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In noisy evolutionary optimization, sampling is a common strategy to deal with noise. By the sampling strategy, the fitness of a solution is evaluated multiple times (called sample size) independently, and its true fitness is then approximated by the average of these evaluations. Most previous studies on sampling are empirical, and the few theoretical studies mainly showed the effectiveness of sampling with a sufficiently large sample size. In this paper, we theoretically examine what strategies can work when sampling with any fixed sample size fails. By constructing a family of artificial noisy examples, we prove that sampling is always ineffective, while using parent or offspring populations can be helpful on some examples. We also construct an artificial noisy example to show that when using neither sampling nor populations is effective, a tailored adaptive sampling (i.e., sampling with an adaptive sample size) strategy can work. These findings may enhance our understanding of sampling to some extent, but future work is required to validate them in natural situations. [ABSTRACT FROM AUTHOR]

In many real-world optimization problems, the objective function evaluation is subject to noise, and we cannot obtain the exact objective value. Evolutionary algorithms (EAs), a type of general-purpose randomized optimization algorithm, have been shown to be able to solve noisy optimization problems well. However, previous theoretical analyses of EAs mainly focused on noise-free optimization, which makes the theoretical understanding largely insufficient for the noisy case. Meanwhile, the few existing theoretical studies under noise often considered the one-bit noise model, which flips a randomly chosen bit of a solution before evaluation; while in many realistic applications, several bits of a solution can be changed simultaneously. In this paper, we study a natural extension of one-bit noise, the bit-wise noise model, which independently flips each bit of a solution with some probability. We analyze the running time of the (1+1)-EA solving OneMax and LeadingOnes under bit-wise noise for the first time, and derive the ranges of the noise level for polynomial and super-polynomial running time bounds. The analysis on LeadingOnes under bit-wise noise can be easily transferred to one-bit noise, and improves the previously known results. Since our analysis discloses that the (1+1)-EA can be efficient only under low noise levels, we also study whether the sampling strategy can bring robustness to noise. We prove that using sampling can significantly increase the largest noise level allowing a polynomial running time, that is, sampling is robust to noise. [ABSTRACT FROM AUTHOR]

Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits. [ABSTRACT FROM AUTHOR]

We have fabricated an interdigitated double-coil microelectrode chip for the determination of traces of phosphate by making use of a MEMS technique and enzyme immobilization technology. The chip is composed of two 3-dimensional strip microelectrodes which form a double coil microelectrode configuration with steep sidewalls and high aspect ratio. This novel configuration results in a high current response during amplification by redox cycling. The enzyme pyruvate oxidase was immobilized on the chip using gold nanoparticles as a support. Phosphate can be determined by using this chip with good sensitivity and linearity and in concentrations ranging from 0.5 μM to 7 μM. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

The authors describe a microsensor for the determination of biochemical oxygen demand. Different from established BOD detection schemes that incorporate a film of immobilized microbes, the sensitive element of this BOD microsensor consists of magnetite-functionalized Bacillus subtilis that can be immobilized and regenerated on an ultramicroelectrode array (UMEA). Modification and regeneration are magnetically controlled. The oxygen consumed is amperometrically quantified by using an UMEA modified with palladium nanoparticles and reduced carboxy graphene. The assay can be performed within 5 min owing to the fast mass transfer of the magnetite-functionalized microbes on the surface of the UMEA. The calibration plot, best acquired at a voltage of -0.4 V vs. Ag/AgCl, is linear in the 2 to 15 mg⋅L BOD concentration range. A critical comparison with other BOD sensor shows the sensitivity of this sensor to be largely improved. It was successful applied to the determination of BOD in spiked water samples. [ABSTRACT FROM AUTHOR]

Land subsidence along significant linear engineering is mainly affected by long-term over-extraction of groundwater, mining of mineral resources, and karst collapse. In this paper, combined with the engineering geological and hydrogeological conditions, a three-dimensional fluid-solid model of land subsidence is established based on groundwater seepage and Biot's consolidation theories, in order to analyze and forecast the evolution law of the groundwater and land subsidence. The numerical results are verified using field monitoring data (InSAR and high-precision level measurement results). On the basis of monitoring and numerical results, the induced factors and distribution characteristics of land subsidence along the high-speed railway line are determined. According to different groundwater exploitation schemes, the development and evolution laws of ground subsidence in the future are predicted to analyze the influence of ground subsidence on high-speed railway line. The results suggest that (1) the main influencing factors of land subsidence in DK306~DK313 and DK411~DK414 sections are groundwater over-extraction, while DK276~DK279 section is coal mining, DK368~DK372 section requires a special research; (2) the decrease of land subsidence rate and differential subsidence are shown to be nonlinear with the reduction of groundwater withdrawal; (3) under the same mining conditions of groundwater, the land subsidence rate and differential subsidence are declining with time; (4) the surface differential subsidence is obviously sensitive to groundwater exploitation. [ABSTRACT FROM AUTHOR]

A correction to the article “The genome sequence of the orchid Phalaenopsis equestris" that was published online on November 24, 2014 is presented.

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers. [ABSTRACT FROM AUTHOR]

Chinese hamster ovary (CHO) cells, first isolated in 1957, are the preferred production host for many therapeutic proteins. Although genetic heterogeneity among CHO cell lines has been well documented, a systematic, nucleotide-resolution characterization of their genotypic differences has been stymied by the lack of a unifying genomic resource for CHO cells. Here we report a 2.4-Gb draft genome sequence of a female Chinese hamster, Cricetulus griseus, harboring 24,044 genes. We also resequenced and analyzed the genomes of six CHO cell lines from the CHO-K1, DG44 and CHO-S lineages. This analysis identified hamster genes missing in different CHO cell lines, and detected >3.7 million single-nucleotide polymorphisms (SNPs), 551,240 indels and 7,063 copy number variations. Many mutations are located in genes with functions relevant to bioprocessing, such as apoptosis. The details of this genetic diversity highlight the value of the hamster genome as the reference upon which CHO cells can be studied and engineered for protein production. [ABSTRACT FROM AUTHOR]

We report the ∼2.66-Gb genome sequence of a female Yunnan black goat. The sequence was obtained by combining short-read sequencing data and optical mapping data from a high-throughput whole-genome mapping instrument. The whole-genome mapping data facilitated the assembly of super-scaffolds >5× longer by the N50 metric than scaffolds augmented by fosmid end sequencing (scaffold N50 = 3.06 Mb, super-scaffold N50 = 16.3 Mb). Super-scaffolds are anchored on chromosomes based on conserved synteny with cattle, and the assembly is well supported by two radiation hybrid maps of chromosome 1. We annotate 22,175 protein-coding genes, most of which were recovered in the RNA-seq data of ten tissues. Comparative transcriptomic analysis of the primary and secondary follicles of a cashmere goat reveal 51 genes that are differentially expressed between the two types of hair follicles. This study, whose results will facilitate goat genomics, shows that whole-genome mapping technology can be used for the de novo assembly of large genomes. [ABSTRACT FROM AUTHOR]

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C4 biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (?423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C4 photosynthesis pathway were also identified. [ABSTRACT FROM AUTHOR]

A correction to the article “The genome sequence of the orchid Phalaenopsis equestris" that was published online on November 24, 2014 is presented.