Prevalence and Prognostic Significance of HPV in Laryngeal Squamous Cell Carcinoma in Northeast China

Background/Aims: Human papillomavirus (HPV) is an etiological risk factor for a subset of head and neck squamous cell carcinomas. HPV has been proven to be a powerful prognostic biomarker for oropharyngeal cancer, but its role in the larynx has not been explored in depth. Here, we sought to evaluate the prevalence and genotype distribution of HPV in patients with laryngeal squamous cell carcinoma (LSCC) in northeast China. Methods: HPV DNA in specimens from 211 patients diagnosed with LSCC was analyzed by the polymerase chain reaction and in situ hybridization, and p16 overexpression was evaluated by immunohistochemistry. p16 expression was scored positive if strong and diffuse nuclear and cytoplasmic staining was present in > 75% of tumor cells. Results: In this study, infection with HPV and p16 expression were not absolutely consistent. Among all patients, 132 (62.6%) were positive for HPV DNA (HPV+), while 23 (10.9%) were inconsistent for HPV and p16. Multivariate analysis indicated that HPV, but not p16, is an independent prognostic factor for overall survival in LSCC. Overall survival was significantly improved in HPV+ LSCC patients compared with the HPV-negative group (hazard ratio, 0.395; 95% confidence interval, 0.185–0.843; p = 0.016). Among the 132 HPV+ patients, 28 (21.2%) were HPV-16 single infection. Conclusion: This study indicates that HPV DNA is a more reliable surrogate marker than p16 for the prediction of survival in patients with LSCC

Two high-risk susceptibility loci at 6p25.3 and 14q32.13 for Waldenström macroglobulinemia

Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a rare, chronic B-cell lymphoma with high heritability. We conduct a two-stage genome-wide association study of WM/LPL in 530 unrelated cases and 4362 controls of European ancestry and identify two high-risk loci associated with WM/LPL at 6p25.3 (rs116446171, near EXOC2 and IRF4; OR = 21.14, 95% CI: 14.40–31.03, P = 1.36 × 10 −54 ) and 14q32.13 (rs117410836, near TCL1; OR = 4.90, 95% CI: 3.45–6.96, P = 8.75 × 10 −19 ). Both risk alleles are observed at a low frequency among controls (~2–3%) and occur in excess in affected cases within families. In silico data suggest that rs116446171 may have functional importance, and in functional studies, we demonstrate increased reporter transcription and proliferation in cells transduced with the 6p25.3 risk allele. Although further studies are needed to fully elucidate underlying biological mechanisms, together these loci explain 4% of the familial risk and provide insights into genetic susceptibility to this malignancy. © 2018, The Author(s).Peer reviewe

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

Retrotransposons consist of significant portions of many complex eukaryotic genomes and are often enriched in heterochromatin. The centromeric retrotransposon (CR) family in grass species is colonized in the centromeres and highly conserved among species that have been diverged for >50 MY. These unique characteristics have inspired scientists to speculate about the roles of CR elements in organization and function of centromeric chromatin. Here we report that the CRR (CR of rice) elements in rice are highly enriched in chromatin associated with H3K9me2, a hallmark for heterochromatin. CRR elements were transcribed in root, leaf, and panicle tissues, suggesting a constitutive transcription of this retrotransposon family. However, the overall transcription level was low and the CRR transcripts appeared to be derived from relatively few loci. The majority of the CRR transcripts had chimerical structures and contained only partial CRR sequences. We detected small RNAs (smRNAs) cognate to nonautonomous CRR1 (noaCRR1) and CRR1, but not CRR2 elements. This result was also confirmed by in silico analysis of rice smRNA sequences. These results suggest that different CRR subfamilies may play different roles in the RNAi-mediated pathway for formation and maintenance of centromeric heterochromatin

Preparation and properties of epoxy resin-coated micro-sized ferrosilicon powder

Ferrosilicon powder surface coated with a dense epoxy resin membrane was prepared via coating precipitation methods using silane coupling agents as the modifier and epoxy resin as the coating agent. FTIR, FESEM, MPMS-XL, and TG-DSC were used to analyze the morphology, surface composition, magnetic property and thermostability of ferrosilicon powder before and after the modification and coating. The experimental results indicate that epoxy resin membranes of a certain thickness were successfully coated onto the surface of ferrosilicon powder; coatings of epoxy resin contributed to the decreased the rate of weight loss via the reduced wear of the coatings and provided resistance to corrosion; the apparent viscosity of medium suspension with coated ferrosilicon was smaller than that of magnetite. Meanwhile, analysis reveals that room-temperature magnetic hysteresis loops of ferrosilicon powder remain basically unchanged before and after coating

Simulation and observation of magnetic mineral particles aggregating into chains in a uniform magnetic field

Based on the theory of magnetic dipoles, the 3D characteristics of the magnetic potential energy of magnetic particles in a magnetic field were analyzed, and the interaction force formula between the magnetic particles was derived. Additionally, the Velocity Verlet algorithm was adopted to simulate the interaction of soft magnetic particles, which were compared against the observed 2D dynamic processes of magnetite particles. The observational results are largely consistent with the simulation, which considers both the magnetic dipole force and the viscous resistance that occurs during the interaction of soft magnetic particles. Nevertheless, significant difference exists between the 2D dynamic observation and the simulation for the interaction of magnetite particles. Three series of experiments and simulation show that all the magnetic particles are arranged in chain structures and orientated along the direction of the external magnetic field. Furthermore, the results show that the time required for magnetic particles to form magnetic chains is negatively correlated with the intensity of the magnetic field, and positively correlated with the viscosity of the chosen medium

Additional file 2: Table S1. of Impact of post-alignment processing in variant discovery from whole exome data

Five public exome-seq data in NA12878. Table S2: Change of SNP calling sensitivity and precision rate after local realignment. (PDF 49 kb

Additional file 2: Table S1. of An analytical workflow for accurate variant discovery in highly divergent regions

Five mappers and five variant callers used in the study. Table S2. SNP and INDEL calling precision rate in simulated data. Table S3. Percent of SNP calling sensitivity for three callers in simulated data. Table S4. INDEL calling sensitivity for two callers in simulated data. Table S5. Known INDELs in the HLA region of NA12878. Table S6. Novel INDELs in the HLA region of NA12878. Table S7. Number of novel SNPs in 22 CLL samples. Table S8. Number of INDELs in 22 CLL samples. (PDF 170 kb

Additional file 1: Figure S1. of Impact of post-alignment processing in variant discovery from whole exome data

Change of INDEL calling precision rate following local realignment. Figure S2: Local realignment and BQSR for SAMtools/BCFtools consensus-caller and multiallelic-caller. Figure S3: BQSR changed variant calling sensitivity in NA12878. Figure S4: Change of known and novel SNPs in NA12878 after BQSR. Figure S5: Change of known and novel INDELs in NA12878 by BQSR. Figure S6: Local realignment and BQSR with hg19 versus hg38. (PDF 769 kb