The changing incidence of human papillomavirus-associated oropharyngeal cancer using multiple imputation from 2000 to 2010 at a Comprehensive Cancer Centre

Introduction Human papillomavirus (HPV) is a risk and prognostic factor for oropharyngeal cancer (OPC). Determining whether the incidence of HPV-associated OPC is rising informs health policy. Methods HPV status was ascribed using p16 immunohistochemistry in 683/1474 OPC patients identified from the Princess Margaret Hospital's Cancer Registry (from 2000 to 2010). Missing p16 data was estimated using multiple (n = 100) imputation (MI) and validated using an independent OPC cohort (n = 214). Non-OPC head and neck squamous cell carcinoma (HNSCC) (n = 3262) were also used for time-trend comparison. Regression was used to compare HNSCC subsets and time-trends. The c-index was used to measure the predictive ability of MI. Results The incidence of OPC rose from 23.3% of all HNSCC in 2000 to 31.2% in 2010 (p = 0.002). In the subset of OPC tested for p16, there was no change in p16 positivity over time (p = 0.9). However, p16 testing became more frequent over time (p < 0.0001), but was nonetheless biased, favouring never-smokers [OR 1.87 (95% CI 1.29–2.70)] and tumors of the tonsil [OR 2.30 (1.52–3.47)] or base-of-tongue [OR 1.72 (1.10–2.70)]. These same factors were also associated with p16-positivity [ORs 3.22 (1.27–8.16), 7.26 (3.50–15.1), 5.83 (2.70–12.7), respectively]. Following MI and normalization, the proportion of OPC that was p16-associated rose from 39.8% in 2000 to 65.0% in 2010, p = 0.002, fully explaining the rise in OPC in our patient population. Conclusion The rise in HNSCC referrals seen from 2000 to 2010 at our institution was driven primarily by p16-associated OPC. MI was necessary to derive reliable conclusions when cases with missing data are considerable.     

Spectral feature differences between shrub and grass communities and shrub coverage retrieval in shrub-encroached grassland in Xianghuang Banner,Nei Mongol,China北大核心CSCD

Aims: Shrub-encroached grassland has become an important vegetation type in China's arid and semi-arid region. Our study objective is to explore the spectral features of shrub and grass communities, as well as their empirical relationships with shrub coverage. The quantitative estimation of shrub cover based on medium-resolution Landsat satellite imagery provides the practical basis for long term retrieval of large areas of shrub expansion in the grassland region. Methods: Linear models and Multiple Endmember Spectral Analysis Model (MESMA) based on medium resolution Landsat satellite imagery were developed to quantify the shrub coverage in a shrub-encroached grassland region in Xianghuang Banner, Nei Mongol using the spectral features and their seasonal differences between the shrub and grass communities. Important findings: Compared to Leymus chinensis and Stipa krylovii dominated grass communities, Caragana microphylla community had a higher normalized difference vegetation index (NDVI), modified red edge normalized difference vegetation index (mNDVI705), and red edge slope. The red edge position of C. microphylla community shifted to longer wavelengths. The average and the maximum shrub coverage was 13% and 25%, respectively, in the shrub-encroached grassland based on both models. The correlation coefficient of determination (R2) and root mean square error (RMSE) of the linear model was 0.31 and 0.05, respectively. We found that the linear model based on seasonal differences of shrub and grass community was more suitable for retrieving shrub coverage in the study area from medium resolution imagery than the MESMA model that is based on mid-summer images.     

Fluorescence in situ hybridization with multiple repeated DNA probes applied to the analysis of wheat-rye chromosome pairing

 Fluorescence in situ hybridization (FISH) with multiple probes has been applied to meiotic chromosome spreads derived from ph1b common wheat x rye hybrid plants. The probes used included pSc74 and pSc 119.2 from rye (the latter also hybridizes on wheat, mainly B genome chromosomes), the Ae. squarrosa pAs1 probe, which hybridizes almost exclusively on D genome chromosomes, and wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH with a two-by-two combination of these probes allowed unequivocal identification of all of the rye (R) and most of the wheat (W) chromosomes, either unpaired or involved in pairing. Thus not only could wheat-wheat and wheat-rye associations be easily discriminated, which was already feasible by the sole use of the rye-specific pSc74 probe, but the individual pairing partners could also be identified. Of the wheat-rye pairing observed, which averaged from about 7% to 11% of the total pairing detected in six hybrid plants of the same cross combination, most involved B genome chromosomes (about 70%), and to a much lesser degree, those of the D (almost 17%) and A (14%) genomes. Rye arms 1RL and 5RL showed the highest pairing frequency (over 30%), followed by 2RL (11%) and 4RL (about 8%), with much lower values for all the other arms. 2RS and 5RS were never observed to pair in the sample analysed. Chromosome arms 1RL, 1RS, 2RL, 3RS, 4RS and 6RS were observed to be exclusively bound to wheat chromosomes of the same homoeologous group. The opposite was true for 4RL (paired with 6BS and 7BS) and 6RL (paired with 7BL). 5RL, on the other hand, paired with 4WL arms or segments of them in more than 80% of the cases and with 5WL in the remaining ones. Additional cases of pairing involving wheat chromosomes belonging to more than one homoeologous group occurred with 3RL, 7RS and 7RL. These results, while adding support to previous evidence about the existence of several translocations in the rye genome relative to that of wheat, show that FISH with multiple probes is an efficient method by which to study fundamental aspects of chromosome behaviour at meiosis, such as interspecific pairing. The type of knowledge attainable from this approach is expected to have a significant impact on both theoretical and applied research concerning wheat and related Triticeae. Received: 21 February 1996 / Accepted: 12 July 1996     

