Label2label: Training a neural network to selectively restore cellular structures in fluorescence microscopy

Immunofluorescence (IF) microscopy is routinely used to visualise the spatial distribution of proteins that dictates their cellular function. However, unspecific antibody binding often results in high cytosolic background signals, decreasing the image contrast of a target structure. Recently, convolutional neural networks (CNNs) were successfully employed for image restoration in IF microscopy, but current methods cannot correct for those background signals. We report a new method that trains a CNN to reduce unspecific signals in IF images; we name this method label2label (L2L). In L2L, a CNN is trained with image pairs of two non-identical labels that target the same cellular structure. We show that after L2L training a network predicts images with significantly increased contrast of a target structure, which is further improved after implementing a multi-scale structural similarity loss function. Here, our results suggest that sample differences in the training data decrease hallucination effects that are observed with other methods. We further assess the performance of a cycle generative adversarial network, and show that a CNN can be trained to separate structures in superposed IF images of two targets.

Study on Mechanical Problems of Complex Rock Mass by Composite Material Micromechanics Methods: A Literature Review

The mechanical analysis of complex rock mass is a difficult problem, which often occurs in scientific research and practical engineering. Many achievements have been made in the study of rock mass composite problems by composite material micromechanics method, but it has not been well summarized so far. This paper summarizes in detail the research status of complex rock mass problems by composite material micromechanics method at home and abroad, including the application of the Eshelby equivalent inclusion theory and self-consistent model in rock mass composite problems, and the application of the homogenization method in jointed rock mass and other rock mass composite problems such as anchored rock mass, layered rock mass, and salt rock mass with impurities. It is proposed that the structural similarity and mechanical analysis similarity should be satisfied when the composite material micromechanics method is used to study the complex rock mass. Finally, the problems that need to be further studied are put forward. The research results provide a valuable reference for the study of complex rock mass by the composite material micromechanics method.

Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.

Master Frame Extraction of Fetal Cardiac Images Using B Mode Ultrasound Images

Fetal Echocardiography is used for monitoring the fetal heart and for detection of Congenital Heart Disease (CHD). It is well known that fetal cardiac four chamber view has been widely used for preliminary examination for the detection of CHD. The end diastole frame is generally used for the analysis of the fetal cardiac chambers which is manually picked by the clinician during examination/screening. This method is subjected to intra and inter observer errors and also time consuming. The proposed study aims to automate this process by determining the frame, referred to as the Master frame from the cine loop sequences that can be used for the analysis of the fetal heart chambers instead of the clinically chosen diastole frame. The proposed framework determines the correlation between the reference (first) frame with the successive frames to identify one cardiac cycle. Then the Master frame is formed by superimposing all the frames belonging to one cardiac cycle. The master frame is then compared with the clinically chosen diastole frame in terms of fidelity metrics such as Dice coefficient, Hausdorff distance, mean square error and structural similarity index. The average value of the fidelity metrics considering the dataset used for this study 0.73 for Dice, 13.94 for Hausdorff distance, 0.99 for Structural Similarity Index and 0.035 for mean square error confirms the suitability of the proposed master frame extraction thereby avoiding manual intervention by the clinician. .

Gold (III) Derivatives in Colon Cancer Treatment

Cancer is one of the leading causes of morbidity and mortality worldwide. Colorectal cancer (CRC) is the third most frequently diagnosed cancer in men and the second in women. Standard patterns of antitumor therapy, including cisplatin, are ineffective due to their lack of specificity for tumor cells, development of drug resistance, and severe side effects. For this reason, new methods and strategies for CRC treatment are urgently needed. Current research includes novel platinum (Pt)- and other metal-based drugs such as gold (Au), silver (Ag), iridium (Ir), or ruthenium (Ru). Au(III) compounds are promising drug candidates for CRC treatment due to their structural similarity to Pt(II). Their advantage is their relatively good solubility in water, but their disadvantage is an unsatisfactory stability under physiological conditions. Due to these limitations, work is still underway to improve the formula of Au(III) complexes by combining with various types of ligands capable of stabilizing the Au(III) cation and preventing its reduction under physiological conditions. This review summarizes the achievements in the field of stable Au(III) complexes with potential cytotoxic activity restricted to cancer cells. Moreover, it has been shown that not nucleic acids but various protein structures such as thioredoxin reductase (TrxR) mediate the antitumor effects of Au derivatives. The state of the art of the in vivo studies so far conducted is also described.

