Use of signal quality measurements to gain efficiency in the analysis of cDNA microarray data

This research provides a new way to measure error in microarray data in order to improve gene expression analysis.Microarray data contains many sources of error.In order to glean information about mRNA expression levels,the true signal must first be segregated from noise.This research focuses on the variation that can be captured at the spot level in cDNA microarray images.Variation at other levels,due to differences at the array,dye,and block levels,can be corrected for by a variety of existing normalization procedures.Two signal quality estimates that capture the reliability of each spot printed on a microarray are described.A parametric estimate of within-spot vari ance,referred to here as σ s2pot,assumes that pixels follow a normal distribution and are spatially correlated.A non-parametric estimate of error,called the mean square prediction error(MSPE),assumes that spots of high quality possess pixels that are similar to their neighbors.This paper will provide a framework to use either spot quality measure in downstream analysis,specifically as weights in regression models.Using these spot quality estimates as weights can result in greater efficiency,in a statistical sense,when modeling microarray data.     

Use of signal quality measurements to gain efficiency in the analysis of cDNA microarray datacDNA microarray data

This research provides a new way to measure error in microarray data in order to improve gene expression analysis. Microarray data contains many sources of error. In order to glean information about mRNA expression levels, the true signal must first be segregated from noise. This research focuses on the variation that can be captured at the spot level in cDNA microarray images. Variation at other levels, due to differences at the array, dye, and block levels, can be corrected for by a variety of existing normalization procedures. Two signal quality estimates that capture the reliability of each spot printed on a microarray are described. A parametric estimate of within-spot variance, referred to here as σ²_spot, assumes that pixels follow a normal distribution and are spatially correlated. A non-parametric estimate of error, called the mean square prediction error (MSPE), assumes that spots of high quality possess pixels that are similar to their neighbors. This paper will provide a framework to use either spot quality measure in downstream analysis, specifically as weights in regression models. Using these spot quality estimates as weights can result in greater efficiency, in a statistical sense, when modeling microarray data.     

利用人工智能预测癌症的易感性、复发性和生存期

癌症具有较高的发病率和致死率,对人类健康具有重大威胁。癌症预后分析可以有效避免过度治疗及医疗资源的浪费,为医务人员及家属进行医疗决策提供科学依据,已成为癌症研究的必要条件。随着近年来人工智能技术的迅速发展,对癌症患者的预后情况进行自动化分析成为可能。此外,随着医疗信息化的发展,智慧医疗的理念受到广泛关注。癌症患者作为智慧医疗的重要组成部分,对其进行有效的智能预后分析十分必要。本文综述现有基于机器学习的癌症预后方法。首先,对机器学习与癌症预后进行概述,介绍癌症预后及相关的机器学习方法,分析机器学习在癌症预后中的应用;然后,对基于机器学习的癌症预后方法进行归纳,包括癌症易感性预测、癌症复发性预测、癌症生存期预测,梳理了它们的研究现状、涉及到的癌症类型与数据集、用到的机器学习方法及预后性能、特点、优势与不足;最后,对癌症预后方法进行总结与展望。     

Photobioreactor cultivation strategies for microalgae and cyanobacteria

The current burden on fossil‐derived chemicals and fuels combined with the rapidly increasing global population has led to a crucial need to develop renewable and sustainable sources of chemicals and biofuels. Photoautotrophic microorganisms, including cyanobacteria and microalgae, have garnered a great deal of attention for their capability to produce these chemicals from carbon dioxide, mineralized water, and solar energy. While there have been substantial amounts of research directed at scaling‐up production from these microorganisms, several factors have proven difficult to overcome, including high costs associated with cultivation, photobioreactor construction, and artificial lighting. Decreasing these costs will substantially increase the economic feasibility of these production processes. Thus, the purpose of this review is to describe various photobioreactor designs, and then provide an overview on lighting systems, mixing, gas transfer, and the hydrodynamics of bubbles. These factors must be considered when the goal of a production process is economic feasibility. Targets for improving microalgae and cyanobacteria cultivation media, including water reduction strategies will also be described. As fossil fuel reserves continue to be depleted and the world population continues to increase, it is imperative that renewable chemical and biofuel production processes be developed toward becoming economically feasible. Thus, it is essential that future research is directed toward improving these processes. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:811–827, 2018     