Reprint of: Saprolegnia strains isolated from river insects and amphipods are broad spectrum pathogens

Saprolegnia species are destructive pathogens to many aquatic organisms and are found in most parts of the world. Reports based on phylogenetic analysis suggest that Saprolegnia strains isolated from aquatic animals such as crustaceans and frogs are close to Saprolegnia strains isolated from infected fish or fish eggs and vice versa. However, it has often been assumed that host specificity occurs for each individual isolate or strain. Here we demonstrate that Saprolegnia spp. can have multiple hosts and are thus capable of infecting different aquatic organisms. Saprolegnia delica, Saprolegnia hypogyna, and 2 strains of Saprolegnia diclina were isolated from aquatic insects and amphipods while S. delica, Saprolegnia ferax, Pythium pachycaule, and a Pythium sp. were isolated from the water of a medium to fast flowing river. The ITS region of the rRNA gene was sequenced for all isolates. In challenge experiments, all four isolates from insects were found to be highly pathogenic to eggs of Atlantic salmon (Salmo salar) and embryos of the African clawed frog (Xenopus laevis). We found that Saprolegnia spp. isolated from salmon eggs were also able to successfully establish infection in nymphs of stonefly (Perla bipunctata) and embryos of X. laevis). These results suggest that Saprolegnia spp. are capable of infecting multiple hosts, which may give them an advantage during seasonal variation in their natural environments.     

REDHORSE-REcombination and Double crossover detection in Haploid Organisms using next-geneRation SEquencing data

Background

Next-generation sequencing technology provides a means to study genetic exchange at a higher resolution than was possible using earlier technologies. However, this improvement presents challenges as the alignments of next generation sequence data to a reference genome cannot be directly used as input to existing detection algorithms, which instead typically use multiple sequence alignments as input. We therefore designed a software suite called REDHORSE that uses genomic alignments, extracts genetic markers, and generates multiple sequence alignments that can be used as input to existing recombination detection algorithms. In addition, REDHORSE implements a custom recombination detection algorithm that makes use of sequence information and genomic positions to accurately detect crossovers. REDHORSE is a portable and platform independent suite that provides efficient analysis of genetic crosses based on Next-generation sequencing data.

Results

We demonstrated the utility of REDHORSE using simulated data and real Next-generation sequencing data. The simulated dataset mimicked recombination between two known haploid parental strains and allowed comparison of detected break points against known true break points to assess performance of recombination detection algorithms. A newly generated NGS dataset from a genetic cross of Toxoplasma gondii allowed us to demonstrate our pipeline. REDHORSE successfully extracted the relevant genetic markers and was able to transform the read alignments from NGS to the genome to generate multiple sequence alignments. Recombination detection algorithm in REDHORSE was able to detect conventional crossovers and double crossovers typically associated with gene conversions whilst filtering out artifacts that might have been introduced during sequencing or alignment. REDHORSE outperformed other commonly used recombination detection algorithms in finding conventional crossovers. In addition, REDHORSE was the only algorithm that was able to detect double crossovers.

Conclusion

REDHORSE is an efficient analytical pipeline that serves as a bridge between genomic alignments and existing recombination detection algorithms. Moreover, REDHORSE is equipped with a recombination detection algorithm specifically designed for Next-generation sequencing data. REDHORSE is portable, platform independent Java based utility that provides efficient analysis of genetic crosses based on Next-generation sequencing data. REDHORSE is available at http://redhorse.sourceforge.net/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1309-7) contains supplementary material, which is available to authorized users.     

Novel aspects of osteoclast activation and osteoblast inhibition in myeloma bone disease

Increased bone resorption is a major characteristic of multiple myeloma and is caused by osteoclast activation and osteoblast inhibition (uncoupling). Myeloma cells alter the local regulation of bone metabolism by increasing the receptor activator of NF-kappaB ligand (RANKL) and decreasing osteoprotegerin expression within the bone marrow microenvironment, thereby stimulating the central pathway for osteoclast formation and activation. In addition, they produce the chemokines MIP-1alpha, MIP-1beta, and SDF-1alpha, which also increase osteoclast activity. On the other hand, myeloma cells suppress osteoblast function by the secretion of osteoblast inhibiting factors, e.g., the Wnt inhibitors DKK-1 and sFRP-2. Moreover, they inhibit differentiation of osteoblast precursors and induce apoptosis in osteoblasts. The resulting bone destruction releases several cytokines, which in turn promote myeloma cell growth. Therefore, the inhibition of bone resorption could stop this vicious circle and not only decrease myeloma bone disease, but also the tumor progression.     