Group-Based Sparse Representation for Compressed Sensing Image Reconstruction with Joint Regularization

Achieving high-quality reconstructions of images is the focus of research in image compressed sensing. Group sparse representation improves the quality of reconstructed images by exploiting the non-local similarity of images; however, block-matching and dictionary learning in the image group construction process leads to a long reconstruction time and artifacts in the reconstructed images. To solve the above problems, a joint regularized image reconstruction model based on group sparse representation (GSR-JR) is proposed. A group sparse coefficients regularization term ensures the sparsity of the group coefficients and reduces the complexity of the model. The group sparse residual regularization term introduces the prior information of the image to improve the quality of the reconstructed image. The alternating direction multiplier method and iterative thresholding algorithm are applied to solve the optimization problem. Simulation experiments confirm that the optimized GSR-JR model is superior to other advanced image reconstruction models in reconstructed image quality and visual effects. When the sensing rate is 0.1, compared to the group sparse residual constraint with a nonlocal prior (GSRC-NLR) model, the gain of the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) is up to 4.86 dB and 0.1189, respectively.

Subpixel-Scale Topography Retrieval of Mars Using Single-Image DTM Estimation and Super-Resolution Restoration

We propose using coupled deep learning based super-resolution restoration (SRR) and single-image digital terrain model (DTM) estimation (SDE) methods to produce subpixel-scale topography from single-view ESA Trace Gas Orbiter Colour and Stereo Surface Imaging System (CaSSIS) and NASA Mars Reconnaissance Orbiter High Resolution Imaging Science Experiment (HiRISE) images. We present qualitative and quantitative assessments of the resultant 2 m/pixel CaSSIS SRR DTM mosaic over the ESA and Roscosmos Rosalind Franklin ExoMars rover’s (RFEXM22) planned landing site at Oxia Planum. Quantitative evaluation shows SRR improves the effective resolution of the resultant CaSSIS DTM by a factor of 4 or more, while achieving a fairly good height accuracy measured by root mean squared error (1.876 m) and structural similarity (0.607), compared to the ultra-high-resolution HiRISE SRR DTMs at 12.5 cm/pixel. We make available, along with this paper, the resultant CaSSIS SRR image and SRR DTM mosaics, as well as HiRISE full-strip SRR images and SRR DTMs, to support landing site characterisation and future rover engineering for the RFEXM22.

Fuzzy Proximity based Robust Data Hiding Scheme with Interval Threshold

In 2020, Ashraf et al. proposed an interval type-2 fuzzy logic based block similarity calculation using color proximity relations of neighboring pixels in a steganographic scheme. Their method works well for detecting similarity, but it has drawbacks in terms of visual quality, imperceptibility, security, and robustness. Using Mamdani fuzzy logic to identify color proximity at the block level, as well as a shared secret key and post-processing system, this paper attempts to develop a robust data hiding scheme with similarity measure to ensure good visual quality, robustness, imperceptibility, and enhance the security. Further, the block color proximity is graded using an interval threshold. Accordingly, data embedding is processed in the sequence generated by the shared secret keys. In order to increase the quality and accuracy of the recovered secret message, the tampering coincidence problem is solved through a post-processing approach. The experimental analysis, steganalysis and comparisons clearly illustrate the effectiveness of the proposed scheme in terms of visual quality, structural similarity, recoverability and robustness.

The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

High Yielding, One-Pot Synthesis of Bis(1H-indazol-1-yl)methane Catalyzed by 3d-Metal Salts

Synthetic access to poly(indazolyl)methanes has limited their study despite their structural similarity to the highly investigated chelating poly(pyrazolyl)methanes and their potentially important indazole moiety. Herein is presented a high yielding, one-pot synthesis for the 3d-metal catalyzed formation of bis(1H-indazol-1-yl)methane from 1H-indazole utilizing dimethylsulfoxide as the methylene source. Complete characterization of bis(1H-indazol-1-yl)methane is given with 1H and 13C NMR, UV/Vis, FTIR, high resolution mass spectrometry and for the first time, single crystal X-ray diffraction. This simple, inexpensive pathway to yield exclusively bis(1H-indazol-1-yl)methane provides synthetic access to further investigate the coordination and potential applications of the family of bis(indazolyl)methanes.