Robust Selection of Cancer Survival Signatures from High-Throughput Genomic Data Using Two-Fold Subsampling

Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature. The software is available as an R package rsig at CRAN (http://cran.r-project.org).     

天童常绿阔叶树种栲树生殖个体大小及其生殖构件特征

对浙江天童木荷-栲树林内的常绿阔叶树种栲树(Castanopsis fargesii Franch.)的生殖个体大小、生殖构件的分布及其动态变化特征进行了研究。结果表明, 该地区栲树生殖个体的胸径在17~50 cm 间, 平均胸径为31. 2±8.0 cm, 平均年龄约36.3±6.6 年;林缘附近的生殖个体小于木荷-林内。相对稳定的群落和比较丰富的土壤养分条件有利于生殖枝数量和花序数量的增多。栲树生殖个体的数量在两年中变化较大, 部分栲树个体可以在连续年份中生殖。从枝系水平分析:在持续生殖的栲树个体上, 生殖枝数量有明显变化, 并非所有的生殖枝在两年中都可开花或结果, 保持连续生殖的枝系约占48.2%。栲树果序枝数量在连续年份有明显差异(p < 0.01), 而且果序枝上的幼蕾数、果实数量及结实率等都有明显差异(p < 0.05)。     

Alaskan marine mammal tissue archival project

A project to establish an archive of Alaskan marine mammal tissues was conceived in 1987 to be a part of the National Biomonitoring Specimen Bank (NBSB). Protocols and field collection of marine mammals, long-term storage, and analysis are summarized in this paper. Instrumental neutron activation analysis has been used for an initial evaluation of trace element content in samples of northern fur seal (Callorhinus ursinus) from the Pribilof Islands. The findings agree with previously observed trace element levels in northern fur seals. The archived specimens can be used in future studies when comparisons of past and present pollution levels are needed.

     

Application of the upflow anaerobic sludge bed (UASB) process for treatment of complex wastewaters at low temperatures

The feasibility of the upflow anaerobic sludge bed (UASB) process for the treatment of potato starch wastewater at low ambient temperatures was demonstrated by operating two 5.65-L reactors at 14 degrees C and 20 degrees C, respectively. The organic space loading rates achieved in these laboratory-scale reactors were 3 kg COD/m(3)/day at 14 degrees C and 4-5 kg COD/m(3)/day at 20 degrees C. The corresponding sludge loading rates were 0.12 kg COD/kg VSS/day at 14 degrees C and 0.16-0.18 kg COD/kg VSS/day at 20 degrees C.These findings are of considerable practical importance because application of anaerobic treatment at low ambient temperatures will lead to considerable savings in energy needed for operating the process. As compared with various other anaerobic wastewater treatment processes, a granular sludge upflow process represents one of the best options developed so far. Although the overall sludge yield under psychrophilic conditions is slightly higher than under optimal mesophilic conditions, this doesn't seriously hamper the operation of the process. The extra sludge yield, due to accumulation of slowly hydrolyzing substrate ingredients, was 4.75% of the COD input at 14 degrees C and 1.22% of the COD input at 20 degrees C.     

Sugars and desiccation tolerance in seeds

Soluble sugars have been shown to protect liposomes and lobster microsomes from desiccation damage, and a protective role has been proposed for them in several anhydrous systems. We have studied the relationship between soluble sugar content and the loss of desiccation tolerance in the axes of germinating soybean (Glycine max L. Merr. cv Williams), pea (Pisum sativum L. cv Alaska), and corn (Zea mays L. cv Merit) axes. The loss of desiccation tolerance during imbibition was monitored by following the ability of seeds to germinate after desiccation following various periods of preimbibition and by following the rates of electrolyte leakage from dried, then rehydrated axes. Finally, we analyzed the soluble sugar contents of the axes throughout the transition from desiccation tolerance to intolerance. These analyses show that sucrose and larger oligosaccharides were consistently present during the tolerant stage, and that desiccation tolerance disappeared as the oligosaccharides were lost. The results support the idea that sucrose may serve as the principal agent of desiccation tolerance in these seeds, with the larger oligosaccharides serving to keep the sucrose from crystallizing.     