条斑紫菜EST-SSR引物种间转移扩增真实性研究

当条斑紫菜EST-SSR引物在坛紫菜几个品系上进行种间扩增时,微卫星引物的扩增结果中也出现了多带形式。为了研究的假阳性问题,扩增产物被从胶上回收克隆测序。在回收的坛紫菜扩增产物中,同阳性对照条斑紫菜扩增产物大小相同的产物中有微卫星序列重复,但在大分子量的条带中却没有,显现出典型的假阳性问题。在坛紫菜扩增中产生的假阳性带不适合进行建立在微卫星突变基础上的遗传研究,然而,在确定相关的遗传性状后,这些引物也可以用来进行品系鉴定等遗传研究。     

Are “multiple cross-multiple pollen hybrids’ an answer for productive populations in Brassica campestris var. ‘brown sarson’?

Summary A set of complex crosses with multiple crosses as female parents were made using multiple pollen in turnip rape (Brassica campestris L.). These multiple cross — multiple pollen hybrids (mucromphs) were evaluated for a large number of quantitative characters including yield. New methods were proposed to study such genetic material in depth so as to formulate suitable strategies to breed for attractive seed yield.Part of the Ph. D. Thesis of junior author submitted to Indian Agricultural Research Institute, New Delhi     

Integrating ecological features of species in spatial pattern analysis of a plant community

Objective: This empirical study was designed to explore the role of ecological features of species in the spatial patterning of a grassland community. Location: Banks of the river Rhône in France. Material and Methods: First, we explored the spatial pattern of 29 species recorded in the community using spatial autocorrelation analysis of species cover values. Second, we then explored the relationship between the patterns found and a set of life attributes that characterized the ecological features of species for resource foraging or dispersion. Finally, we explored the spatial relationship of groups of species that shared the same ecological features using cross‐correlation analysis. Results: We found a significant relationship between the spatial pattern and life attributes of the species highlighting three groups of species: (1) species characterized as competitors, reproducing by runner clonal organs and forming large, dense patches; (2) species characterized as competitive‐rud‐erals, dispersing exclusively by seed production and forming small periodic patches; and (3) species classified as CSR, characterized by rosette morphology and short rhizomes as clonal organs without any significant spatial autocorrelation. Spatial segregation was found between group 1 and group 2 up to 14 m; no significant cross‐correlation between groups 1 and 3 between 0 and 3.5 m, and association between groups 2 and 3 up to 14 m. Conclusions: These results helped to understand how species attributes (relative to stature or dispersion abilities); external factors (such as disturbance) and biotic processes (competition) interplay in structuring the plant community under study in space.     

RIFLE标准在高容量血液滤过治疗MODS患者疗效的评价

目的：探讨不同肾功能损害时期行高容量血液滤过（HVHF）治疗对多器官功能障碍综合征（MODS）疗效的影响。方法：采用RIFLE标准,将入选的MODS患者按急性肾损伤（AKI）分为AKIⅠ期（A组）、AKIⅡ期（B组）、AKIⅢ期（C组）,以不同AKl分期作为HYI-IF治疗的时机,对比分析不同时期行HVHF治疗MODS患者的死亡率、平均重症监护病房0CU）住院时间（T1）、平均机械通气时间（T2）、平均连续血液滤过治疗时间（T3）,并将HVHF治疗前和治疗24h后的APACHEⅡ评分、SOFA评分、血浆白介素-6（IL-6）、氧合指数、血浆肌酐（Cr）、平均动脉压-（MAP）等结果进行比较。结果：1、AKIⅢ期患者死亡率显著高于AKIⅠ期和AKIⅡ期患者（P〈0．01）;AKIⅡ期患者T1、T2和T3显著高于AKIⅠ期患者（P〈0．01）;2、与AKIⅠ期和AKIⅡ期患者比较,AKIⅢ期患者HVHF治疗前APACHEⅡ评分、SOFA评分、IL-6和Cr均显著增高（P〈0．05）;AKIⅡ期患者HVHF治疗前血浆IL-6显著高于AKIⅠ期患者（P〈0．01）;3、与HVHF治疗前比较,三组患者HVHF治疗24h后IL-6、氧合指数、cr和MAP均显著改善（P〈0．01）：AKIⅢ期患者治疗后的IL-6仍显著高于AKIⅠ期和AKIⅡ期患者;AKIⅠ期和AKIⅡ期患者HVHF治疗24h后APACHEⅡ评分SOFA评分显著降低（P〈0．01）,AKIⅢ期患者治疗前后APACHEⅡ评分和SOFA评分变化无显著统计学差异。结论：RIFLE标准及IL-6对判断预后有指导意义;AKIⅠ期和Ⅱ期行HVHF可明显改善MODS的预后,而AKIⅠ期行HVHF的疗效更好。