Use of signal quality measurements to gain efficiency in the analysis of cDNA microarray data

This research provides a new way to measure error in microarray data in order to improve gene expression analysis.Microarray data contains many sources of error.In order to glean information about mRNA expression levels,the true signal must first be segregated from noise.This research focuses on the variation that can be captured at the spot level in cDNA microarray images.Variation at other levels,due to differences at the array,dye,and block levels,can be corrected for by a variety of existing normalizati...     

Lectinomics II. A highway to biomedical/clinical diagnostics

The review assesses current status and attempts to forecast trends in the development of lectin biorecognition technology. The progressive trend is characterized scientometrically and reflects the current transient situation, when standard low-throughput lectin-based techniques are being replaced by a novel microarray-based techniques offering high-throughput of detection. The technology is still in its infancy (validation phase), but already shows promise as an efficient tool to decipher the enormous complexity of the glycocode that influences physiological status of the cell. Further enhancement in robustness and flexibility of lectin microarrays is predicted by using recombinant and artificial lectins that will render production of lectin microarrays cost-effective and more affordable. Mass spectrometry is expected to play an important role to characterize the binding profile of new lectins. Differences in glycan recognition by lectins and anti-carbohydrate antibodies are given on a molecular basis, and strong and weak points of both biorecognition molecules in diagnosis are briefly discussed.     

AN OPTICAL DETECTION SYSTEM FOR THE STUDY OF FINE SCALE VERTICAL DISPLACEMENT OF MICROALGAE IN AN ARTIFICIAL WATER COLUMN

A proper knowledge of the vertical organization of the phytoplankton is of fundamental importance for our understanding of the functions of pelagic ecosystems. Essential in this context is the existence of vertical gradients in environmental parameters. However, little is known about how the fine vertical structures of phytoplankton species are formed and maintained. In situ study of phytoplankton is biased by the fact that submersing instruments can disturb or even destroy the fine vertical gradients in species composition and/or cell numbers. We have designed and constructed an optical instrumentation system by which fine-scale vertical displacements of microalgae can be studied in an artificial water column without influencing fine physical, chemical, and biological structures of the water column. This enables us to find out more about the fine-scale behavioral responses of microalgae to vertical gradients in environmental parameters. We describe the main system, present some test results, and conclude that our optical system is able to reveal fine-scale vertical displacements of microalgae in an artificial water column and that the system can detect differences in cell densities down to 100 cells·mL⁻¹.     

Combined influence of light and temperature on growth rates of <Emphasis Type="Italic">Nannochloropsis oceanica</Emphasis>: linking cellular responses to large-scale biomass production

The interaction effects between irradiance and temperature on growth rates ofNannochloropsis oceanicawere determined in both laboratory cultures and large-scale tubular photobioreactors. Growth responses were investigated in 48 batch cultures subjected to crossing light/temperature gradients ranging from 34–80μmol photons m⁻²s⁻¹and 14.5–35.7^∘C respectively. Comparisons were made to growth responses observed in production systems (200L biofences) operated in climate-regulated greenhouses with controlled temperature and artificial light gradients. Cellular responses showed increasing specific growth rates as a function of temperature, with a peak at 25–29^∘C, after which the growth became increasingly unstable. The optimum temperature for growth increased with higher light intensities up to approximately 28^∘C at 80μmol photons m⁻²s⁻¹. At low light intensities the specific growth rate was less affected by temperature. The maximum daily production measured in the biofence systems increased proportionally with irradiation and reached approximately 0.7gL⁻¹d⁻¹at 1030μmol photons m⁻²s⁻¹average daily radiation for a culture temperature of 24^∘C. This corresponds to a daily yield of 140g per day in a 200L biofence system. When specific growth rates for the biofence cultures were measured at different densities and plotted against temperature, results showed a peak with the 24^∘C temperature treatment. This peak became less pronounced as the density increased in the cultures. This is consistent with the laboratory results; increasing cell density in the biofence cultures resulted in less average light cell⁻¹, which produced the same temperature dependent response as seen by reducing the external irradiance exposure for the dilute laboratory cultures.     

