Robust container slot allocation with uncertain demand for liner shipping services

Flexible Services and Manufacturing Journal - Container slot allocation for liner shipping services is to allocate the limited container slots of ships to different segments of demands in order to...     

Photosynthate allocation and productivity of latex vessels inHevea brasiliensis

Manipulations of production systems in rubber tree which were intended to improve sucrose translocation in tapped bark resulted in an increase of latex sucrose and of latex production and reduced the incidence of nonyielding laticiferous tissue. This was achieved by shortening the tapping cut from full to half spiral, by changing the descending direction into an ascending mode of tapping or by annual change-over of tapping panel allowing for a longer time the regeneration of bark removed above the location of the cut. The increase of latex yield did not result in a significant decrease in the growth of trees over a period of three years. Clonal differences in nonyielding bark appeared to be related to differences in sucrose depletion by tapping. In clone PB 235 which exhibited low latex sucrose, a reduction of tapping frequency resulted in an increase in sucrose level and in a decrease of bark “dryness” tending to an increase in total yield. The tapping manipulations examined did not affect latex flow characteristics such as the plugging index of latex vessels and the bursting index of lutoids. The results stress the importance of photosynthate allocation for the physiology of laticiferous system productivity and indicate the possibilities of improving assimilate economy in rubber trees. On mission as export of the International Atomic Energy Agency.     

Variation in allocation to sexual and asexual reproduction among clones of cyclically parthenogenetic Daphnia pulex (Crustacea: Gladocera)

Organisms reproducing by cyclical parthenogenesis combine the benefits of both sexual and asexual reproduction within the same life cycle. Few studies have examined the evolution of variation in the pattern of investment in parthenogenetic compared to sexual reproduction. Seven clones of Daphnia pulex (Crustacea: Cladocera) varying in allocation to sexual reproduction, as measured by the production of males, were raised in isolation and together in a microcosm to study the pattern of sexual reproduction and the effect of this variation on clone fitness. Sex allocation for clones raised together a microcosm was similar to their allocation when raised in isolation, suggesting a genetic basis to the variation. Three clones showed a cost of producing males that lead to their extinction after about 30 days due to the lack of females required for the clones to persist by parthenogenetic reproduction. The remaining four clones persisted until the end of the 72-day experiment. Clones with little or no allocation to males showed no increased allocation to sexual females. The seven clones showed a greater variation in estimated fitness through male and female function than in total estimated fitness. The clone with the greatest total fitness gained most of its fitness through male function but also had a relatively high fitness through female function. Although one clone produced only females it had the next highest fitness. The three clones that went extinct because of a high investment in males had estimated fitness as high as some clones that persisted in the microcosm because of a higher investment in parthenogenetic reproduction. The similarity in total fitness among clones suggests that Daphnia pulex populations in temporary habitats maintain a sex polymorphism where different genotypes vary-in functional gender ranging from female to primarily male.     

Strategic aspects of time allocation in the ecology of a freshwater pulmonate snail

Summary The paper describes experiments designed to investigate the influence of starvation on responses to various constant stimuli by Biomphalaria glabrata (Say). The results are discussed in the context of the economic priorities involved in decisions to switch from one conflicting behaviour to another. Two pairs of conflicting behaviour patterns are discussed: to aggregate as opposed to feeding in isolation, and to move to the surface for pulmonary gaseous exchange as opposed to remaining submersed involved in feeding behaviour. This evolutionary, strategic perspective is pursued with a consideration of the tactics adopted by starved individuals in relation to obtaining food.formerly School of Biological Sciences, University of Sussex, Sussex     

新课改呼唤开放的生物学教学

《新课程标准》要求体现培养学生科学探究方法和创新思维,发展学生的能力,形成科学素养。在教学中实施开放性有利于达到以上目标。     

基于第二代测序数据识别肿瘤基因突变的工具比较

使用第二代测序数据来发现癌细胞中的基因组突变,一直是很重要的科学应用问题。此研究使用一个癌症病人的大量数据,评估了甄别基因组突变的几个现有工具。经过比较各工具的方法和正确率,本文发现各自都有自己的优点和缺点。针对这些优缺点,本文提供一些建议,让工具使用者能更好地选择合适的工具。     

Validation and assessment of variant calling pipelines for next-generation sequencing

Background

The processing and analysis of the large scale data generated by next-generation sequencing (NGS) experiments is challenging and is a burgeoning area of new methods development. Several new bioinformatics tools have been developed for calling sequence variants from NGS data. Here, we validate the variant calling of these tools and compare their relative accuracy to determine which data processing pipeline is optimal.

Results

We developed a unified pipeline for processing NGS data that encompasses four modules: mapping, filtering, realignment and recalibration, and variant calling. We processed 130 subjects from an ongoing whole exome sequencing study through this pipeline. To evaluate the accuracy of each module, we conducted a series of comparisons between the single nucleotide variant (SNV) calls from the NGS data and either gold-standard Sanger sequencing on a total of 700 variants or array genotyping data on a total of 9,935 single-nucleotide polymorphisms. A head to head comparison showed that Genome Analysis Toolkit (GATK) provided more accurate calls than SAMtools (positive predictive value of 92.55% vs. 80.35%, respectively). Realignment of mapped reads and recalibration of base quality scores before SNV calling proved to be crucial to accurate variant calling. GATK HaplotypeCaller algorithm for variant calling outperformed the UnifiedGenotype algorithm. We also showed a relationship between mapping quality, read depth and allele balance, and SNV call accuracy. However, if best practices are used in data processing, then additional filtering based on these metrics provides little gains and accuracies of >99% are achievable.

