Data visualization in yield component analysis: an expert study

Even though data visualization is a common analytical tool in numerous disciplines, it has rarely been used in agricultural sciences, particularly in agronomy. In this paper, we discuss a study on employing data visualization to analyze a multiplicative model. This model is often used by agronomists, for example in the so-called yield component analysis. The multiplicative model in agronomy is normally analyzed by statistical or related methods. In practice, unfortunately, usefulness of these methods is limited since they help to answer only a few questions, not allowing for a complex view of the phenomena studied. We believe that data visualization could be used for such complex analysis and presentation of the multiplicative model. To that end, we conducted an expert survey. It showed that visualization methods could indeed be useful for analysis and presentation of the multiplicative model

Gene Conversion Tracts from Double-Strand Break Repair in Mammalian Cells

Mammalian cells are able to repair chromosomal double-strand breaks (DSBs) both by homologous recombination and by mechanisms that require little or no homology. Although spontaneous homologous recombination is rare, DSBs will stimulate recombination by 2 to 3 orders of magnitude when homology is provided either from exogenous DNA in gene-targeting experiments or from a repeated chromosomal sequence. Using a gene-targeting assay in mouse embryonic stem cells, we now investigate the effect of heterology on recombinational repair of DSBs. Cells were cotransfected with an endonuclease expression plasmid to induce chromosomal DSBs and with substrates containing up to 1.2% heterology from which to repair the DSBs. We find that heterology decreases the efficiency of recombinational repair, with 1.2% sequence divergence resulting in an approximately sixfold reduction in recombination. Gene conversion tract lengths were examined in 80 recombinants. Relatively short gene conversion tracts were observed, with 80% of the recombinants having tracts of 58 bp or less. These results suggest that chromosome ends in mammalian cells are generally protected from extensive degradation prior to recombination. Gene conversion tracts that were long (up to 511 bp) were continuous, i.e., they contained an uninterrupted incorporation of the silent mutations. This continuity suggests that these long tracts arose from extensive degradation of the ends or from formation of heteroduplex DNA which is corrected with a strong bias in the direction of the unbroken strand

Multivariate analysis of an LA-ICP-MS trace element dataset for pyrite

Application of multivariate statistics to trace element datasets is reviewed using 164 multi-element LA-ICP-MS spot analyses of pyrite from the Moonlight epithermal gold prospect, Queensland, Australia. Multivariate analysis of variance (MANOVA) is used to demonstrate that classification of pyrite on morphological and other non-numeric factors is geochemically valid. Parallel coordinate plots and correlation cluster analysis using Spearman’s coefficients are used to discover unexpected elemental relationships without making assumptions a priori. Finally, principal component analysis and factor analysis are used to demonstrate the presence of sub-classes of pyrite. Corroborated with geological data, statistical analysis provides evidence for successive generations of hydrothermal fluids, each introducing specific metals, and for partial or complete replacement of different minerals. The data permit reinterpretation of Moonlight as a telescoped system where epithermal-Au (± base metals) is superposed onto early porphyry-Mo mineralization.Lyron Winderbaum, Cristiana L. Ciobanu, Nigel J. Cook, Matthew Paul, Andrew Metcalfe, Sarah Gilber

Texturing industrial multicrystalline silicon solar cells

Three potential techniques for texturing commercial multicrystalline silicon solar cells are compared on the basis of reflectance measurements. Wet acidic texturing, which would be the least costly to implement, produces a modest improvement in reflection before antirflection coating and encapsulation, whereas maskless reactiveion etching texturing, and especially masked reactive-ion etched ‘pyramids’, generate a larger gain in absorption. After antireflection coating and encapsulation however, the differences between the methods are reduced. Short-circuit current measurements on wet acidic textured cells reveal that there is a significant additional current gain above that expected from the reduced reflection. This is attributed to both light-trapping and oblique coupling of incident light into the cell, resulting in generation closer to the junction

Balancing sufficiency and impact in reporting standards for mass spectrometry imaging experiments

Reproducibility, or a lack thereof, is an increasingly important topic across many research fields. A key aspect of reproducibility is accurate reporting of both experiments and the resulting data. Herein, we propose a reporting guideline for mass spectrometry imaging (MSI). Previous standards have laid out guidelines sufficient to guarantee a certain quality of reporting; however, they set a high bar and as a consequence can be exhaustive and broad, thus limiting uptake.To help address this lack of uptake, we propose a reporting supplement-Minimum Information About a Mass Spectrometry Imaging Experiment (MIAMSIE)-and its abbreviated reporting standard version, MSIcheck. MIAMSIE is intended to improve author-driven reporting. It is intentionally not exhaustive, but is rather designed for extensibility and could therefore eventually become analogous to existing standards that aim to guarantee reporting quality. Conversely, its abbreviated form MSIcheck is intended as a diagnostic tool focused on key aspects in MSI reporting.We discuss how existing standards influenced MIAMSIE/MSIcheck and how these new approaches could positively impact reporting quality, followed by test implementation of both standards to demonstrate their use. For MIAMSIE, we report on author reviews of four articles and a dataset. For MSIcheck, we show a snapshot review of a one-month subset of the MSI literature that indicated issues with data provision and the reporting of both data analysis steps and calibration settings for MS systems. Although our contribution is MSI specific, we believe the underlying approach could be considered as a general strategy for improving scientific reporting

MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney

Recent developments in spatial proteomics have paved the way for retrospective in situ mass spectrometry (MS) analyses of formalin-fixed paraffin-embedded clinical tissue samples. This type of analysis is commonly referred to as matrix-assisted laser desorption/ionization (MALDI) imaging. Recently, formalin-fixed paraffin-embedded MALDI imaging analyses were augmented to allow in situ analyses of tissue-specific N-glycosylation profiles. In the present study, we outline an improved automated sample preparation method for N-glycan MALDI imaging, which uses in situ PNGase F-mediated release and measurement of N-linked glycans from sections of formalin-fixed murine kidney. The sum of the presented data indicated that N-glycans can be cleaved from proteins within formalin-fixed tissue and characterized using three strategies: (i) extraction and composition analysis through on-target MALDI MS and liquid chromatography coupled to electrospray ionization ion trap MS; (ii) MALDI profiling, where N-glycans are released and measured from large droplet arrays in situ; and (iii) MALDI imaging, which maps the tissue specificity of N-glycans at a higher resolution. Thus, we present a complete, straightforward method that combines MALDI imaging and characterization of tissue-specific N-glycans and complements existing strategies.Ove J. R. Gustafsson, Matthew T. Briggs, Mark R. Condina, Lyron J. Winderbaum, Matthias Pelzing, Shaun R. McColl, Arun V. Everest-Dass, Nicolle H. Packer, Peter Hoffman

Lymph node metastasis of primary endometrial cancers : associated proteins revealed by MALDI imaging

Metastasis is a crucial step of malignant progression and is the primary cause of death from endometrial cancer. However, clinicians presently face the challenge that conventional surgical-pathological variables, such as tumour size, depth of myometrial invasion, histological grade, lymphovascular space invasion or radiological imaging are unable to predict with accuracy if the primary tumour has metastasized. In the current retrospective study, we have used primary tumour samples of endometrial cancer patients diagnosed with (n = 16) and without (n = 27) lymph node metastasis to identify potential discriminators. Using peptide matrix assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI), we have identified m/z values which can classify 88% of all tumours correctly. The top discriminative m/z values were identified using a combination of in situ sequencing and LC-MS/MS from digested tumour samples. Two of the proteins identified, plectin and -Actin-2, were used for validation studies using LCMS/MS data independent analysis (DIA) and immunohistochemistry. In summary, MALDIMSI has the potential to identify discriminators of metastasis using primary tumour samples

Influence of the high-temperature "firing" step on high-rate plasma deposited silicon nitride films used as bulk passivating antireflection coatings on silicon solar cells

The influence of a short high-temperature step, comparable to the so-called "firing" of the metallization on silicon solar cells, on properties of high-rate (>0.5 nm/s) plasma deposited silicon nitride (a-SiNx:H) films has been investigated. These a-SiNx:H films are used as antireflection coating on multicrystalline silicon (mc-Si) solar cells and, after the firing process, they also induce hydrogen bulk passivation in the mc-Si. Three different types of remote plasma deposited a-SiNx:H films have been investigated: (i) expanding thermal plasma (ETP) deposited a-SiNx:H films from a N2–SiH4 gas mixture, (ii) ETP deposited a-SiNx:H films from a NH3–SiH4 mixture, and (iii) microwave plasma deposited a-SiNx:H films from a NH3–SiH4 mixture. The atomic composition and optical and structural properties of the films have been studied before and after the high-temperature step by the combination of elastic recoil detection, spectroscopic ellipsometry, and Fourier transform infrared spectroscopy. It has been observed that the high-temperature step can induce significant changes in hydrogen content, bonding types, mass density, and optical absorption of the films. These thermally induced effects are more enhanced for Si- than for N-rich films, which in some cases have a high thermal stability. Furthermore, the material properties and the influence of the high-temperature step have been related to the bulk passivation properties of the a-SiNx:H coated mc-Si solar cells. It is found that in particular the density and thermal stability of the a-SiNx:H films seem to be important for the degree of the bulk passivation obtained

Multivariate Analysis of an LA-ICP-MS Trace Element Dataset for Pyrite

Application of multivariate statistics to trace element datasets is reviewed using 164 multi-element LA-ICP-MS spot analyses of pyrite from the Moonlight epithermal gold prospect, Queensland, Australia. Multivariate analysis of variance (MANOVA) is used to demonstrate that classification of pyrite on morphological and other non-numeric factors is geochemically valid. Parallel coordinate plots and correlation cluster analysis using Spearman’s coefficients are used to discover unexpected elemental relationships without making assumptions a priori. Finally, principal component analysis and factor analysis are used to demonstrate the presence of sub-classes of pyrite. Corroborated with geological data, statistical analysis provides evidence for successive generations of hydrothermal fluids, each introducing specific metals, and for partial or complete replacement of different minerals. The data permit reinterpretation of Moonlight as a telescoped system where epithermal-Au (± base metals) is superposed onto early porphyry-Mo mineralization.Lyron Winderbaum, Cristiana L. Ciobanu, Nigel J. Cook, Matthew Paul, Andrew Metcalfe, Sarah Gilber