中国桑寄生科植物叶表皮微形态

通过扫描电镜对中国桑寄生科桑寄生亚科8属18种和槲寄生亚科1属2种植物成熟叶的上、下叶表皮内表面和下表皮外表面进行了研究。内面观发现桑寄生科植物叶上、下表皮形状为多边形,垂周壁式样平直或稍弓形,常具有角质增厚,平周壁常覆盖厚角质或颗粒状、丝状角质增厚;气孔存在于上下表皮,通常下表皮较多,气孔的形状,特别是保卫细胞的形态在亚科间、属间或种间都具有一定的差异,气孔器类型为平列型或单圈型。下表皮表面观察了的角质膜和蜡质纹饰、气孔的形状,外部气孔缘及外部气孔缘内缘的特征。这些特征在亚科或属级水平上较为稳定,有的也表现出种间差异,有一定的分类价值。从气孔形态和外部气孔周围角质膜来看,两亚科显示出明显的不同:桑寄生亚科上、下表皮均具有内部气孔缘,而槲寄生亚科没有此结构;桑寄生亚科外部气孔周围角质膜增厚成环状,其上具增厚的条纹,而槲寄生亚科外部气孔周围角质膜增厚成脊状,不具条纹。这些特征支持槲寄生亚科作为独立1个科来处理。     

Disease signatures are robust across tissues and experiments

Meta‐analyses combining gene expression microarray experiments offer new insights into the molecular pathophysiology of disease not evident from individual experiments. Although the established technical reproducibility of microarrays serves as a basis for meta‐analysis, pathophysiological reproducibility across experiments is not well established. In this study, we carried out a large‐scale analysis of disease‐associated experiments obtained from NCBI GEO, and evaluated their concordance across a broad range of diseases and tissue types. On evaluating 429 experiments, representing 238 diseases and 122 tissues from 8435 microarrays, we find evidence for a general, pathophysiological concordance between experiments measuring the same disease condition. Furthermore, we find that the molecular signature of disease across tissues is overall more prominent than the signature of tissue expression across diseases. The results offer new insight into the quality of public microarray data using pathophysiological metrics, and support new directions in meta‐analysis that include characterization of the commonalities of disease irrespective of tissue, as well as the creation of multi‐tissue systems models of disease pathology using public data.     

Effect of ammonium load on the growth of attached microalgae in the northern Baltic Sea

The effect of ammonium discharge from a food factory on the growth of attached microalgae was monitored north of the Hanko peninsula, on the southwestern coast of Finland. The impact of the discharge was studied at twelve localities, at four stages of seasonal succession. The microalgae were sampled from glass slides exposed at 0.4 m depth for two weeks. The variables measured for the microalgal growth were chlorophylla, primary production and total organic carbon (TOC). These were compared with planktonic chlorophylla and nutrient concentrations. The growth of attached microalgae displayed a consistent pattern of spatial distribution. Depending on season, TOC and primary production values were 7 to 70 times higher and chlorophylla values up to 1000 times higher close to the effluent outlet than in undisturbed areas of the archipelago. The microalgal samples near the discharge were characterized by low TOC/chlorophylla and TOC/primary production ratios. The temporal consistency of microalgal distribution illustrates the advantages of using attached algal assemblages in monitoring programmes.