Conclusions

Our findings will help to determine the best approach for processing NGS data to confidently call variants for downstream analyses. To enable others to implement and replicate our results, all of our codes are freely available at http://metamoodics.org/wes.

     

A short review of variants calling for single-cell-sequencing data with applications

The field of single-cell sequencing is fleetly expanding, and many techniques have been developed in the past decade. With this technology, biologists can study not only the heterogeneity between two adjacent cells in the same tissue or organ, but also the evolutionary relationships and degenerative processes in a single cell. Calling variants is the main purpose in analyzing single cell sequencing (SCS) data. Currently, some popular methods used for bulk-cell-sequencing data analysis are tailored directly to be applied in dealing with SCS data. However, SCS requires an extra step of genome amplification to accumulate enough quantity for satisfying sequencing needs. The amplification yields large biases and thus raises challenge for using the bulk-cell-sequencing methods. In order to provide guidance for the development of specialized analyzed methods as well as using currently developed tools for SNS, this paper aims to bridge the gap. In this paper, we firstly introduced two popular genome amplification methods and compared their capabilities. Then we introduced a few popular models for calling single-nucleotide polymorphisms and copy-number variations. Finally, break-through applications of SNS were summarized to demonstrate its potential in researching cell evolution.     

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays

Background  

Microarray measurements are susceptible to a variety of experimental artifacts, some of which give rise to systematic biases that are spatially dependent in a unique way on each chip. It is likely that such artifacts affect many SNP arrays, but the normalization methods used in currently available genotyping algorithms make no attempt at spatial bias correction. Here, we propose an effective single-chip spatial bias removal procedure for Affymetrix 6.0 SNP arrays or platforms with similar design features. This procedure deals with both extreme and subtle biases and is intended to be applied before standard genotype calling algorithms.     

The effect of visual input on calling song attractiveness for female Acheta domesticus

ABSTRACT. Of twelve mature phonotactically-responsive female Acheta domesticus L., ten responded phonotactically to a wider range (30 or SO to 100 ms) of model calling song (CS) syllable periods (SP) on the Kramer treadmill in the dark than in a lighted visually structured arena (50–70 ms). When given a choice between the visually attractive target and the invisible loudspeaker, seven of the ten females that tracked a visually attractive target (black square) when presented alone in the light reduced the range of SPs they tracked phonotactically to 50–70 ms. Three of the ten females that were not strongly attracted to the visual target when presented alone, continued to respond to model calling songs with a wide range of SPs (30–100 ms) when given a choice between visual and acoustical targets under the same conditions. Two of the twelve females responded only to model calling songs with a 50–70 ms SP on the Kramer treadmill in the dark. These females did not change their choice for model calling song SPs when presented with the visually attractive target.     

Use of plastics for suspension culture vessels

Summary Plastic containers were found to facilitate the adaptation of a number of mammalian cell lines derived from normal tissues to growth in continuous suspension culture. Several different types of plastic materials were studied and a variety of culture vessels were designed.     

A model system for the study of food container leakage

A model system to study food container leakage was developed. The model system allows the independent investigation of the effect of physical factors such as vacuum and contents viscosity, and microbial factors on the leakage process. The design, construction and operation of the container leakage model system is described.     

Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.     

Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling

Background

To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq™ Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer.

Results

Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3 % in four samples, whereas the concordance of co-detected variant loci reached 99 %. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5 %) was higher than the SNPs specific to TargetSeq-Proton (60.0 %) or specific to SureSelect-HiSeq (88.3 %). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0 %) and SureSelect-HiSeq-specific (89.6 %) were higher than those of TargetSeq-Proton-specific (15.8 %).

Conclusions

In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the sequencing of platform-specific variants, the accuracy of variant calling by HiSeq 2000 was higher than that of Ion Proton, specifically for the InDel detection. Moreover, the variant calling software also influences the detection of SNPs and, specifically, InDels in Ion Proton exome sequencing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1796-6) contains supplementary material, which is available to authorized users.     

A model system for the study of food container leakage

A model system to study food container leakage was developed. The model system allows the independent investigation of the effect of physical factors such as vacuum and contents viscosity, and microbial factors on the leakage process. The design, construction and operation of the container leakage model system is described.     

Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays

Multiple algorithms have been developed for the purpose of calling single nucleotide polymorphisms (SNPs) from Affymetrix microarrays. We extend and validate the algorithm CRLMM, which incorporates HapMap information within an empirical Bayes framework. We find CRLMM to be more accurate than the Affymetrix default programs (BRLMM and Birdseed). Also, we tie our call confidence metric to percent accuracy. We intend that our validation datasets and methods, refered to as SNPaffycomp, serve as standard benchmarks for future SNP calling algorithms.