Identification of softwood species using convolutional neural networks and raw near-infrared spectroscopy

Previous reports have shown that wood species identification result based on near-infrared (NIR) spectroscopy was intimately entwined with spectra preprocessing. However, there is no universal recipes for a suitable preprocessing method, and misuse of preprocessing may bring on worse model performance for new species identification. Therefore, a convolutional neural network (CNN) model incorporating a residual connection structure is created aiming at replacing the preprocessing and identifying 21 Pinaceae species at the species level. The model is compared to the other two CNN models on different wavelength range raw transverse section NIR spectra. 12 preprocessing methods are carried out for 780–2440 nm spectra to evaluate the influence of spectra preprocessing on the model. The model outperforms the other two CNN models on raw and preprocessed spectra and provides the highest macro F1 of 0.9787 and 0.9792 for raw and preprocessed spectra at the wavelength range of 780–2440 nm. The model is further compared to three conventional methods. The results indicated that created model is capable to replace the spectra preprocessing and identify 21 wood species at the species level. It is indicated that a suitable CNN structure can replace the multifarious data preprocessing in traditional methods. It potentially provides a generic raw NIR spectra discrimination method for wood species identification.</p

CTCF and Rad21 mediate the spatial organization of the <i>kcnq5</i> gene locus.

<p>(A) 3C quantitative PCR assay determined the interaction frequencies between the chromatin fragments of the <i>kcnq5</i> gene locus in MCF-7 cells with CTCF and Rad21 repression, respectively. The amplification efficiencies of the independent PCR reactions were normalized with respect to the control template. Error bars represent mean ± s.d. (n = 3). (B) Western blot (panel up) and reverse transcription quantitative PCR (RT-qPCR) (panel down) analyses of the CTCF expression level in MCF-7 cells after CTCF knockdown by CTCF shRNA. (C) Western blot (panel up) and RT-qPCR (panel down) analyses of the Rad21 expression level in MCF-7 cells after Rad21 knockdown by Rad21 shRNA. Transfection of MCF-7 cells with non-target shRNA was performed as a control. The relative transcription levels in the cells were normalized with respect to the endogenous control GAPDH. Error bars represent mean ± s.d. (n = 3). (D) Anti-CTCF and Rad21 ChIP-loop assays were performed with MCF-7 cells. The amplification efficiencies of the independent PCR reactions were normalized with the respect to the control template. Error bars represent mean ± s.d. (n = 3).</p

MOESM1 of Rapid determination of chemical composition and classification of bamboo fractions using visible–near infrared spectroscopy coupled with multivariate data analysis

Additional file 1: Table S1. The experimental values and estimated values for cellulose, xylan and lignin. Table S2. Results of calibration and prediction PLS2 models for the quantitative compositional analysis of bamboo using raw spectra. Table S3. Results of calibration and prediction PLS1 models for the quantitative compositional analysis of bamboo using pretreated visible-near infrared spectra. Table S4. The experimental values and estimated values for glucose and xylose

4C assay and limited screening.

<p>(A) The bait sequence for 4C assay was a highly conserved DNA fragment of the 28 vertebrate species analyzed using the UCSC Genome Browser. (B) Gel electrophoresis analysis of the product of 4C nested reverse PCR amplification. The results showed the smear-like trails stained with ethidium bromide (EtBr, 0.5 µg/ml). (C) The sequencing results of three interaction partners (No. 319, 202, and 225) were identified by the 4C assay.</p

The dynamic spatial organization of <i>Kcnq5</i> locus and local gene regulation.