Biogeographical patterns of endemic diversity and its conservation in Australia's artesian desert springs

Aim

Springs in the Australian arid zone are distinct from other waterways because they house a large number of endemic species. We aimed to assess spatial patterns in endemic diversity at a basin‐wide scale and whether environmental features can help to explain them. In doing so, we take the opportunity to summarize the current state of conservation in the system.

Location

Great Artesian Basin (GAB), arid and semiarid regions of eastern Australia

Methods

We combine data regarding the location of springs with published GIS layers regarding environmental characteristics and a literature review of all species and subspecies documented in the published literature to be endemic to GAB springs.

Results

We found evidence of 96 species and subspecies of fishes, molluscs, crustaceans and plants endemic to these springs. The majority of endemic species are invertebrates with geographical distributions limited to a single spring complex (<61 km²). Endemic taxa are concentrated in 75 of the 326 spring complexes. Spring complexes with a large number of springs, high connectivity via drainage basins and low rainfall were more likely to contain endemic taxa, but environmental models were poor predictors of diversity. Only 24% spring complexes with high conservation value are within conservation reserves, and the majority of endemic species are unassessed under the IUCN and Australian conservation legislation, particularly the invertebrates.

Main conclusions

Diversity in this system is underestimated given the current rate of species discovery and prevailing data deficiency for many taxa. Historical processes and species‐specific environmental requirements may be more important for explaining why diversity is concentrated in particular complexes. Almost a decade after this system was listed as endangered, most complexes of high conservation value remain outside of conservation reserves, and the endangered species status of many taxa, and particularly the invertebrates, remain unassessed.

     

Indoor and outdoor winter activity of Culicoides biting midges,vectors of bluetongue virus,in Italy

Indoor and outdoor winter activity of Culicoides spp. (Diptera: Ceratopogonidae) in central Italy was investigated in order to evaluate whether indoor activity might account for the overwintering of bluetongue virus, as has been hypothesized by some authors. Weekly Culicoides collections were performed at three farms over three consecutive winter seasons. At each farm, two black‐light traps were operated simultaneously, indoors and outdoors. Culicoides were identified using both morphological and molecular means. The Culicoides obsoletus group accounted for 98.2% of sampled specimens. Within this group, C. obsoletus s.s. accounted for 56.8% and Culicoides scoticus for 43.2% of samples. Nulliparous, parous and engorged females were caught throughout the entire winter, both indoors and outdoors. At times, indoor catch sizes outnumbered outdoor collections. A significant inverse correlation was found between minimum temperature and the proportion of indoor Culicoides of the total midge catch, thus indicating that lower outdoor temperatures drive Culicoides midges indoors. High rates of engorged females were recorded indoors, possibly as the result of the propensity of C. obsoletus females to feed indoors. Higher proportions of parous females were found in indoor than in outdoor catches, indicating higher survival rates indoors and, consequently, higher vectorial capacities of midges sheltering indoors compared with those remaining outdoors.     

Desiccation tolerance in Physcomitrella patens: Rate of dehydration and the involvement of endogenous abscisic acid (ABA)

The moss Physcomitrella patens , a model system for basal land plants, tolerates several abiotic stresses, including dehydration. We previously reported that Physcomitrella patens survives equilibrium dehydration to ?13 MPa in a closed system at 91% RH. Tolerance of desiccation to water potentials below ?100 MPa was only achieved by pretreatment with exogenous abscisic acid (ABA). We report here that gametophores, but not protonemata, can survive desiccation below ?100 MPa after a gradual drying regime in an open system, without exogenous ABA. In contrast, faster equilibrium drying at 90% RH for 3–5 days did not induce desiccation tolerance in either tissue. Endogenous ABA accumulated in protonemata and gametophores under both drying regimes, so did not correlate directly with desiccation tolerance. Gametophores of a Ppabi3a/b/c triple knock out transgenic line also survived the gradual dehydration regime, despite impaired ABA signaling. Our results suggest that the initial drying rate, and not the amount of endogenous ABA, may be critical in the acquisition of desiccation tolerance. Results from this work will provide insight into ongoing studies to uncover the role of ABA in the dehydration response and the underlying mechanisms of desiccation tolerance in this bryophyte.