prognosis. By conducting expression profiling in para-carcinoma, carcinoma and relapse of human pancreatic tissues, 319 genes or transcripts with differential expression levels >3-fold between these tissue types were identified. Further analysis with Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes demonstrated that the translation, nucleus assembly processes and molecular functions associated with vitamin B6 and pyridoxal phosphate binding in pancreatic carcinoma were abnormal. Pancreatic cancer was additionally identified to be closely associated with certain autoimmune diseases, including type I diabetes mellitus and systemic lupus erythematosus.