<p>(A) Reverse transcriptional quantitative PCR (RT-qPCR) analysis of KCNQ5 expression levels in MCF-7 and Jurkat cells. (B) RT-qPCR analysis of KCNQ5 relative transcription levels in MCF-7 cells transfected with CTCF shRNA, Rad21 shRNA, or shRNA control. The relative transcription levels in the cells were normalized with respect to the endogenous control GAPDH. Error bars represent mean ± s.d. (n = 3). (C) The quantitative PCR of the FAIRE assay with MCF-7 cells. The independent quantitative PCR amplification efficiency was normalized with the input template. Error bars represent mean ± s.d. (n = 3). (D) The <i>cis</i> regulatory element assays were performed in MCF-7 cells using the Luciferase Reporter System (Promega). Three DNA fragments of No. 225 (sense), No. 319 (sense), and CT6 (sense and antisense) were directly cloned into the <i>Bam</i> HI/<i>Sal</i> I site of the pGL3-promoter. The property of each target chromatin fragment was determined by the relative activity of the luciferase reporter. The values of the fluorescence units of firefly luciferase activities were normalized with Renilla luciferase activities (Firefly/Renilla). The values represent the average of independent quadruple repetition experiments and the error bars represent the standard deviation (n = 4); *: <i>P</i><0.05; **: <i>P</i><0.01. (E) A schematic representation of dynamic spatial organization at the <i>Kcnq5</i> locus. A schematic model representation of the CTCF-mediated dynamic spatial organization of the <i>kcnq5</i> locus, which regulates the local gene activity. CTCF mediates the contact of the repressive chromatin fragments within the inner gene locus and confines them within the hub with the assistance of cohesin.</p

Daphnia galeata microsats data

Daphnia galeata microsats dat

Genetic diversity of <i>Daphnia galeata</i> populations from Eastern China, based on 15 microsatellite loci.

<p>N, Total number of individuals; N*, Number of individuals excluding those lacking a complete multilocus genotype, i.e. all 15 loci; MLG, number of unique multi-locus genotypes; <i>N</i>_<i>a</i>, number of alleles, <i>H</i>_<i>o</i>, observed heterozygosity; <i>H</i>_<i>e</i>, expected heterozygosity; HWE, Hardy-Weinberg-Equilibrium; <i>F</i>_<i>IS</i>, inbreeding coefficient; *** P < 0.001.</p><p>Genetic diversity of <i>Daphnia galeata</i> populations from Eastern China, based on 15 microsatellite loci.</p

Taxon identity of individuals from the <i>D</i>. <i>longispina</i> complex sampled from eight lakes in Eastern China.

<p>(a) Similarity of Chinese samples to 49 reference clones representing three species and two hybrid taxa (indicated by crosses; for a list of all reference clones see Yin <i>et al</i>. 2010). Factorial correspondence analysis scores from the first two axes are shown. FCA based on allelic variation at up to 15 microsatellite loci was used to extract factorial axes. (b) Individuals were reclassified by discriminant functions to taxa using FCA scores from four axes to discriminate among groups. Shown are values from the first two discriminant functions per individual and five group centroids representing the five taxa.</p

Analysis of Trx-ARTN.

<p>Cation exchange chromatography using a HiTrap CM FF column for Trx-ARTN produced by a combination of dilution and dialysis refolding technique (A) and a combination of reverse-dilution and dialysis refolding technique (B). Monomeric and dimeric Trx-ARTN proteins were eluted at low and high NaCl concentrations, respectively. Protein-containing fractions were analyzed by non-reduced SDS-PAGE (top) and reduced SDS-PAGE (bottom) to determine the molecular weight of refolded and partially folded protein (C). (D) Size-exclusion chromatography of Trx-ARTN produced by dilution and dialysis combination refolding technique (dotted line) and reverse-dilution and dialysis combination refolding technique (solid line). Molecular weight values were determined by column calibration with protein standards (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045891#pone-0045891-g006" target="_blank">Figure 6S</a>). The retention volumes for B-lactoglobulin (Mr 35,000 Da) and BSA (Mr 67,000 Da) on the Superdex-200 10/300 HR column were 15.5 ml and 14 ml, respectively.</p

Indirect immunofluorescence confirmed that anti-serum collected from immunized mice directly binds <i>H</i>. <i>pylori in vitro</i>.

<p>No immunofluorescence was detected in the absence of antigen specific pcAb (A and B). Positive indirect immunofluorescence signals indicate binding of rHspA-GGT pcAb with <i>H</i>. <i>pylori</i> 26695 (C) and the existence of <i>H</i>. <i>pylori</i> (D). This study was performed twice, yielding similar results.</p